Microbiology Lab Manual and Guide

W ritten by:
Donna Cain, Hershell Hanks, Mary Weis, Carroll Bottoms , and

Jonathan Lawson
Table of Contents
Experiment #
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Appendix A
Appendix B
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Title
Web Address for Tutorial Website
Biosafety Guidelines
Microorganisms/Biosafety Levels
Aseptic Technique
Microscopy
Staining of Bacterial Specimens
Preparing a Smear
Gram Stain
Capsule Stain
Acid Fast Stain
Endospore Stain
Culture Transfer Techniques
Isolation of Pure Cultures
Viable Plate Counts
Effect of Temperature on Microbial Growth
Atmospheric Oxygen Requirements
Cultivation of Anaerobic Organisms
Use of Selective, Differential, and Enriched Media
Chemical Control of Microorganisms
Chemotherapeutic Agents
Additive and Synergistic Effects of Antibiotics
Microbiota of the Mouth
Normal Microbiota of the Throat and Skin
Cultivation of Urine Specimens
Identification of Bacillus Species
Transformation
Catalase Test
Identification of Streptococcus Species
Rapid Strep Test
Identification of Staphylococcus Species
Coagulase Test
Rapid Staph Test
Identification of Gram-negative Species
Epidemiology
HIV Testing Using an Enzyme-Linked Immunosorbent Assay
Yogurt Production
Water Microbiology
Food Microbiology
Unknowns
Unknown Lab Report Guidelines
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Tutorial Website for

Microbiology Laboratory
Available at
http://iws2.collin.edu/dcain/CCCCD%20Micro/index.htm
METRIC SYSTEM
This is a scientific laboratory course, and thus a working understanding of the metric system is
expected. If you require a review of the metric system (units, conversions, scientific notation
etc) please refer yourself to previous textbooks or utilize one of the many online tutorials. We
have provided a url below that presents a good review of the metric system. Please talk with
your instructor now if you have questions or need additional assistance.
http://www.swtc.edu:8082/mscenter/mthsci/science/1tools/p02amtrc.pps
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BIOSAFETY GUIDELINES
BACKGROUND ON BIOSAFETY
In addition to following general laboratory safety rules, additional rules must be
implemented in the microbiology lab since students are working with living organisms and the
risk of student exposure to these organisms must be minimized. The four basic routes of
exposure to microorganisms are (1) contact with skin and mucous membranes, (2) ingestion, (3)
inhalation, and (4) inoculation. Specific lab safety guidelines are designed to address each of
these potential routes of exposure. Contact with skin and mucous membranes can be
minimized by wearing proper personal protective equipment such as lab coats or aprons, gloves,
goggles, respirators, and face shields. In addition, students should be prohibited from inserting
contact lenses in the lab. Ingestion of microorganisms can be minimized by prohibiting eating,
drinking, or applying cosmetics in the lab. Inhalation of microorganisms can be minimized by
adopting measures which decrease the likelihood of generating aerosols. Inoculation can be
minimized by instituting rigid protocols for the use and disposal of sharps (needles, slides,
broken glass, etc.)
Microorganisms are divided into 4 Biosafety Levels (BSL) by the Centers for Disease
Control and Prevention. The microbes used in our micro lab fall into the BSL-1 and BSL-2
categories.
Biosafety Level 1 organisms are defined as well-characterized strains of microorganisms
not known to cause disease in healthy human adults. Precautions in BSL-1 labs include general
lab safety rules such as no eating or drinking, prohibition of mouth pipetting, practicing aseptic
technique, and proper disposal of sharps and microbiological waste. Examples of BSL-1
organisms include non-pathogenic laboratory strains of Escherichia coli, Staphylococcus
xylosus, and Bacillus megaterium.
Biosafety Level 2 organisms are defined as moderate-risk microorganisms that are
associated with less serious human diseases whose potential for transmission is limited and a
proven treatment for the disease exists. Many BSL-2 pathogens are opportunistic, meaning they
dont ordinarily cause disease in healthy human adults, but may cause disease in children and
immunocompromised adults. Additional precautions in BSL-2 labs include using personal
protective equipment (PPE) such as disposable gloves and lab coats and limiting lab access to
trained individuals. Examples of BSL-2 organisms include Staphylococcus aureus,
Pseudomonas aeruginosa, and Salmonella.
Biosafety Level 3 organisms are defined as high-risk microorganisms with a true
potential for infection by aerosols and in which the resulting disease may have serious or lethal
consequences. Researchers in BSL-3 labs generally wear double gloves, respirators, and
disposable surgical scrubs and gowns, and work in biological safety cabinets in isolated,
negative-pressure containment rooms. Examples of BSL-3 organisms include Mycobacterium
tuberculosis and Bacillus anthracis.
Biosafety Level 4 organisms are defined as easily transmitted, very-high risk
microorganisms which cause life-threatening diseases for which there is no vaccine or therapy.
Workers in BSL-4 labs work in impermeable positive pressure space suits with an external
oxygen supply, and precautions such as chemical showers must be taken before exiting the lab.
Examples of BSL-4 organisms include Ebola virus, Marburg virus, and Lassa fever virus.
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BIOSAFETY RULES:
1. Do not eat or drink in the laboratory, chew gum, or place any object on or near your mouth.
All books, backpacks, coats, purses, etc. should be cleared from your table before beginning any
procedure. While actively working with microbial cultures, keep your laboratory manual /
instructions at a reasonable distance from your work area. Do not wear loose articles of clothing,
such as scarves or bulky jackets.
2. Practice good aseptic technique by performing the following at the beginning each class:
a) tie back long hair
b) wear closed footwear to protect the feet
c) wear lab coats (preferred) or aprons to protect clothes
d) clean lab table with an antiseptic wash
e) wash hands thoroughly before starting any lab exercise
f) wear disposable gloves when handling BSL-2 organisms
g) wear safety goggles when conducting procedures that pose a splash or aerosol risk, and
when dealing with certain chemicals, such as staining reagents.
3. All cultures, whether test tubes or Petri plates, should be labeled with your name or initials,
the date, and the name of the organism. Plates can be written on directly; tape labels should be
used for test tubes. Permanent markers designated only for laboratory use must be used to label
cultures.
4. Most microbial cultures will be inoculated using a sterile loop or needle; once the transfer is
complete the loop or needle should be sterilized again. Liquid cultures should be transferred
using a sterile pipette and mechanical pipetting apparatus. No mouth pipetting!
5. All test tubes should be placed in a rack before transporting them from one area of the lab to
another. All lids on all test tubes must be secure.
6. All Petri plates should be taped on both sides before carrying to the incubators.
7. All disposable microbiological waste should be discarded in the BIOHAZARD bag. Used test
tubes (labels removed) should be placed in the designated pan to be autoclaved and cleaned.
Used pipettes should be placed immediately into the provided waste container. Do not place any
hazardous or infectious materials in the regular trash. Do not place any hazardous or
infectious materials in the sink.
8. All used glass slides and coverslips should be placed in SHARPS boxes. Do not discard
slides in the biohazard bags.
9. Practice good aseptic technique by performing the following at the end of each lab exercise:
a) remove gloves inside out and place them in the biohazard bag
b) remove lab coats or aprons, fold them inside out, and place them in the assigned
drawer
c) remove goggles (if used) and clean with alcohol wipes before placing in cabinet for
sterilization
d) decontaminate your work bench by applying an antiseptic wash
e) wash your hands thoroughly
10. Practice good aseptic technique when making notes or recording results from your
experiments in your lab manual -- Do not write in your lab manual or notebook until AFTER you
have removed your gloves and apron and washed your hands!
11. If an accident should occur, such as a spill or a broken test tube:
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a) inform your instructor immediately

b) soak the area with disinfectant and cover with paper towels
c) dispose of contaminated paper towels in the biohazard bag
d) dispose of contaminated broken glass in the SHARPS container
e) wash hands thoroughly
12. If an accident results in bacterial culture coming in contact with eyes, mucous membranes or
an open wound:
a) eyes should be flushed immediately at the eye wash station
b) affected wound should be washed thoroughly with soap and water
c) the student should contact their personal physician for advice on further treatment
13. Accident reports must be filed with the Biosafety committee no more than 48 hours
following the accident.
14. Students who are pregnant or have a medical condition which could compromise their
immune system must have written permission from their attending physician in order to
participate in microbiology lab.
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MICROORGANISMS / BIOSAFETY LEVEL:

Below is a list of microorganisms that may be used in Biol2421 lab at Collin College, grouped
according to their designated Biosafety Level*:
Biosafety Level 1
Alcaligenes faecalis
Bacillus brevis
Bacillus coagulans
Bacillus licheniformis
Bacillus megaterium
Bacillus polymyxa
Bacillus sphaericus
Bacillus stearothermophilus
Bacillus subtilis
Staphylococcus intermedius
Staphylococcus saprophyticus
Staphylococcus xylosus
Streptococcus bovis
Streptococcus mutans
Biosafety Level 2
Acinetobacter lwoffii
Bacillus cereus
Edwardsiella tarda
Enterococcus faecalis
Klebsiella pneumonia
Morganella morganii
Proteus mirabilis
Proteus vulgaris
Pseudomonas aeruginosa
Salmonella typhimurium
Salmonella cholerasuis
Shigella boydii
Staphylococcus aureus
Streptococcus agalactiae
Streptococcus pyogenes
Streptococcus equi
Streptococcus equi subspecies zooepidemicus
Citrobacter freundii
Clostridium sporogenes
Enterobacter aerogenes
Enterobacter cloacae
Escherichia coli
Flavobacterium capsulatum
Klebsiella oxytoca
Micrococcus luteus
Mycobacterium smegmatis
Providencia alcalifaciens
Pseudomonas fluorescens
Pseudomonas putida
Saccharomyces cerevesiae
Serratia marcescens
Staphylococcus epidermidis
*Note: The Biosafety designation is based on the particular strain of the species that we use in the lab; other strains
of a given species may be a different biosafety level.
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ASEPTIC TECHNIQUE
1. Disinfect the tables with antibacterial cleaner.
2. Wear gloves and lab aprons.
3. When labeling Petri plates, always write on the bottom of the plate.
4. When using incinerators, give them ample time to warm up before sterilizing loops or
needles. DO NOT leave loops or needles unattended in the incinerators. They will melt!
You will burn your fingers!
5. When inoculating cultures, always sterilize your loop or needle before going into a
culture and after transferring it. Sterilize the loop even if you are going back into the
same culture again.
6. Make sure you let your loop cool first you dont want to kill the bacteria.
7. After removing the lid of a test tube, briefly flame the mouth of the tube before inserting
your inoculating loop, and flame again before replacing the cap.
8. Dont put anything down on the table loops, needles, pipettes, test tube lids, etc. Once
they touch the table they are no longer sterile.
9. Loops/needles can be placed temporarily in slots on the sides of incinerators.
10. Test tube lids can be held with pinky finger.
11. Pipettes should remain in canister until just before use.
12. Dont leave media open to the air bacteria and fungi in the air can contaminate the
media.
13. Dont over-inoculate! It doesnt take much inoculum to start a culture. Simply touch the
loop or needle to the bacterial growth and obtain a small amount on the loop. Dont
scrape the culture, and dont dig into the agar.
14. When streaking onto an agar plate or slant, make sure the loop doesnt break the surface
of the agar. A gentle gliding motion is all that is necessary to distribute the bacteria on
the plate.
15. When finished, disinfect the tables again with antibacterial cleaner. Dispose of gloves in
the biohazard trash, and place aprons back in your designated drawers. Wash your
hands!
NOTES:
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EXPERIMENT #1: MICROSCOPY

Brightfield Compound Light Microscope
The light microscope is an important tool in the study of microorganisms. The compound light
microscope uses visible light to directly illuminate specimens in a two lens system, resulting in
the illuminated specimen appearing dark against a bright background. The two lenses present in
a compound microscope are the ocular lens in the eyepiece and the objective lens located in the
revolving nosepiece. Compound light microscopes typically have the following components:
Illuminator: the light source in the base of the microscope.
Abbe Condensor: a two lens system that collects and concentrates light from the illuminator
and directs it to the iris diaphragm.
Iris Diaphragm: regulates the amount of light entering the lens system.
Mechanical Stage: a platform used to place the slide on which has a hole in the center to let
light from the illuminator pass through. Often contains stage clips to hold the slide in place.
Body tube: Houses the lens system that magnifies the specimens
Upper end of body tube -- Oculars/Eye pieces: what you view through
Lower end of body tube -- Nose-piece: revolves and contains the objectives
Principles of Microscopy
Basically, a light microscope magnifies small objects and makes them visible. The science of
microscopy is based on the following concepts and principles:
Magnification is simply the enlargement of the specimen. In a compound lens system, each
lens sequentially enlarges or magnifies the specimen. The objective lens magnifies the
specimen, producing a real image that is then magnified by the ocular lens resulting in the final
image. The total magnification can be calculated by multiplying the objective lens value by the
ocular lens value.
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Resolving power is the ability of a lens to show two adjacent objects as discrete entities. In
general, the shorter the wavelength of light, the better the resolution, which is why a blue filter
is usually connected to the condenser to produce short light waves for optimum resolution.
Resolving power is also dependent on the refractive index or the bending power of light.
Because air has a lower refractive index than glass, light waves have a tendency to bend and
scatter as they pass through the air from the glass slide to the objective lens. Addition of
immersion oil, which has the same refractive index as glass, diminishes the loss of refracted
light and improves resolution.
Contrast is the ability to distinguish an object from its background. Since most microbes are
relatively transparent when viewed under a standard light microscope they are difficult to
identify. Using a stain (labs 2-5) that will bind to the microorganism and not the glass slide,
dramatically enhances their contrast enabling them to be observed more clearly.
Depth-of-focus is the thickness of the sample that appears in focus at a particular
magnification. As the magnification increases the depth-of-focus decreases, or the slice of the
sample that appears in focus gets thinner. Many of the newer compound microscopes are par
focal, which means that if one objective lens has the object in focus, and you go to the next
objective lens, only minor adjustment (fine focus) is needed to bring the image back into focus.
This is due to the fact that as you increase the magnification, and thus the slice of the sample that
appears in focus becomes thinner, the correct plane-of-focus will always be within the depth of
focus of the previous objective. After you get the sample into focus at scanning or low power
using the course adjustment knob, you should only have to use the fine focus knob at the higher
magnifications.
Field-of-View is the area of the slide that you are observing through the microscope. As you
increase the magnification the actual area of the slide that you are looking at is getting smaller.
You can think of the field-of-view as a dartboard. At low magnification you are able to see the
entire dartboard, but as you increase the magnification you are only observing the bulls-eye, a
much smaller portion of the dartboard.
These microscopes are also par central, which refers to the ability to keep an object in the
middle of your field-of-view when changing from one objective to another. It is useful to
remember this as you are increasing magnification. Always keeping your sample in the center of
your field-of-view will avoid unnecessary searching of the slide for your sample.
Working distance is the distance between the objective and the slide. As you increase
magnification (by using more powerful objective lenses) the working distance decreases. So
much so that by the time you are using the oil-immersion objective (100X) the objective is
almost touching the slide, allowing the immersion oil to connect the slide and objective. It is
important to consider working distance in a number of applications, but practically there are two
reasons you should be aware of your working distance. The first is so that you do not
inadvertently push the objective through the slide, causing damage to the objective and your
sample slide. The second is to estimate whether you are in the correct plane-of-focus.
Care of Microscopes
Microscopes are very expensive pieces of scientific equipment and must be treated with care.
Each pair of students will be assigned a microscope to use throughout the semester, and will be
required to sign a microscope agreement form acknowledging responsibility for that microscope.
Some basic rules of microscope care include the following:
(1) Always carry a microscope with two hands, one on the base and one on the arm.
(2) Use the coarse focus knob on the lowest objective only. NEVER use coarse focus on
high power or oil immersion, or you may damage the objective lenses.
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(3) Always clean all lenses thoroughly with lens paper and lens cleaner before putting away.
Immersion oil which is not removed immediately can dry on the lenses, making it
difficult to view any specimen. Dried immersion oil is also quite difficult to remove from
the lenses.
(4) Always store the microscope with the lowest objective (4X) in place. NEVER store the
microscope with the oil immersion objective in place, as it can damage the lens.
MATERIALS NEEDED:
Commercially prepared slides of:
Any Staphylococcus species
Any Bacillus species
Saccharomyces cerevisiae (yeast)
Microscope
Immersion Oil
Lens Paper
Lens Cleaner
PROCEDURE:
1. Place the slide on the stage and use the coarse and fine focus knobs to bring the specimen
into focus under 4X magnification. Tip: Bring the stage all the way to the highest
position with the coarse focus knob. While looking through the ocular, gradually turn the
knob to lower the stage until the specimen comes into focus. Once you have it in focus
with the coarse focus knob, fine-tune with the fine focus.
2. Turn the revolving nose piece to bring the 10X objective into place and observe the
specimen. Repeat with the 40X objective. Draw several cells observed under 40X in the
spaces provided below.
3. Turn the revolving nose piece to bring the 100X objective into place and observe the
specimen. Move the nosepiece slightly so you can add a drop of immersion oil to the
slide, then bring the oil immersion objective back into place and fine-tune the focus.
Observe the specimen. You may need to turn down the amount of light in order to
observe the specimen under oil immersion.
4. Draw several cells observed under 100X in the spaces provided below.
5. Repeat steps 1-4 for the remaining prepared slides.
6. When finished, clean all lenses thoroughly with lens paper and lens cleaner. Have your
instructor check your microscope to make sure it is clean.
_______ (Instructors initials)
7. Store the microscope according to the instructions written on the inside of your
microscope cabinet.
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RESULTS:
Staphylococcus, 400X
Bacillus, 400X
Staphylococcus, 1000X
Bacillus, 1000X
Saccharomyces, 400X
Saccharomyces, 1000X
STUDY QUESTIONS:
1. State the purpose of each of the following microscope components:
a. Condenser
b. Fine-adjustment knob
c. Coarse-adjustment knob
d. Iris Diaphragm
e. Mechanical stage control
2. What is the purpose of adding immersion oil when using the 100X objective?
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3. Compare the relative sizes of the bacteria (Staphylococcus and Bacillus) and yeast
(Saccharomyces) under 10X, 40X, and 100X magnification.
4. Were you able to distinguish any internal structures, such as a nucleus, in any of the
specimens viewed under oil immersion (100X)? Explain.
5. If the ocular lens has a magnification of 10X and the objective lens has a magnification of
40X, what is the total magnification?
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STAINING OF BACTERIAL SPECIMENS

Bacterial specimens are often stained prior to microscopy studies, which allows better
visualization of specimens using microscopy. Simply speaking, a stain is a substance that
adheres to a cell, giving the cell color. Different stains have different affinities for different
organisms, or different parts of organisms. They may be used to differentiate different types of
organisms or to view specific parts of organisms.
There are several types of stains which are commonly used in microbiology. The first is
a simple stain, which uses only one reagent which provides contrast between the background
and the heat-fixed bacterium itself. The bacterium takes up stain and becomes colored, while the
background remains unstained. Simple stains are typically used on bacterial smears which have
been heat-fixed and thus contain non-living microbes.
A second type of stain is a negative stain, which uses a single reagent to provide contrast
between the background and the living bacterium. Thus, the background is stained, while
bacterium does not take up any stain. Negative stains are typically used when observing live
bacteria is desired.
A differential stain is a type of staining that allows you to distinguish between types of
bacteria or between specific structures in a bacterium. A differential stain typically uses two or
more reagents a primary stain and a counter stain.
Chemically, there are two main types of stains: basic stains, which have a positive
charge (cationic) and acidic stains, which have a negative charge (anionic). Basic stains have an
affinity for negative components of cells, and include dyes such as methylene blue, crystal violet,
and carbol fuchsin. Acidic stains have an affinity for positive components of cells, and include
dyes such as nigrosin, India ink, and picric acid. Since cell walls are negatively charged, a
positive dye will be attracted to and stain the cell wall, whereas a negative dye will be repulsed
by the cell wall and not directly stain the cell.
PREPARATION OF BACTERIAL SPECIMENS
In order to stain bacterial specimens, the bacteria must be placed on a glass slide and
prepared for the specific staining process. This is typically done by preparing a bacterial smear.
A smear is a small volume (a loopful) of specimen-containing medium that is spread (smeared)
onto a microscope slide. In preparing smears, the Goldilocks principle applies everything
has to be done just right! If smears are too thick, you will have trouble seeing individual cells. If
smears are too thin, you may not find the organism. If you stir the drop of medium too much as
you spread it on the slide, you will disrupt cell arrangements such as chains or clusters.
Following preparation of a bacterial smear, most smears need to be heat fixed before
they are stained. Heat fixation accomplishes three things: (1) it kills the organisms; (2) it causes
the organisms to adhere to the slide; and (3) it alters the organisms so that they more readily
accept stains (dyes). Again, the Goldilocks principle applies. Slides must be completely dry
before heat-fixing, or the organism will be boiled and destroyed. If you heat-fix too little, the
organism will wash off the slide. If you heat-fix too much, the organisms may be incinerated.
Specific instructions for preparing a bacterial smear and heat fixing the smear are outlined on the
following page.
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PROCEDURE FOR PREPARING A BACTERIAL SMEAR

1. Obtain a glass slide and clean if necessary.
2. Using a broth culture:
a. Gently agitate your culture broth tube to disperse the bacteria.
b. Sterilize your inoculating loop using an incinerator or a Bunsen burner, and let
cool for 20-30 seconds.
c. Place loop in the bacterial broth and put the loopful of the broth onto the glass
slide. Rub the drop into a nickel-sized smear. Sterilize the loop again to kill any
remaining bacteria. Let the smear air dry completely. Do not use heat to dry
your smear!
3. Using an agar plate:
a. Place a small drop of water in the center of the slide.
b. Sterilize your inoculating loop using an incinerator or a Bunsen burner, and let
cool for 20-30 seconds.
c. Use the sterile loop to pick up a small amount of bacterial growth from the
surface of the plate. Do not dig into the agar. Put the loopful of bacteria into the
drop of water on the glass slide, and rub the drop into a nickel-sized smear.
Sterilize the loop again to kill any remaining bacteria Let the smear air dry
completely. Do not use heat to dry your smear!
4. Heat fix the slide.
a. Incinerator method: Hold the slide with a wooden clothes pin approximately 1
cm over the barrel of a hot incinerator for 2030 seconds. Let the slide cool.
b. Bunsen burner method: Hold the slide with a wooden clothes pin, and pass 1012 times through the flame. Let the slide cool.
5. Optional: After the slide has cooled us a marker or wax pencil to outline the area of the
smear on the underside of the slide. This will help you locate your sample later.
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EXPERIMENT #2: GRAM STAIN

The Gram stain is a differential stain which distinguishes bacteria based on cell wall
properties. Bacterial cell walls are composed primarily of peptidoglycan and bacteria can be
classified into two main groups dependent on the amount of peptidoglycan present in their cell
wall. Gram-positive organisms have a thick layer of peptidoglycan, whereas Gram-negative
organisms have a thin layer of peptidoglycan, plus an additional outer membrane that is absent
in Gram-positive organisms.
Lipopolysaccharide
(LPS)
Teichoic acid
Outer
membrane
Peptidoglycan
Lipoteichoic acid
Peptidoglycan
Cytoplasmic
membrane
Cytoplasmic
membrane
Gram-positive cell wall
Gram-negative cell wall
In the gram staining procedure, the primary stain is crystal violet, and all cells take up
the purple crystal violet stain. Following the primary stain, Grams Iodine is applied to the
bacterial smears. The iodine acts as a mordant, enhancing the ability of the stain to enter and
bind to the bacteria. Specifically, the iodine binds with crystal violet and locks it into
peptidoglycan of bacteria. It also intensifies the purple color. The decolorizing agent used in
the gram staining procedure is 95% ethanol, which is a lipid solvent that melts the Gramnegative outer membrane and leads to decolorization of Gram-negative cells. It also dehydrates
proteins, helping the primary stain to remain in Gram-positive cell walls. The counter stain
then used is Safranin, which stains the decolorized Gram-negative cells pink. Thus, at the end of
the staining procedure, Gram-positive cells are purple and Gram-negative cells are pink. Note:
It is preferable to use fresh cultures for the Gram stain. Old cultures may stain Gram-variable
(a mix of purple and pink) because they decolorize easily.
Overview of Gram Stain:
Primary Stain
Mordant
Decolorizer
Counter Stain
Crystal Violet
Grams Iodine
95% Ethanol
Safranin
CULTURES NEEDED:
Nutrient broth tubes or plates of the following:
Escherichia coli
Bacillus megaterium
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PROCEDURE:
Note: This is an individual lab exercise each student will perform their own Gram stain.
1. Prepare a bacterial smear with a mixture of all 3 organisms (i.e. 1-2 loopfuls of each)
listed above and heat fix as described on page 13.
2. Place the slide on a staining tray, and cover the smear with crystal violet. Allow to stain
for 60 seconds.
3. Tilt the slide and gently rinse with distilled water until the stain is removed.
4. Cover the smear with Grams Iodine, and allow to sit for 60 seconds.
5. Tilt the slide and gently rinse with distilled water.
6. IMPORTANT STEP: Tilt the slide and let 2-3 drops of Decolorizer run over the slide.
If the last drop is still purple, continue decolorizing, 2-3 drops at a time, until the
decolorizer runs clear. Rinse with distilled water.
7. Cover the smear with Safranin, and stain for 45 seconds.
8. Tilt the slide and rinse with distilled water.
9. Place the slide in a book of Bibulous paper and blot to dry. You do not need a cover slip!
Observe the slide under oil immersion, and draw what you see in the results section
below. You should see: Small purple cocci (spheres) which are the gram-positive S.
xylosus, large purple rods, which are the gram-positive B. megaterium, and small pink
rods, which are the gram-negative E. coli. Label these in your drawing.
10. Clean your microscope with lens cleaner, paying extra attention to the 40X and 100X
objectives. Have your instructor check your microscope to make sure it is clean.
_______ (Instructors initials)
11. Dispose of staining waste in designated waste receptacle. Dispose of slides in red
SHARPS container.
RESULTS:
Using colored pencils, draw and label S. xylosus, B. megaterium, and E. coli in the circle
below.
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STUDY QUESTIONS:
1. Describe several advantages of differential staining procedures compared with simple
staining techniques.
2. Give the purpose of each of the following reagents in a differential staining procedure:
a. Primary stain
b. Counter stain
c. Decolorizing agent
d. Mordant
3. Why is it important for the counter stain to be a lighter color than the primary stain?
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EXPERIMENT #3: CAPSULE STAIN

The capsule stain is a type of differential stain which selectively stains bacterial
capsules. A capsule is a substance that is synthesized in the cytoplasm and secreted to the
outside of the cell where it surrounds the
DNA
bacterium. Capsules can be polysaccharide,
polypeptide, or glycoprotein. Capsules are
associated with virulence in several
capsule
microorganisms, including Streptococcus
cell wall
pneumoniae and Neisseria meningitidis, because
capsules provide a mechanism for these
cell membrane
pathogens to evade the host immune system.
Because of their structure and composition, heat
and water will dislodge capsules from bacteria
Bacterial capsule
during laboratory procedures.
In the capsule staining procedure, the primary stain is crystal violet, and all parts of the
cell take up the purple crystal violet stain. There is no mordant in the capsule staining procedure.
A 20% copper sulfate solution serves a dual role as both the decolorizing agent and counter
stain. It decolorizes the capsule by washing out the crystal violet, but will not decolorize the
cell. As the copper sulfate decolorizes the capsule, it also counter stains the capsule. Thus, the
capsule appears as a faint blue halo around a purple cell.
CULTURES NEEDED:
Milk broth tubes of Flavobacterium capsulatum
(Note: your instructor may provide additional organisms for staining)
PROCEDURE:
Note: Students will work in pairs to perform the capsule stain.
1. Obtain a clean glass slide. Choose one of the above broth cultures, and agitate your broth
culture to disperse the bacteria.
2. Prepare a smear using 2-3 loopfuls of the broth culture. Allow the smear to air-dry, but
DO NOT HEAT FIX THIS SLIDE! Heat will cause the capsule to dislodge.
3. Cover the smear with crystal violet, and stain the smear for 2 minutes.
4. Tilt the slide and rinse with 20% copper sulfate solution. DO NOT RINSE WITH
WATER! Water will remove the capsule from the cell.
5. Let the slide air dry for a few minutes. DO NOT blot the slide! Blotting will remove the
bacteria from the slide and/or distort the capsule.
6. Observe the slide under oil immersion, and draw what you see in the results section
below. Look for purple cells surrounded by a clear or faint blue halo on a purple
background. (The halo is the capsule.) You may need to decrease the amount of light in
order to make the capsule easier to see.
7. Clean your microscope with lens cleaner, removing all oil from lenses. Have your
instructor check your microscope to make sure it is clean. _______ (Instructors initials)
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SHARPS container.
RESULTS:
Using colored pencils, draw the results from the capsule stain:
______________________
(name of organism)
STUDY QUESTIONS:
1. Why are capsule stains NOT rinsed with water? (Hint: think about what capsules are
made of.)
2. Explain the clinical significance of a bacterial capsule.
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EXPERIMENT #4: ACID-FAST STAIN

The acid-fast stain is a
differential stain which distinguishes
bacteria based on cell wall properties.
Bacteria which are acid-fast are
Gram-positive microorganisms that
are resistant to the Gram stain, so
implementing the acid-fast stain
allows us to visualize these bacteria.
Acid-fast bacteria have a waxy
substance called mycolic acid in their
cell walls, which comprises up to 60%
of the cell wall components. They
also contain polymers called
arabinogalactan and
lipoarabinomannan. Genera which
are acid-fast include Mycobacterium and Nocardia, which include pathogenic organisms such as
M. leprae and M. tuberculosis.
The primary stain in the acid-fast staining procedure is carbol fuchsin, which contains
phenol to solubilize the cell wall and allow the stain to enter the cell. The procedure requires the
application of heat in order for the stain to penetrate the waxy cell wall. All cells will take up
the reddish-pink primary stain. Once the cells have been allowed to cool after the primary stain,
the cells are decolorized. The decolorizer used in the acid-fast staining procedure is acid
alcohol, which decolorizes all cells except acid-fast cells. The acid alcohol is unable to penetrate
the waxy cell wall of acid-fast microorganisms. The counterstain then used is methylene blue,
which stains the decolorized non acid-fast cells blue. Thus, at the end of the staining procedure,
acid-fast cells are reddish-pink and all other cells are blue.
CULTURES NEEDED:
Nutrient broth tubes or plates of Mycobacterium smegmatis
Nutrient broth tubes or plates of Staphylococcus xylosus
PROCEDURE:
Note: Students will work in pairs to perform the acid-fast stain.
1. Fill a beaker about 1/3 to 1/2 full of tap water and place on a hot plate. Turn hot plate on
high and allow water to boil. Once the water comes
to a boil, reduce the heat to low.
2. Prepare a bacterial smear with a mixture of M.
smegmatis and S. xylosus (i.e. 2-3 loopfuls of M.
smegmatis + 1 loopful S. xylosus) and heat fix as
described on page 13.
3. Place the slide on top of the beaker of water and let
steam for 5 minutes.
4. Place a paper towel square on top of the smear area.
This will hold the stain in place and keep it from
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running off the slide.

5. Apply enough Carbol Fuchsin to soak the paper towel square and allow to sit for 5
minutes, keeping the paper towel moist with stain. Do not let it dry!
6. Carefully remove the slide with a clothes pin (slide will be hot!) and place on the staining
tray to cool. Remove paper towel square.
8. Tilt the slide and rinse with Acid Alcohol, drop by drop, until the acid alcohol runs clear.
10. Cover the slide with Methylene Blue and allow it to sit for 2 minutes.
12. Blot your slide dry with Bibulous paper and observe your slide under oil immersion using
proper microscope techniques. Record your results below. You should observe acid fast
(reddish-pink) rods.
13. Clean your microscope with lens paper and lens cleaner, paying extra attention to the
40X and 100X objectives.
SHARPS container.
RESULTS:
1. Using colored pencils, draw the results of the acid-fast stain, labeling the M. smegmatis
and S. xylosus:
STUDY QUESTIONS:
1. Why must heat be used with the application of the primary stain during acid-fast
staining?
2. When and why would the acid-fast stain be used in a hospital or clinical lab?
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EXPERIMENT #5: ENDOSPORE STAIN

The endospore stain is a differential stain which stains bacterial endospores or spores.
Some bacteria, including those belonging to the genera Clostridium and Bacillus, have the
capacity to produce metabolically inactive cells called spores. Spores are highly resistant to
hostile chemical and physical conditions and are produced by a process called sporulation if
environmental conditions become unfavorable for normal vegetative growth. The spore
structures have a tough outer covering composed primarily of keratin which makes them
resistant to heat, radiation, disinfectants, and
desiccation. The bacteria will remain in this suspended
state until conditions become favorable again and they
can germinate and return to their vegetative state. The
term endospore refers to the spore structure contained
within a mother cell. The term spore refers to the
spore structure that exists free of the mother cell.
Endospores may be located in the middle of the cells
(central), at the end (terminal), or between the end and the middle of the cells (subterminal). The
endospores themselves may be round or oval.
The primary stain in the endospore staining procedure is malachite green, which stains
both vegetative cells and endospores. As with the acid-fast stain, heat is required to penetrate
the endospore coat. Once the cells have cooled, the cells are decolorized with water, which
selectively removes the malachite green from all vegetative cells but not from endospores. The
counterstain then applied is safranin, which stains the decolorized vegetative cells pink. Thus,
at the end of the staining procedure, the endospores are dark green, and vegetative cells are pink.
Note: Sometimes the endospores dont take up the malachite green very well. In those cases,
the endospores will appear as clear ovals or circles within a pink vegetative cell.
CULTURES NEEDED:
Bacillus megaterium
PROCEDURE:
Note: Students will work in pairs to perform the endospore stain.
1. Fill a beaker about 1/4 to 1/3 full of tap water and place on a hot plate. Turn hot plate on
high and allow water to boil. Once the water comes to a boil, reduce the heat.
2. Obtain a clean glass slide and prepare a bacterial smear as described on page 13. Air dry
and heat fix the slide. Be sure to label your slide!
3. Place the slide on top of the beaker of water and let
steam for 5 minutes.
4. Place a paper towel square on top of the smear area.
This will hold the stain in place and keep it from
running off the slide.
5. Apply enough Malachite Green to soak the paper
towel square and allow to sit for 2-3 minutes, keeping
the paper towel moist with stain. Do not let it dry!
6. Carefully remove the slide with a clothes pin (slide
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will be hot!) and place on the staining tray to cool. Remove paper towel square.
8. Cover the slide with Safranin and allow to sit for 30 seconds.
10. Blot your slide dry with Bibulous paper and observe your slide under oil immersion using
proper microscope techniques. Record your results below. Endospores will appear as
dark green or clear circles or ovals, whereas vegetative cells will be pink rods.
11. Clean your microscope with lens paper and lens cleaner, paying extra attention to the
40X and 100X objectives.
SHARPS container.
RESULTS:
1. Using colored pencils, draw the results of the endospore stain. Label an endospore and a
free spore in the drawing. Are the endospores central, terminal, or subterminal? (circle
one)
B. megaterium
STUDY QUESTIONS:
1. Why must heat be used with the application of the primary stain during endospore
staining?
2. What advantage does the ability to sporulate give to pathogenic bacteria such as
Clostridium tetani, Clostridium botulinum and Bacillus anthracis?
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EXPERIMENT #6 CULTURE TRANSFER TECHNIQUES

The purpose of this lab exercise is to learn how to subculture microorganisms in various
types of microbiological media. Simply stated, subculturing is transferring microorganisms
from one media type to another. Various media types used in microbiology labs include agar
slants, agar deeps, agar plates, and broths. An agar slant is a solid media in a test tube with a
slanted surface on which to culture the microorganism. These are typically inoculated by
streaking the surface of the slant with a sterile loop. An agar deep is a solid media in a test tube
which does not have a slanted surface. These are typically inoculated by stabbing the media with
a sterile needle. An agar plate is a solid media which is contained in a Petri plate, providing an
optimal surface on which to culture microorganisms. Like the agar slants, these are inoculated
by streaking the surface with a sterile loop. Broth tubes are a liquid medium which can be
inoculated by a sterile loop, needle, or pipette. Remember that when inoculating any cultures, it
is essential to practice sterile technique at all times!
It is important to know what sterile media looks like. Take a minute to observe your
uninoculated cultures. You will be responsible for making sure there are no contaminates
present in the media we provide for you.
MEDIA NEEDED:
1 Nutrient agar slant
1 Nutrient agar deep
1 Nutrient broth tube
CULTURES NEEDED:
Serratia marcescens broth cultures and slants
PROCEDURE:
1. Label each tube appropriately.
2. Using a sterile needle, obtain a small amount of culture from the broth tube containing
Serratia marcescens. Use the needle to inoculate a nutrient agar deep tube by stabbing
the needle into the agar deep.
3. Using a sterile loop, obtain a loop full of culture from the broth tube containing Serratia
marcescens. Use the loop to inoculate a nutrient agar slant tube by streaking the agar
slant with a zig-zag motion.
4. Using a sterile loop, obtain a loop full of culture from the slant of Serratia marcescens.
Use the loop to inoculate a nutrient broth tube by gently swishing the loop around in the
liquid broth.
5.
Make sure all caps are loose, but secure.
6. Incubate at 30 C for 48 hours.
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RESULTS:
Examine broth tubes, agar deep tubes and agar slant tubes. Complete the chart below:
Nutrient Broth
Nutrient Agar Slant
Nutrient Agar Deep
Growth (+) or (-)
Red pigmentation
(+) or (-)
Sketch the distribution
of growth
STUDY QUESTIONS:
1. Why is it important to sterilize the inoculating instrument before and after each
inoculation?
2. Why did we use an inoculating needle to inoculate the agar deep tube?
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EXPERIMENT #7 ISOLATION OF PURE CULTURES

The purpose of this experiment is to separate a mixed culture of Serratia marcescens and
Escherichia coli and obtain single, isolated colonies of each bacterial species. When working
with microorganisms, it is desirable to start with single, isolated colonies to ensure you are
working with a pure culture. Cultures that are visible on the surface of solid media are called
colonies. A colony forms on a plate when a
single microbe is inoculated onto the surface of
the plate and reproduces until there are enough
cells to form a visible colony. Since a colony
theoretically forms from a single cell, a colony
should then represent a pure culture. One way
to obtain single, isolated colonies is using the
quadrant streak method. The quadrant streak
plate method allows sequential dilution of the
original microbial material over the entire
surface of a fresh plate. As the original sample
is diluted by streaking it over successive
quadrants, the number of organisms decreases.
Usually by the third or fourth quadrant only a
few organisms are transferred, and these
produce single, discrete colonies.
MEDIA: (per student)
Nutrient agar plate
CULTURES:
Mixed broth culture of Serratia marcescens and Escherichia coli.
PROCEDURE:
(NOTE: YOUR INSTRUCTOR MAY PRESENT AN ALTERNATE METHOD.)
1. Divide the agar plate into 4 quadrants.
2. Place a loopful of culture onto the plate in Quadrant 1 with a sterile loop and streak the
loop very gently using a back and forth motion.
3. Sterilize loop. Go back to the edge of Quadrant 1 and extend the streaks into Quadrant 2,
going back into Quadrant 1 twice.
going back into Quadrant 2 twice.
going back into Quadrant 3 twice. Be careful NOT to go back into Quadrant 1!
6. Tape plate closed on both sides. Make sure the plate is labeled with your name, date, and
the organism(s), and incubate upside down (to prevent condensation from getting on to
agar) at 30 C.
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RESULTS:
Examine your isolation streak plate. Did you obtain single, isolated colonies of Serratia
marcescens and Escherichia coli?
Do you see two distinct colony types on the agar plate? Hint: S. marcescens should be pinkishred and E. coli should be cream-colored.
Draw the distribution of the growth and colonies on the plate.
STUDY QUESTIONS:
1. Why is it important to start a bacterial culture with a single, isolated colony?
2. Suppose you suspect that a supposedly pure bacterial culture is contaminated with
another bacterium. Could you use this technique to determine if a contaminant is
present? Explain.
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EXPERIMENT #8: VIABLE PLATE COUNTS

The purpose of this exercise is to quantify the number of bacteria in a broth culture of E.
coli. In microbiological research, it is often necessary to be able to quantify the number of
living bacteria in a particular sample. One of the major ways to do this is using viable plate
counts, in which bacterial cells from a liquid culture are spread onto an agar plate. The plate is
incubated, the number of colonies that grow on the plate are counted, and the number of original
bacterial cells in the culture is determined. In most cases, however, the liquid culture being
quantified contains too many cells to be directly plated onto agar plates there would be so
much growth that it would be impossible to count individual colonies! Therefore, the liquid
culture needs to be diluted, often 1-million-fold, before it can be plated.
When such a large dilution is required, an accurate dilution cannot be made in a single
dilution step and it is necessary to make serial dilutions. Serial dilutions are a step-wise set of
dilutions which sequentially dilute the bacterial culture. One or more of the dilutions are then
plated on the agar plates to determine the number of colonies present in the original culture.
Only plates containing between 30 and 300 colonies are counted to ensure statistically significant
data. To estimate the number of bacterial in the original culture, the # of colonies on the plate is
multiplied by the total dilution plated. For example, suppose 0.1 ml of a 10-6 dilution was plated,
and 123 colonies were counted following incubation. The total dilution plated would be 10-7
(since only 0.1 ml was plated), and the number of bacteria/ml of the original culture would be:
(123) x 1/10-7 = 1.23 x 109 CFU/ml. Note that the results are expressed as colony forming units
(CFU) per ml.
1 ml original
culture
1.0 ml
9 ml broth +
1 ml original
culture
1.0 ml
1:10
dilution
(10-1)
1.0 ml
1:100
dilution
(10-2)
1:1000
dilution
(10-3)
1.0 ml
1:10,000
dilution
(10-4)
1:100,000
dilution
(10-5)
0.1 ml
-6
(10 )
# Colonies
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MEDIA NEEDED: (per group of four)

3 Nutrient agar plates
7 Dilution blanks containing 9 ml water
CULTURES NEEDED:
Overnight broth culture of Escherichia coli
PROCEDURE:
1. Label the dilution blanks as follows: 10-1, 10-2, 10-3, 10-4, 10-5, 10-6, 10-7.
2. Label the agar plates as follows: 10-6, 10-7, 10-8.
3. Using a sterile pipette, transfer 1 ml of the E. coli broth culture into the tube labeled 10-1.
Mix thoroughly.
4. Using a new sterile pipette, transfer 1 ml of the 10-1 tube into the tube labeled 10-2. Mix
thoroughly.
thoroughly.
thoroughly.
thoroughly.
thoroughly.
thoroughly.
10. Using a new sterile pipette, transfer 0.1 ml of the 10-5 tube to the nutrient agar plate
labeled 10-6, and spread the liquid thoroughly and evenly over the surface of the plate
using a sterile disposable spreader. Be careful not to let the spreader dig into the agar!
[Note: Since were only plating 0.1 ml of the 10-5 dilution, the total dilution plated is 106
.]
using a sterile disposable spreader.
using a sterile disposable spreader.
13. After the liquid has absorbed into the plates, tape them closed on both sides. Make sure
your plates are labeled with your name, date, and the organism, and incubate upside
down at 30 C.
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RESULTS:
Examine the nutrient agar plates for growth, and count the number of colonies on each plate.
Remember, the number has to be between 30 and 300 in order to be statistically accurate. If your
plate has fewer than 30 colonies, record the number as TFTC for too few to count. If your
plate has more than 300 colonies, record the number as TNTC for too numerous to count.
Then, use the formula on the previous page to determine the number of CFU/ml of the original
broth culture.
Dilution
Number of colonies
Number of CFU/ml of original broth culture

(Remember to use scientific notation!)
10-6
10-7
10-8
STUDY QUESTIONS:
1. Why do you think it is important to be able to quantify the number of viable bacteria in a
sample?
2. Give an example of an industrial setting where quantifying viable bacteria would be a

useful tool.
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EXPERIMENT #9 EFFECT OF TEMPERATURE ON GROWTH OF MICROORGANISMS

Bacterial growth is dependent on the ability of bacterial enzymes to carry out metabolic
processes, and is therefore dependent on temperature. In general, enzymes are less active at low
temperatures due to low kinetic energy, and are increasingly active as temperatures increase.
However, when temperatures become too high, enzymes will become denatured and will cease to
function properly. Another important factor in bacterial growth is membrane fluidity. At low
temperatures, the lipids in a cell membrane can pack too tightly and solidify, prohibiting the
membrane from functioning properly. When temperatures become excessively high, the lipid
bilayer can become too fluid and lose its integrity. As a group, bacteria are capable of growth
within a range from -5 C to 80 C, with some archea able to withstand even higher
temperatures. However, each individual bacterial species will have a more narrow range in
which it can grow. For every organism there are three cardinal temperatures: the minimum
growth temperature, the optimum growth temperature, and the maximum growth temperature.
The minimum growth temperature is the lowest temperature at which a specific organism will
grow and reproduce. The optimum growth temperature is the temperature at which a specific
organism exhibits maximum growth and reproduction. The maximum growth temperature is
the highest temperature at which a specific organism will grow and reproduce. Although the
optimum growth temperature is different for each organism, it is generally closer to the
maximum growth temperature than the minimum.
All prokaryotes can be classified into four general groups depending on their temperature
requirements. If an organism grows at temperatures ranging from -5 to 20 C, its classified as a
psychrophile. An organism that grows in a range from 20 to 45 C is classified as a mesophile.
(The term psychrotroph is often used to describe organisms which are able to grow at
temperatures below 10 C, but also grow in the mesophile range.) Thermophiles are able to
grow in a range from 45 to 80 C. Some archaea are classified as hyperthermophiles, which
can grow at temperatures greater than 80 C, some up to 105 C.
It is important to note that the specific growth range will vary for each species in a given
temperature class. For example, while Staphylococcus aureus and Staphylococcus epidermidis
are both classified as mesophiles, the maximum growth temperature for S. epidermidis is only 40
C, whereas S. aureus will grow at 45 C.
For this lab exercise, each group will design and conduct an experiment to determine the
temperature classification of five different species of bacteria, using the provided media and
equipment.
MEDIA AVAILABLE: (per group of four)
4 nutrient agar plates
EQUIPMENT AVAILABLE:
Incubators set at various temperatures (4 C, 25 C, 37 C, 55 C)
(Note: the 4 C incubator is the refrigerator, and 25 C is approximately room temperature)
CULTURES NEEDED:
Escherichia coli, Bacillus stearothermophilus, Pseudomonas fluorescens, Serratia
marcescens, Micrococcus luteus
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PROCEDURE:
(Outline your experimental design in the space provided below.)
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DATA:
Serratia
marcescens
Pseudomonas
fluorescens
Escherichia
coli
Bacillus
stearothermophilus
Micrococcus
luteus
CONCLUSIONS:
Organism
Temperature Class*
Serratia marcescens
Pseudomonas fluorescens
Escherichia coli
Bacillus stearothermophilus
Micrococcus luteus
(*psychrophile, psychrotroph, mesophile, or thermophile)
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STUDY QUESTIONS:
1. If a bacterial culture is incubated at a temperature that is above the maximum growth
temperature of that organism, what effect will that have on its cellular enzymes?
2. If an organism grew at 20 C, how could you experimentally determine whether it was a

psychrophile or a mesophile?
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EXPERIMENT #10 -- ATMOSPHERIC OXYGEN REQUIREMENT FACTORS

Bacterial growth is also dependent on the presence of oxygen in the environment, as
different bacteria have different oxygen requirements depending on the types of enzymes they
possess. The major bacterial oxygen classes are aerobes, microaerophiles, obligate anaerobes,
aerotolerant anaerobes, and facultative anaerobes. Aerobes require atmospheric O2 (20%), and
use O2 as the final electron acceptor in the electron transport system. Microaerophiles require
O2 at below atmospheric concentrations, typically 2-10%. Microaerophiles have a limited
ability to neutralize toxic oxygen, so excess O2 will kill the bacteria. However, microaerophiles
do use O2 as final electron acceptor in the electron transport system. Obligate Anaerobes
cannot survive in the presence of any oxygen. Obligate anaerobes lack the enzymes necessary to
break down the toxic by-products of oxygen. In these bacteria, the final electron acceptor in the
electron transport system is a molecule other than O2. Aerotolerant Anaerobes grow equally
well in the presence or absence of oxygen. They do possess enzymes necessary to neutralize
toxic oxygen by-products, but they never use O2 as a final electron acceptor. Facultative
Anaerobes are also able to live either in the presence or absence of oxygen, but they prefer
oxygen so they can carry out aerobic respiration with O2 as final electron acceptor to maximize
ATP yields. These organisms can use other electron acceptors if O2 is not available, such as
fumarate and nitrate. They can also utilize fermentative metabolism in the absence of oxygen.
One simple way to determine the oxygen requirements of a bacterium is to inoculate the
bacterial culture into a melted agar deep tube of brain heart infusion (BHI) media, mixing well to
evenly distribute the bacteria throughout the liquefied agar. Once the agar solidifies, an oxygen
gradient is created, with atmospheric oxygen concentrations at the top of the tube and little to no
oxygen present at the bottom of the tube. The bacteria present in the agar deep tube will only be
able to grow where their oxygen requirements are met, and will localize to the area(s) of their
oxygen requirements in the tube.
Based on your knowledge of oxygen requirements, sketch where you think growth would occur
in the BHI tube for each oxygen class:
Obligate
Aerobe
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36
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Obligate
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Revised Spring 2013
MEDIA NEEDED: (per group of 4)

4 Brain Heart Infusion (BHI) deeps
CULTURES NEEDED:
Staphylococcus xylosus, Mycobacterium smegmatis, Bacillus megaterium, Micrococcus
luteus, Saccharomyces cerevisiae, Clostridium sporogenes, Enterococcus faecalis,
Serratia marcescens
PROCEDURE:
1. Obtain 4 melted BHI tubes from the water bath and label with 4 of the above bacteria.
Each person in the group should be responsible for one BHI tube. Coordinate with
another group so that all microorganisms are tested!!
2. While the BHI tube is still liquefied, add 2 drops of the appropriate inoculum into the
BHI tube using a sterile Pasteur pipette. Alternatively, you may gently inoculate the
liquefied BHI tube using a sterile loop or needle. Place cap loosely (but securely) on the
tube. You need to work quickly so the agar doesnt solidify!
3. Roll the BHI tube between the palms of your hands to disperse the bacteria throughout
the tube, taking care not to create bubbles or aerate the agar.
4. Place the BHI tube in ice bath until solidified.
5. Remove from ice bath, and place in incubator. Incubate at 37 C for 48 hours.
RESULTS:
Examine the BHI deep tubes for presence/absence of microbial growth and location of growth.
Record results in the table below.
Species
Distribution of growth
Oxygen Requirement Classification
Mycobacterium smegmatis
Bacillus megaterium
Micrococcus luteus
Saccharomyces cerevisiae
Clostridium sporogenes
Serratia marcescens
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STUDY QUESTIONS:
1. Why is it important to avoid creating bubbles or aerating the liquefied BHI tubes when
mixing the bacteria into the agar?
2. What do the following classes of bacteria have in common?

a. Obligate aerobes and Microaerophiles?
b. Aerotolerant and Obligate anaerobes?
c. Facultative and Aerotolerant?
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EXPERIMENT #11 CULTIVATION OF ANAEROBIC ORGANISMS

Specialized methods are necessary to culture organisms anaerobically. One such
method is the use of fluid thioglycollate broth, which is a reducing medium. It contains
sodium thioglycollate, which reacts with molecular oxygen keeping free oxygen levels low.
The sodium thioglycollate in the broth creates a redox potential in the tube, with higher levels
of oxygen at the top of the tube, and a complete absence of oxygen at the bottom of the tube.
Fluid thioglycollate broth also typically contains a redox potential indicator such as resazurin,
which produces a pink coloration in an oxidized environment. As with the BHI media described
in Experiment #10, organisms will only be able to grow where their oxygen requirements are
met, and will localize to the area(s) of their oxygen requirements in the fluid thioglycollate broth
A second method used to culture organisms anaerobically is the use of a GasPak Jar.
This is a specialized culture vessel in which an anaerobic environment is generated after
inoculated media are sealed into the chamber. Anaerobic conditions are created by adding water
to a gas generator envelope that is placed in the jar just before sealing. There are two chemical
tablets in the envelope, sodium
borohydride and sodium
bicarbonate. Water reacts with these
chemicals, producing hydrogen gas
from the sodium borohydride and
carbon dioxide from the sodium
bicarbonate. The hydrogen gas
combines with free oxygen in the
chamber to produce water, thus
removing all free oxygen from the
chamber. This reaction is catalyzed by
the element palladium (#46 on the
periodic table), which is attached to
the underside of the lid of the jar. The
carbon dioxide replaces the removed
oxygen, creating a completely anaerobic environment.
For this lab exercise, each group will design and conduct an experiment to determine the
oxygen classification of four different species of bacteria, using the provided media and
equipment.
MEDIA AVAILABLE: (per group of four)
4 thioglycollate broth tubes
2 nutrient agar plates
EQUIPMENT AVAILABLE:
Gas Pak Jar
Incubators set at 37 C
CULTURES NEEDED:
Bacillus megaterium, Pseudomonas aeruginosa, Escherichia coli, Clostridium
sporogenes
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PROCEDURE:
(Outline your experimental design in the space provided below.)
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RESULTS/CONCLUSIONS:
Species
Oxygen Requirement
Classification
Pseudomonas.
aeruginosa
Bacillus
megaterium
Escherichia coli
Clostridium
sporogenes
STUDY QUESTIONS:
1. At the molecular level, why are strict aerobes unable to grow in the absence of oxygen?
2. Since humans require oxygen in cellular respiration, we are classified as aerobic

organisms. Therefore, how are obligate anaerobes such as Clostridium tetani (causative
agent of tetanus) and Clostridium difficile (causes diarrhea) able to infect the human
body?
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EXPERIMENT #12: USE OF SELECTIVE, DIFFERENTIAL,
AND ENRICHED MEDIA
Microbiologists often used multiple types of media to cultivate microorganisms in order

to either specifically grow a particular organism, or to obtain information about the biochemical
properties of the organisms that grow. Three commonly used types of media are selective media,
differential media, and enriched media.
Selective media is designed to suppress the growth of some microorganisms while
allowing the growth of others (i.e., it selects for certain microbes). Solid media is usually
employed with selective media so that individual colonies may be isolated.
Examples of selective media include mannitol salt agar, MacConkey agar, eosin-methylene blue
agar, and Columbia C-CNA agar.
Differential media allow the growth of more than one microorganism of interest but
with morphologically distinguishable colonies based on specific biochemical properties of the
organisms. Most differential media contain a substrate and a chemical indicator, often a pH
indicator. As with selective media, solid media is usually employed so individual colonies may
be observed. Examples of differential media include mannitol salt agar, DNAse agar, blood
agar, MacConkey agar and eosin-methylene blue agar.
Enriched media contains specific growth factors needed by fastidious bacteria to support
their growth. Examples of enriched media include blood agar and chocolate agar.
Described below are the specific properties of some of the more commonly used
selective, differential, and enriched media. Note that a particular type of media can have
multiple properties e.g. it can be both selective and differential!
Mannitol Salt Agar:
Mannitol salt agar (MSA) is both selective and differential. MSA contains 7.5% NaCl, which
selects for halotolerant organisms such as members of the Staphylococcus genus. The media
also contains the carbohydrate substrate mannitol, and a pH indicator, phenol red. Organisms
which are able to ferment the mannitol will produce acid fermentation products which lower the
pH, causing the phenol red indicator to turn yellow.
Blood Agar:
Blood agar is a differential medium. It is also commonly used as an enriched medium for
growing fastidious bacteria. Some bacteria produce exotoxins called hemolysins that cause lysis
of red blood cells. The degree of the hemolysis is an especially useful tool for differentiation
among Gram-positive cocci. The three types of hemolysis are:
1. Beta hemolysis, which is the complete lysis of red blood cells and hemoglobin. This
results in complete clearing of the blood around colonies.
2. Alpha hemolysis refers to the partial lysis of red blood cells and hemoglobin. This results
in a greenish-grey or greenish-yellow discoloration of the blood around the colonies.
3. No hemolysis, sometimes called gamma hemolysis results in no change in the medium.
MacConkey Agar:
MacConkey Agar is both selective and differential. This media contains crystal violet and bile
salts, which inhibit most gram-positive organisms and select for gram-negative organisms. It
also contains the substrate lactose and the pH indicator neutral red, which allow differentiation
among gram-negative bacteria based on their ability to ferment lactose. When lactose is
fermented by coliforms such as Escherichia coli, acid end-products lower the pH of the media
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below 6.8, with the resulting colonial growth turning pinkish-red. If an organism is unable to
ferment lactose, the colonies will be colorless, taking on the color of the medium.
Eosin Methylene Blue Agar:
Eosin Methylene Blue (EMB) agar is both selective and differential. This media contains the
dyes eosin and methylene blue, which inhibit gram-positive growth and select for gram-negative
organisms. It also contains lactose, allowing differentiation between organisms which ferment
lactose and produce acid end-products, and organisms that do not ferment lactose. Small
amounts of acid production result in a pink colored growth (e.g. Enterobacter aerogenes) while
large amounts of acid cause the acid to precipitate on the colony, resulting in a characteristic
greenish, metallic sheen (e.g. E. coli). Organisms which do not ferment lactose will be colorless,
taking on the color of the medium.
Columbia C-NA Agar:
Columbia C-NA (CCNA) agar is both selective and differential. This media contains two
antibiotics, colistin and nalidixic acid, which prohibit the growth of most gram-negative
organisms. Gram-positive organisms such as members of the Staphylococcus and Streptococcus
genera are allowed to grow. Addition of blood to the agar allows differentiation by hemolytic
patterns.
1 Mannitol Salt agar plate
1 Blood agar plate
1 MacConkey agar plate
1 Eosin-Methylene Blue (EMB) agar plate
1 Columbia C-NA (CCNA) agar plate
CULTURES NEEDED:
Enterobacter aerogenes, Escherichia coli, Pseudomonas aeruginosa, Streptococcus
zooepidemicus, Streptococcus mutans, Enterococcus faecalis, Staphylococcus xylosus,
Staphylococcus epidermidis, Salmonella typhimurium
PROCEDURE:
1. Label each plate according to the diagram on the following page. Dont forget to also put
your name/initials and the date.
2. Using a sterile loop, inoculate each one of the plates using a straight line streak according
to the diagram on the following page.
3. Tape all plates on both sides.
4. Place the blood agar plates and CCNA plates into a GasPak jar or Anaeropak box so they
can be incubated in an environment enriched with carbon dioxide.
5. Incubate all plates at 37 C for 48 hours.
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S. mutans
S. xylosus
S. xylosus
S. zooepidermicus
S. mutans
MSA
Blood
S. mutans
P. aeruginosa
E. coli
S. typhimurium
E. coli
E. aerogenes
S. mutans
E. aerogenes
EMB plate
MacConkey plate
E. faecalis
S. xylosus
E. aerogenes
S. typhimurium
C-CNA
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RESULTS:
Examine plates for the following:
1. Mannitol Salt Agar Plates: Growth on mannitol salt agar indicates the organism is
halotolerant. A change in the color of the agar from pink to yellow indicates the organism
has the ability to ferment mannitol. Note: this yellow coloration can usually be seen
around the sides of the bacterial growth.
2. Blood Plates: All organisms should grow on the blood plates they are NOT selective.
Growth surrounded by a complete clearing of the blood indicates beta hemolysis.
Growth surrounded by a partial clearing of the blood (often a greenish-grey color)
indicates alpha hemolysis. Growth which produces no changes in the blood indicates the
bacteria are non-hemolytic. (This lack of hemolysis is sometimes called gamma
hemolysis.)
3. MacConkey Agar Plates: Growth on MacConkey agar indicates the organism is resistant
to crystal violet and bile salts, and is likely to be gram-negative. Growth which is a
pinkish-red color indicates the organism has the ability to ferment lactose, and is
probably a coliform.
4. Eosin Methylene Blue Agar: Growth on Eosin Methylene Blue agar indicates the
organism can grow in the presence of the dyes eosin and methylene blue and is likely a
gram-negative. Growth which is a pink color indicates the organism can ferment lactose
to form weak acid end-products, and growth which exhibits a green metallic sheen
indicates the organism can ferment lactose to form strong acid end-products.
5. C-CNA Agar: Growth on Columbia C-NA agar indicates the organism is resistant to the
antibiotics colistin and naladixic acid, and is likely a gram-positive. Hemolysis patterns
can allow differentiation (see above).
Record your results on the data charts below.
Mannitol Salt Agar
Organism
Growth
Color
Interpretation of Results
Staphylococcus
epidermidis
Staphylococcus
xylosus
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Blood
Organism
Growth
Hemolytic
pattern
Growth
Color
Growth
Color
Streptococcus
zooepidemicus
Staphylococcus
xylosus
MacConkey
Organism
Escherichia coli
Salmonella
typhimurium
Enterobacter
aerogenes
EMB
Organism
Escherichia coli
Pseudomonas
aeruginosa
Enterobacter
aerogenes
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C-CNA
Organism
Growth
Hemolysis
Salmonella
typhimurium
Enterococcus
faecalis
Staphylococcus
xylosus
Enterobacter
aerogenes
STUDY QUESTIONS:
1. What property or properties of gram-negative organisms would likely make them more
resistant to crystal violet and bile salts than gram-positive organisms?
2. An unknown bacterium produces colorless colonies when inoculated onto an EMB plate.
Predict what you would see if you inoculated that same unknown onto the following media, and
why:
MacConkey agar:
C-CNA Agar:
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EXPERIMENT #13: CHEMICAL CONTROL OF MICROORGANISMS

Antimicrobial chemicals, disinfectants, and antiseptic solutions are routinely used to
decontaminate surfaces, objects, and even skin and tissues. Examples include household
cleaners such as Lysol and Clorox, first aid treatments such as isopropanol and hydrogen
peroxide, and hospital cleaners such as Amphyll and Vesphene. Chemical agents work through
two main mechanisms: (1) Alteration of cell walls or cytoplasmic membranes and (2)
Interference with protein and nucleic acid structure. Like antibiotics, chemical agents may be
static or cidal in action, although most of the newer chemical agents are microbiocidal.
There are many methods to test the effectiveness of antimicrobial chemicals, including
the disk diffusion assay. In this assay, small filter disks are impregnated with the chemical to be
tested, and are placed on a plate inoculated to form a bacterial lawn (even, confluent bacterial
growth). The plates are incubated to allow growth of the bacteria and time for the chemicals to
diffuse into the agar. As a chemical diffuses into the agar, it becomes less concentrated. If an
organism is susceptible to a chemical, a clear zone of inhibition will appear around the disk
where the growth has been inhibited. The size of this zone of inhibition depends on the
sensitivity of the bacteria to the specific chemical and the chemical's ability to diffuse through
the agar.
We will be testing four different chemicals today using the disk diffusion assay. Students
may test the chemicals provided in the laboratory, or they are welcome to bring in their own
disinfectants for testing.
MATERIALS NEEDED: (per group of 4)
1 Mueller-Hinton plate
CULTURES NEEDED:
Escherichia coli, Staphylococcus aureus
PROCEDURE:
1. With a marker, divide the bottom of the plate into quadrants. Label A, B, C, and D.
(Key: A = isopropanol; B= hydrogen peroxide; C= Lysol antibacterial disinfectant;
D= Micro-90 dish detergent) Note: If you brought your own disinfectants to test,
record those here: A = _______________________B = ______________________
C = _________________________ D = ______________________
2. Select a broth culture of either E. coli or S. aureus. Coordinate with another lab
group in your class so that each group chooses a different one. Write the name of the
bacteria on the plate, as well as your initials and the date.
3. Gently agitate your broth tube to resuspend any bacteria that have settled to the
bottom of the tube. With a sterile swab, dip into the broth tube and completely swab
the surface of the plate. Rotate the plate 90 and repeat, dipping a fresh sterile swab
into the broth tube and completely swabbing the surface of the plate. There should be
a blanket of uniform growth following incubation.
4. Using forceps, dip a sterile filter disk in Solution A, allow the excess solution to drip
off, and then place the disk in the center of Quadrant A. Repeat with Solutions B, C,
and D.
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5. GENTLY press each disk onto the agar to make sure it stays, but do not puncture the
agar.
6. Tape the plate, and incubate at 37 C for 48 hours.
RESULTS:
Using a plastic ruler, measure the diameter in millimeters (mm) of the zone of inhibition for each
chemical tested. Record your results in the chart below.
Chemical
Isopropanol
Hydrogen peroxide
Clorox cleaner
Lab cleaner
E. coli Zone of Inhibition
S. aureus Zone of Inhibition
Based on your results, which chemical is most effective against E. coli? Which is least effective
against E. coli?
Which is most effective against S. aureus? Which is least effective against S. aureus?
Which chemical would you choose if you wanted maximum effectiveness against both E. coli
and S. aureus?
STUDY QUESTIONS:
1. Using your textbook as a reference, describe the mechanisms of action of isopropanol,
hydrogen peroxide, and Clorox bleach against bacteria.
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EXPERIMENT #14: CHEMOTHERAPEUTIC AGENTS

Antimicrobial chemotherapy is the use of chemicals to inhibit or kill microorganisms in
or on the host. Antimicrobial therapy is based on selective toxicity. This means that the agent
used must inhibit or kill the microorganism in question without seriously harming the host. In
order to be selectively toxic, a chemotherapeutic agent must interact with some microbial
function or microbial structure that is either not present in the host, or is substantially different
from that of the host. For example, in treating infections caused by prokaryotic bacteria, the
agent may prevent peptidoglycan synthesis or inhibit bacterial enzymes such as RNA polymerase
or DNA gyrase. Human cells do not contain peptidoglycan or DNA gyrase, and have structurally
different RNA polymerases. Therefore, drugs with these targets will have little, if any, effect on
the host.
Based on their origin, there are 2 general classes of antimicrobial chemotherapeutic
agents:
(1) Antibiotics, which are substances produced as metabolic products of one microorganism
which inhibit or kill other microorganisms.
(2) Antimicrobial chemotherapeutic chemicals, which are chemicals synthesized in the
laboratory which can be used therapeutically on microorganisms.
Today the distinction between the two classes is not as clear, since many antibiotics are
extensively modified in the laboratory (semisynthetic) or even synthesized without the help of
microorganisms.
Some antimicrobial agents are cidal in action: they kill microorganisms (e.g.,
penicillins, cephalosporins, neomycin). Others are static in action: they inhibit microbial
growth long enough for the body's own defenses to remove the organisms (e.g., tetracyclines,
erythromycin, sulfonamides).
Antimicrobial agents also vary in their spectrum. Drugs that are effective against a
variety of both gram-positive and gram-negative bacteria are said to be broad spectrum (e.g.,
tetracycline, streptomycin, cephalosporins, ampicillin, sulfonamides). Those effective against
just gram-positive bacteria, just gram negative bacteria, or only a few species are termed narrow
spectrum (e.g., penicillin G, erythromycin, clindamycin, gentamicin). The major classes of
antibiotics and their mechanisms of action have been covered in the text used in lecture.
Antibiotic sensitivity testing is used to determine the susceptibility of bacteria to various
antibiotics. This standardized test is used to measure the effectiveness of a variety of antibiotics
on a specific organism in order to prescribe the most suitable antibiotic therapy. A series of
antibiotic-impregnated paper disks are placed on a plate inoculated to form a bacterial lawn
(even, confluent growth). The plates are incubated to allow growth of the bacteria and time for
the antibiotics to diffuse into the agar. As the drug diffuses into the agar, its strength decreases.
If an organism is susceptible to an antibiotic, a clear zone of inhibition will appear around the
disk where the growth has been inhibited. The size of this zone of inhibition depends on the
sensitivity of the bacteria to the specific antibiotic and the antibiotic's ability to diffuse through
the agar. After incubation, the zones of inhibition are measured and compared with tables giving
the interpretation of measurement for each antibiotic.
MEDIA NEEDED: (per pair)
1 Mueller Hinton Agar plate
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CULTURES NEEDED:
Escherichia coli, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus
aureus, Proteus vulgaris
PROCEDURE:
1. Each pair will choose one of the five cultures listed above. Make sure to label your
plate with your names or initials and the name of the organism.
2. Gently agitate your broth tube to resuspend any bacteria that have settled to the
bottom of the tube. With a sterile swab, dip into the broth tube and completely swab
the surface of the M-H plate. Rotate the plate 90 and repeat, dipping a fresh sterile
swab into the broth tube and completely swabbing the surface of the plate. There
should be a blanket of uniform growth following incubation.
3. Carefully place the provided antibiotic discs onto the plate using the disc dispenser
provided. (Your lab instructor will demonstrate how to properly use the disc
dispenser.) You will need to take sterile forceps and lightly touch each disc to make
sure it will stay in place.
4. Incubate plates inverted at 37 C for 48 hours.
RESULTS:
Using a plastic ruler, measure the diameter in millimeters (mm) of the zone of inhibition for each
antibiotic tested. Record your results in the chart below. Refer to the table provided to
determine sensitivity and resistance.
Antibiotic
Inhibition Zone Diameter

(mm)
Susceptible/
Intermediate/ Resistant
Nalidixic Acid (NA30)

Trimethoprin/Sulfamethoxazole (SXT25)
Gentamycin (CN10)
Vancomycin (VA30)
Penicillin (P10)
Cefoxitin (FOX30)
Tetracycline (TE30)
Azithromycin (AZM15)
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Antibiotic Zone Diameters:

Disc Code
AZM15
CN10
VA30 -Enterococcus
VA30 -- other
P10 -Staphylococcus
P10 -- Enterococcus
P10 -Streptococcus
P10 -- other
TE30
FOX30
SXT25
NA30
Resistant (<mm)
13
12
14
Intermediate (mm
range)
14-17
13-14
15-16
Susceptible (>mm)
18
15
17
9
28
10-11
-
12
29
14
19
20-27
15
28
19
14
14
10
13
15-18
15-17
11-15
14-18
20
19
18
16
19
STUDY QUESTIONS:
1. Experimental results indicate that antibiotics such as streptomycin, tetracycline, and
chloramphenicol effectively inhibit the growth of prokaryotic cells, but have little effect on
eukaryotic cells such as fungi and protozoa. Based on your knowledge of the mechanism of
action of these particular antibiotics, why do you think this is the case? (Hint: Consult your
textbook to review mechanisms of action of the different classes of antibiotics.)
2. Distinguish between broad spectrum and narrow spectrum antibiotics, and give an example of
a clinical situation where each type of antibiotic might be prescribed.
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EXPERIMENT #15: ADDITIVE AND SYNERGISTIC EFFECTS OF ANTIBIOTICS (DEMO)

Antibiotics are often used in combination with each other in treatment of bacterial
diseases. For example, treatment of tuberculosis often involves a cocktail of antibiotics
including rifampin, isoniazid, and/or ethambutol. The goal of antibiotic combination therapy is
to (a) reduce the incidence of antibiotic-resistance (b) allow lower doses of antibiotics to be used
and/or (c) enhance the agents antibacterial activity. Antibiotics used in combination can have
either an additive effect or a synergistic effect. An additive effect means that the overall effect
of the antibiotic combination is no greater than the sum of the individual antibiotics. A
synergistic effect means that the overall effect of the antibiotic combination is greater than the
sum of the individual antibiotics. In synergism, the antibiotics enhance the effect of each other.
Additive and synergistic effects of drug combinations can be determined in the lab by
placing the two antibiotic discs on a lawn of cells plated on Mueller-Hinton agar. If each disk
has its own uniform zone of inhibition, the effect of the two antibiotics is additive. If the zones
of inhibition for the antibiotics merge in the middle, the effect is synergistic. Demonstrations of
additive and synergistic effects will be available on the front table during the results lab session.
RESULTS:
Draw the results of the additive and synergistic combinations of drugs:
Additive
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EXPERIMENT #16: MICROBIOTA OF THE MOUTH

That fuzzy feeling that can be felt on unbrushed teeth is an accumulation of a biofilm
of bacteria. There are several bacteria within a persons mouth which make up this biofilm and
are cariogenic, meaning they have a tendency to cause dental caries. These include
Lactobacillus acidophilus, Streptococcus mutans (and S. gordonii, S. salivarius), and
Actinomyces odontolyticus. These organisms are able to ferment carbohydrates to lactic acid,
thus lowering the pH at the surface of the enamel which can decalcify the enamel and lead to
cavities. Enamel decalcification will begin with a pH of 5.5 and accelerates as the pH reaches
4.4. For example, S. mutans produces the enzyme dextransucrase, which polymerizes sucrose
to form a polysaccharide called glucan. L. acidophilus produces a similar polymer called lexan.
Glucan and lexan are both glycocalyces which bind tightly to teeth, allowing the bacteria to form
a biofilm. The bacteria then produce acids as a product of carbohydrate fermentation.
The Snyder Test is used to determine a persons susceptibility to dental caries based on
acid production that is assumed to be a result of the growth of lactobacilli on the teeth or in other
areas of the mouth. (Note that the Snyder Test does not test for cariogenic streptococci or
actinomycetes.) The Snyder Test agar contains 2% glucose and has a pH of about 4.8. This low
pH inhibits the growth of most organisms, but it is ideal for lactobacilli. If growth occurs, and
lactic acid is produced by the lactobacilli, the pH will drop below 4.8 to about 4.4. The indicator
used to show this change in pH is bromcresol green, which will change from green to yellow
upon acid production. The rate of change is another factor to be considered, as it is an indication
of the number of acid-producing organisms present (i.e. the faster the rate of change, the more
organisms present). The extent to which a culture changes color following incubation indicates a
persons susceptibility to the formation of dental caries:
Color of Agar
Green
Light Green
Yellow-Green
Yellow
Susceptibility
Slight
Mild
Moderate
High
Alternatively, the tubes can be read at different time intervals and the amount of time it takes for
the tube to turn yellow will correlates with an individuals susceptibility to dental caries:
24 hours = very high susceptibility
48 hours = high susceptibility
72 hours = moderate susceptibility
MEDIA NEEDED: (per student)
1 Snyder deep agar tube
1 Sterile empty tube or beaker
CULTURES NEEDED: Saliva from students oral cavity
PROCEDURE:
1. Obtain a sterile test tube or small beaker. Collect approximately to inch of saliva
in the test tube or beaker.
2. Obtain a melted Snyder Agar deep tube that has been tempered in a 45 C water bath.
3. While the Snyder Agar deep tube is still liquefied, aseptically pipette 0.2 ml of saliva
into the tube.
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4. Place the cap loosely on the tube and roll the tube gently between the palms of your
hands. Let solidify.
5. Incubate the Snyder tube at 37 C for 48 hours.
RESULTS:
Examine Snyder deep agar tubes from the previous lab period for a change in the color of the
culture medium. Record your results in the table below for yourself and your lab partners:
Tube Identification
(name or initials)
Color of test culture
Caries susceptibility? (Slight,

Mild, Moderate, Severe)
Based on your results, what is your tendency to form dental caries?
STUDY QUESTIONS:
1. Explain how the Snyder agar medium is both a selective and a differential medium. How is
the differential nature of the medium used to detect susceptibility to dental caries?
2. Explain how resident mouth microbiota are responsible for the formation of dental caries. Are
all members of resident mouth microbiota capable of initiating dental caries?
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EXPERIMENT #17: NORMAL MICROBIOTA OF THE THROAT AND SKIN

In healthy humans, the internal organs and tissues such as muscles, the brain, and blood
do not contain microorganisms. However, surface tissues, such as the skin and mucous
membranes, are in continuous contact with environmental microbes and become readily
colonized by specific bacteria. The population of microbes regularly found in the body is
referred to as the normal microbiota. The term transient microbiota refers to members of the
normal microbiota that are present for only a short time before disappearing. A persons normal
microbiota is an important part of the immune system, as the normal microbiota often inhibit
pathogenic microbes from colonizing the host, a process called microbial antagonism.
Different types of bacteria will colonize different niches in a persons body due to variations in
moisture level, pH, atmospheric pressure, oxygen levels, and body secretions. Accordingly,
different types of media must be used to culture the various human microbiota.
Streptococcus
Members of the genus Streptococcus are often found as normal microbiota of the mouth and
throat. S. mutans, S. gordonii, and S. salivarius are examples of resident mouth microbiota. S.
pyogenes (one of the Group A Strep) is found in approximately 5-15% of normal individuals as
part of the normal throat microbiota. Blood agar is typically used to cultivate and differentiate
among Streptococcus species. Since streptococci are capnophiles, blood plates containing these
microbes should be incubated in the presence of carbon dioxide.
Neisseria /Moraxella
Members of the genus Neisseria are fastidious organisms that require special media and
conditions for growth. Neisseria are typically cultivated on chocolate agar, which contains
lysed (boiled) red blood cells and provides the nutrients and growth factors needed for these
organisms. Neisseria are also capnophiles, so chocolate plates containing Neisseria should be
incubated in the presence of carbon dioxide. Many saprophytic strains of Neisseria are normal
microbiota of the mouth and throat. In addition, the pathogen Neisseria meningitidis is found in
approximately 20-40% of young adults as a normal resident of the nasopharynx. Members of the
genus Moraxella, which are closely related to Neisseria, will also grow on chocolate agar. Like
Neisseria, Moraxella are also common microbiota of the nasopharynx, particularly in children
and young adults.
Since chocolate agar is not a selective medium, Neisseria and Moraxella must be
identified using the oxidase test, which tests for the presence of cytochrome c in the electron
transport chain. In this test, a drop of oxidase reagent is added to growth on the agar plate, and
a purple-black coloration that appears within 30 seconds signifies a positive reaction.
Diphtheroids
Diphtheroids are species of the genus Corynebacterium that are non-pathogenic and are part of
normal skin microbiota. Diphtheroids are cultivated on Mueller-Hinton Tellurite (MHT)
plates. If Diphtheroids are present, they will produce gray to black colonies because the tellurite
in the media is reduced intracellularly to tellurium, which appears as a gray precipitate.
Staphylococcus
Staphylococcus epidermidis and Staphylococcus aureus are normal microbiota of the skin. S.
aureus tends to be found in moist environments such as the nostrils and armpits, whereas S.
epidermidis is usually found in drier areas of the skin. S. epidermidis is typically nonpathogenic, whereas S. aureus is widely known as a troublesome opportunistic pathogen.
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Approximately 20% of healthy people are permanently colonized with S. aureus, and 60% of
healthy people are transient carriers of S. aureus. Recent studies have also shown that anywhere
from 1-4% of the U.S. population is colonized with methicillin-resistant S. aureus (MRSA), with
a few studies indicating that the MRSA colonization rate may be as high as 10%. Mannitol salt
agar (MSA) is used to select for both of these members of the Staphylococcus genus. MSA also
allows differentiation between S. aureus and S. epidermidis because S. aureus will ferment
mannitol to produce a golden-yellow colony growth, whereas S. epidermidis will not.
Environmental Organisms
Many of the microbes found in the environment are fungi such as yeasts and molds. Sabouraud
agar is an acidic medium (pH 5.5) which is used to cultivate acidophiles such as fungi from
environmental specimens. Other environmental specimens which are not acidophiles can be
cultured on nutrient agar.
MEDIA NEEDED: (1 each per pair)
Blood agar plate
Mannitol salt plate
Chocolate agar plate
Sabouraud agar plate
M-H Tellurite plate
Nutrient agar plate
0.85% saline tube
CULTURES NEEDED:
Swab of throat
Swab of skin or nose
Swab of ears or palms
Swab of environment
PROCEDURE:
1. Using a permanent marker, divide the blood plate, chocolate agar plate, Mannitol Salt
Agar (MSA) plate and Mueller-Hinton-Tellurite (MHT) plate in half so that each lab
partner will use half of each plate. Label the halves with your names or initials.
2. Swab the back of your lab partners throat with a sterile swab (or you may swab your
own throat, if you prefer) and rub onto the appropriate sector of the blood agar plate
in a zig-zag pattern. Swab the throat again with a fresh swab, and rub onto the
appropriate sector of the chocolate agar plate. Switch roles and swab the other
persons throat with fresh sterile swabs and rub onto the other halves of the blood and
chocolate agar plates. Tape the plates, and place in an Anaeropak box with an
activated CO2 generator.
3. Using a fresh swab, swab anywhere on your skin or up in your nostril and rub onto
your half of the MSA plate. Your lab partner should do the same.
4. Using a fresh swab, swab either your ears or the center of your palms and rub onto
your half of the MHT agar plate. Your lab partner should do the same.
5. Swab anywhere in the environment (bathroom door, toilet seat, door handle, water
fountain, etc.) and rub onto a Sabouraud agar plate. You may want to moisten your
swab with sterile saline prior to taking your environmental sample. (Note: if you
want to divide this plate in half and obtain two environmental samples, that is fine.)
Repeat, this time inoculate the environmental specimens onto a nutrient agar plate.
5. Tape all plates on both sides, invert, and incubate at 37oC for 48 hours.
6. ALL used swabs are to be discarded immediately in the biohazard waste!
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RESULTS:
1. DO NOT OPEN THE BLOOD AGAR PLATE! Examine the blood agar plate
cultures for zones of hemolysis.
2. Open the lid of the chocolate plate just enough to add a drop oxidase reagent to the
growth on plate. Close immediately. A purplish color that develops within 30
seconds on the surface of any of the colonies indicates the presence of Neisseria/
Moraxella.
3. Examine the Mueller-Hinton Tellurite plate for black diphtheroid colonies.
4. DO NOT OPEN THE MANNITOL SALT PLATE! Examine the mannitol salt agar
plate for the presence of growth of Staphylococcus. What color is the media
surrounding the growth? A yellow color indicates S. aureus, which has fermented the
mannitol and lowered the pH of media. No color change indicates S. epidermidis.
5. Environmental Samples -- Examine Sabouraud agar plates for growth. Identify mold
vs. yeast growth on the plate. Compare with the growth on the nutrient agar plate.
6. Record all results in the table below:
Culture
Observations and Results
Blood agar: type(s) of

hemolysis
Types of organisms present?
Chocolate agar: purple
colonies?
Mueller-Hinton-Tellurite agar
(+) or (-) black colonies
Sabouraud Agar
(Environmental sample)
Nutrient Agar
(Environmental sample)
Mannitol Salt Agar
(+) or (-) growth
Color of medium
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STUDY QUESTIONS:
1. What is meant by the term normal microbiota? Are these organisms harmful or beneficial
to their host? Why?
2. Even if all students are healthy, why is it still advisable NOT to open the blood plates on
which throat specimens are grown or the MSA plates on which skin specimens are grown?
3. Compare the growth from the environmental samples inoculated onto the Sabouraud and
Nutrient Agar plates. Are there any differences? Would you expect there to be a difference?
Why or why not?
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EXPERIMENT #18: CULTIVATION OF URINE SPECIMENS

Urine from the urinary bladder should be sterile! The act of voiding or micturation
helps to rid the lower urethra orifice of any bacteria that may try to ascend into the urinary
bladder. Bacteriuria, the presence of bacteria in the urine, can indicate a urinary tract infection,
called a UTI. Such infections include urethritis, cystitis, and pyelonephritis. Urethritis is an
infection involving only the urethra. Cystitis is an infection which involves the urinary bladder.
Pyelonephritis is an infection involving the kidneys, and tends to be a more severe infection,
often resulting in the destruction of renal corpuscles. Bacteria that commonly cause UTIs
include Escherichia coli (primary culprit), Staphylococcus aureus, Enterococcus faecalis,
Proteus mirabilis and P. vulgaris, as well as Pseudomonas aeruginosa and Salmonella and
Shigella species.
The first step usually taken to diagnose a UTI is a dipstick test, which detects the
presence of leukocyte esterase and nitrate reductase activity associated with these types of
infections. If the dipstick test is positive, the next step in diagnosis of a UTI is often the
examination of a urine specimen for the presence of bacteria. Samples may be taken aseptically
using a needle for cystocentesis or a clean sample using a sterile catheter. More commonly, a
clean catch voided sample is obtained. In this procedure, the urine sample is collected
midstream following adequate cleansing of the external genitalia. It is crucial to process fresh,
unrefrigerated urine samples immediately to avoid overgrowth of normal genital microbiota
resulting in false positive results.
MEDIA NEEDED:
1 Nutrient Agar plate
CULTURES NEEDED:
Student urine specimen (voluntary only)
PROCEDURE:
1. Students may collect their own urine specimen using a castile soap pad to cleanse the
urethra area followed by midstream urine collection in a sterile urine cup.
2. Using a sterile 10 l plastic calibrated loop, dip the loop into the urine and streak onto the
surface of the nutrient agar plate. Incubate at 37 C for 48 hours.
3. Discard the used loop and remaining urine sample in the biohazard waste.
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RESULTS:
Examine the urine culture plates for the presence of colonies. Count how many bacterial
colonies are present, and calculate the number of CFU/ml by dividing the number of colonies by
the size of the calibrated loop, which is 0.01 ml:
# of colonies = CFU
0.01 ml
ml
Does there seem to be only one colony type, or are multiple colony types represented?
What do the numbers mean? The critical threshold between bacterial infection and simple
bacterial contamination from a clean catch urine sample is usually considered to be 1 x 105
bacteria per ml of urine. Traditionally, a UTI is diagnosed when the number of bacteria present
in the urine is greater than 1 x 105 per ml, and the patient presents with symptoms consistent
with a UTI. Some recent studies suggest, however, that lower count bacteriuria ranging from 1 x
102 to 1 x 104 bacteria per ml of urine may indicate an early phase of UTI.
STUDY QUESTIONS:
1. How accurate is a lab analysis of a 24-hour, unrefrigerated, non-midstream urine culture?
Explain.
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EXPERIMENT #19: IDENTIFICATION OF BACILLUS SPECIES

Bacillus represents a genus of rod-shaped, Gram-positive bacteria which are ubiquitous in
nature, and are commonly found in places such as soil, water, and airborne dust. All Bacillus
species are able to perform aerobic respiration some are facultative and some are strict aerobes.
Most Bacillus species produce capsules, and all are capable of motility by peritrichous flagella.
A unique characteristic of this genus is its ability to produce endospores when environmental
conditions are stressful. Some Bacillus species are natural flora in the human intestines, and
other Bacillus species are ecologically important as insect pathogens. Several species of Bacillus
are antibiotic producers, including B. brevis, B. cereus, B. licheniformis, B. polymyxa, and B.
subtilis.
Although most species of Bacillus are harmless saprophytes, two species are considered
medically significant: Bacillus anthracis and Bacillus cereus. B. anthracis is the causative agent
of anthrax, which occurs in two main forms in humans: pulmonary anthrax and cutaneous
anthrax. B. cereus is a cause of food poisoning associated with dried foods such as rice and
beans.
In order to differentiate between Bacillus species, several microbiological tests are used
including an assay for the presence of extracellular enzymes, growth and fermentation on
mannitol salt agar, nitrate reduction, citrate utilization, and esculin hydrolysis.
EXTRACELLULAR ENZYMES:
Bacteria secrete extracellular enzymes which are responsible for a variety of enzymatic
activities. Among them are enzymes which hydrolyze substrates such as starch, lipids, and
proteins. We will be assaying for these enzymatic activities using the following kinds of
differential media.
Starch media:
Starch media contains the polysaccharide starch as a substrate. Starch is a polymer of many
glucose monomers joined together in glycosidic linkages. Amylase is the enzyme that breaks the
starch down into smaller subunits of maltose (a disaccharide). Another enzyme, maltase, then
catabolizes the maltose into glucose (a monosaccharide). Organisms which hydrolyze starch will
show a clear zone in the starch agar around the growth of the microorganism following the
edition of iodine to the media.
Lipid media:
Lipid media contains the lipid substrate Tributyrin. Lipids are degraded by an enzyme called
lipase, which breaks the ester bonds of triglyceride molecules to produce glycerol and fatty
acids. Organisms which hydrolyze lipids will show a clear zone in the lipid agar around the
growth of the microorganism.
Casein media:
Casein media contains the substrate casein, which is a major milk protein. Proteins are polymers
of amino acids joined together by peptide bonds. Hydrolysis of proteins is referred to as
proteolysis. Enzymes which degrade casein include protease and casease. In proteolysis of
casein, the protein is broken into peptones, then into polypeptides, then into dipeptides, and
finally into amino acids. This is known as the Peptonization Process. Organisms which
hydrolyze casein will show a clear zone in the casein agar around the growth of the
microorganism.
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Gelatin media:
Gelatin media contains the substrate gelatin, which is a protein produced by the hydrolysis of
collagen. Gelatin is degraded by the enzyme gelatinase into its amino acid components.
Organisms which hydrolyze gelatin will cause the gelatin to liquefy.
OTHER TESTS:
Mannitol Salt Agar:
MSA is both selective and differential. It contains 7.5% NaCl, which selects for organisms
which are halotolerant. The media also contains mannitol and phenol red, which allows
differentiation of organisms based on whether or not they are able to ferment mannitol. If
mannitol is fermented, the acidic fermentation products react with the phenol red pH indicator,
which changes color from red to yellow.
Nitrate Reduction:
Some organisms possess an enzyme called nitrate reducatase which enables them to
anaerobically reduce nitrate into nitrite. Some of these organisms can then further reduce the
nitrite to ammonia or completely to molecular nitrogen. Nitrate broth tubes contain beef extract,
peptone, and nitrate. After incubation of an organism in a nitrate broth tube, reagents are added
to determine if the nitrate has been reduced, and if so, to what extent. Nitrate Reagent A,
containing sulfanilic acid, is added to the test tube, followed by addition of Nitrate Reagent B,
containing alpha-naphthylamine. Formation of a red color indicates the presence of nitrites,
indicating the organism has reduced the nitrate to nitrite and is positive for nitrate reduction. If
no color appears, a pinch of zinc is added to the tube. If a red color appears, the organism is
negative for nitrate reduction, because the zinc has reduced the nitrate to nitrite, causing the red
color. However, if there is still no color change after the addition of zinc, this indicates the
nitrates were reduced beyond nitrites to ammonia or molecular nitrogen, and the organism is
positive for nitrate reduction.
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Citrate Utilization:
The purpose of this test is to determine if an organism can use citrate as a carbon source. The
citrate agar slant contains sodium citrate, bromthymol blue (pH indicator), sodium, and water. If
the organism is able to utilize citrate, an enzyme called citrase will break the citrate into
oxaloacetic acid and acetic acid. The oxaloacetic acid is then broken down into pyruvate and the
acetic acid is converted to CO2. The CO2 reacts with the water and sodium in the media to
produce alkaline sodium carbonate. The sodium carbonate reacts with the pH indicator to
produce a Prussian blue color.
Bile esculin agar (BEA):
BEA is both selective and differential. It contains bile salts, esculin, ferric ammonium citrate,
and beef and gelatin extracts. The bile salts give BEA its selective property, because only some
organisms are able to grow in the presence of bile. The esculin and ferric ammonium citrate give
BEA its differential property, because it distinguishes those organisms which are able to
hydrolyze the carbohydrate esculin. When esculin is hydrolyzed to glucose and esculetin, the
esculetin reacts with ferric ammonium citrate to form a blackish precipitate. The beef and
gelatin extracts provide macromolecules for general growth requirements.
1 Tri-plate made of starch agar, lipid agar, and casein agar
1 Mannitol salt agar (MSA) mini-plate
1 Gelatin deep tube
1 Bile esculin tube
1 Citrate agar slant
1 Nitrate broth tube
CULTURES NEEDED:
Each student will select one of the following:
Bacillus cereus, Bacillus subtilis, Bacillus megaterium, Bacillus coagulans, Bacillus
sphaericus, Bacillus licheniformis, Bacillus brevis, or Bacillus polymyxa.
(Your instructor may supply additional Bacillus species for you to choose from.)
PROCEDURE:
1. Using a straight line streak, inoculate each portion of the tri-plate with your Bacillus.
2. Using a straight line streak, inoculate the MSA mini-plate with your Bacillus.
3. Using a sterile needle, inoculate the gelatin deep tube with your Bacillus by stabbing into
the gelatin. Make sure to replace the cap loosely.
4. Using a sterile loop, inoculate the nitrate broth with your Bacillus.
5. Inoculate the citrate agar slant with your Bacillus by streaking the surface of the slant
with a sterile loop in a zig-zag motion. Do not stab the butt!
6. Using a sterile loop, streak the Bile Esculin slant tube with your Bacillus.
7. Make sure all plates are taped on both sides, and all test tube lids are loose but secure.
Make sure all plates and tubes are labeled with your name and the name of the organism.
Incubate all plates and tubes at 30 C for 48 hours.
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RESULTS:
1. Observe your tri-plates for the following reactions:
a. Positive starch hydrolysis clear zone around bacterial growth upon addition of
iodine
b. Negative starch hydrolysis blackish blue color upon addition of iodine indicates
presence of starch (meaning starch has not been hydrolyzed)
c. Positive lipid hydrolysis clear zone around bacterial growth
d. Positive casein clear zone around bacterial growth
2. Observe your mini MSA plate for growth and mannitol fermentation (yellow).
3. Observe your gelatin deeps for a positive or negative reaction. Positive gelatin hydrolysis
is indicated by liquefication of the gelatin at room temperature.
4. Analyze your nitrate broth tube to determine if nitrate reduction has occurred:
a. Add ____* drops of Nitrate Reagent A to the broth tube and mix thoroughly.
Next, add ____* drops of Nitrate Reagent B and mix. If a red color is produced,
this indicates a positive result for nitrate reduction. This means the organism has
reduced the nitrate to nitrite. *Your instructor will tell you how many drops to
add.
b. If no red color is produced, add a pinch of Zinc and mix thoroughly. Allow to sit
for several minutes. If the broth turns red, this indicates that the zinc has reduced
the nitrates and the organism is negative for nitrate reduction.
c. If the addition of zinc does NOT cause a color reaction, the test is positive. This
means that the organism has reduced the nitrate to nitrites and then reduced the
nitrites to ammonia or molecular nitrogen.
5. Observe your citrate slant for color and bacterial growth. Growth and a blue color
indicate a positive result, which means the organism is able to use citrate as a carbon
source.
6. Observe your bile esculin tube for esculin hydrolysis (black precipitate throughout agar).
7. Record your results below or on the chart provided by your lab instructor.
Bacillus species
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Growth
MSA
Fermentation
Nitrate
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Citrate
Bile
Esculin
Starch
Lipid
Casein
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Gelatin
STUDY QUESTIONS:
1. Why is it important to be able to determine the identity of species of Bacillus in the
laboratory?
2. Why do you think soil-dwelling organisms such as Bacillus possess extracellular enzymes
such as lipase, proteases, casease and gelatinase?
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EXPERIMENT #20: TRANSFORMATION

Transformation refers to the ability of a microorganism to take up free DNA from the
environment, and incorporate that DNA into their genome. Cells that have the capacity to do this
are referred to as competent cells. Some genera of bacteria are naturally competent, such as
Streptococcus, Bacillus, Haemophilus, and Pseudomonas. Those genera which are not naturally
competent can be manipulated in the laboratory to become artificially competent. Artificial
competency is typically induced using chemicals such as calcium chloride to increase the
permeability of the cells. The most commonly used artificially competent species is the genetic
workhorse Escherichia coli, which is an indispensable asset to the fields of genetic engineering
and biotechnology.
Plasmids are often used as vectors in transformation experiments. A vector is a piece of
DNA that delivers a gene to a recipient cell. Plasmids are small, covalently closed circular
pieces of extrachromosomal DNA that replicate independently of the chromosome in a bacterial
cell. Plasmid vectors are typically engineered to contain two things: (1) a selectable marker
such as an antibiotic-resistance gene to allow selection of transformed cells and (2) a multiple
cloning site where a gene of interest can be inserted.
The success of a transformation experiment is determined by calculating the
transformation efficiency, which is simply the number of transformants obtained per
microgram of DNA. For example, if 2 ng of plasmid DNA was transformed into competent E.
coli, and 237 transformants resulted, the transformation efficiency would be calculated as
follows:
Step 1: Convert nanograms to micrograms
2 ng = 0.002 g
Step 2: Divide the # of transformants by the amount of DNA
237 /0.002 g = 118,500 transformants/g DNA = 1.19 x 105 transformants/g DNA
The purpose of todays experiment is to transform the plasmid pGREEN into chemically
competent E. coli cells. The selectable marker on the pGREEN plasmid is a beta-lactamase gene
which confers resistance to the antibiotic ampicillin. The pGREEN plasmid also has a gene
encoding a green fluorescent protein inserted into the cloning site. Recipient cells that are
successfully transformed with the pGREEN plasmid will be ampicillin-resistant and will produce
the green fluorescent protein, giving them a green coloration which is visible under ambient light
conditions, and will fluoresce under UV light.
2- LB plates containing Ampicillin (LB-amp)
2- LB plates
LB broth
Ice-cold Calcium chloride (CaCl2)
CULTURES NEEDED:
Escherichia coli competent cells
pGREEN plasmid DNA (5 ng/l), on ice
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PROCEDURE:
1. Label one of the LB-amp plates Before and the other LB-amp plate After. Label one
of the LB plates Before and the other LB plate After.
2. Pre-warm all 4 plates and the small tube of LB broth at 37 C for 30 min.
3. Label an empty microfuge tube as Tube A. Pipet 250 l of ice-cold CaCl2 into Tube A.
Place Tube A on ice.
4. Use a sterile loop to transfer an isolated colony of E. coli to Tube A. Mix the bacteria
with the CaCl2 until no visible clumps remain in the tube. The CaCl2 will increase the
permeability of the bacterial cells, making them competent to take up DNA. Thus,
they are now referred to as competent cells. Put Tube A back on ice.
5. Using a sterile loop, streak a loopful of the competent cells from Tube A onto the LB
plate labeled Before.
6. Using a sterile loop, streak a loopful of the competent cells from Tube A onto the LBamp plate labeled Before.
7. Pipet 10 l of the pGREEN plasmid solution into Tube A, and mix by tapping gently.
8. Incubate Tube A on ice for 15 minutes.
9. Heat-shock the cells by placing Tube A in a 42 C water bath for 90 seconds. Place the
tube immediately back on ice.
10. Add 250 l of pre-warmed LB broth to Tube A. Incubate the tube at 37 C for 10
minutes.
11. Using a sterile disposable spreader, spread 100 l of cells from Tube A on the prewarmed LB-amp plate labeled After.
12. Using a sterile loop, streak a loopful of the cells from Tube A onto the LB plate labeled
After.
13. Incubate all plates overnight at 37 C.
RESULTS:
1. Examine the LB and LB-amp plates for growth and pigmentation, and record your results
in the table below:
Growth on LB
Growth on LB-amp Pigmentation
Before
After
2. Count the number of colonies on the LB-amp After plate. ___________
3. Calculate the transformation efficiency:
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STUDY QUESTIONS:
1. Was there any growth on the LB-amp Before plate? Was there any growth on the LB-amp
After plate? Explain these results.
2. Why is it important to streak the cells on non-selective media (i.e. plain nutrient agar) both
before and after the transformation procedure?
3. Explain how natural transformation could lead to the spread of antibiotic resistance in
pathogenic bacteria.
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EXPERIMENT #21: CATALASE TEST

Staphylococcus species produce an enzyme called catalase, which reacts with the toxic
oxygen by-product hydrogen peroxide (H2O2), breaking it down into water (H2O) and molecular
oxgyen (O2).
2H2O2
catalase
2H2O + O2
Streptococcus and Enterococcus species do not produce catalase (although they

produce superoxide dismutase and peroxidase). Therefore, the catalase test is widely used to
distinguish Staphylococcus from Streptococcus and Enterococcus.
CULTURES NEEDED:
Your Staphylococcus and Streptococcus/Enterococcus cultures from Experiments 22 and
23.
PROCEDURE:
1. Drop 2 small drops of 3% hydrogen peroxide onto a clean glass slide. Using a sterile
loop, put a loopful of the Staphylococcus organism into one of the drops. Observe for a
bubbling reaction. (The bubbles are the molecular oxygen that is produced as the
catalase breaks down the hydrogen peroxide.)
Catalase-positive: bubbles observed
Catalase-negative: no bubbles
2. Repeat with Streptococcus organism using a sterile loop to put a loopful of the bacteria
into the other drop of hydrogen peroxide.
Staph
Strep
RESULTS:..
Organism: ________________________________ Catalase Reaction: + or (circle one)
Organism: ________________________________ Catalase Reaction: + or (circle one)
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STUDY QUESTIONS:
1. In attempting to distinguish between Staphylococcus and Streptococcus species, what is
the first lab test that should be performed? Why?
2. Streptococcus and Enterococcus species do not produce the enzyme catalase. How are these
aerotolerant bacteria able to survive in the presence of oxygen when they lack this important
enzyme?
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EXPERIMENT #22: STREPTOCOCCUS IDENTIFICATION

Members of the genus Streptococcus are also gram-positive cocci of significant clinical
importance. Due to similarities between the genera Streptococcus and Enterococcus, members
of the Enterococcus genus are grouped into the same family as the Streptococcus species.
Streptococcal species are divided into groups based on their Lancefield classification, which
categorizes streptococci based on similar surface antigens. Most of the clinically important
streptococci fall in the following groups:
Lancefield Group
A
Species
S. pyogenes
S. agalactiae
S. equi
E. faecalis
S. bovis
S. salivarius
S. mutans
S. mitis
S. pneumoniae
K
Viridans
(no Lancefield antigens)
Pneumococci
(no Lancefield antigens)
Significant Human Diseases

Acute pharyngitis, scarlet fever, impetigo
Necrotizing fasciitis
Glomerulonephritis, rheumatic fever
Neonatal meningitis, pneumonia, bacteremia
Puerperal fever
Veterinary pathogen (equine strangles)
Urinary tract infections, Biliary tract
infections
Dental caries, endocarditis
Dental caries, endocarditis
Pneumonia, meningitis, bacteremia
Acute S. pyogenes (Group A Strep or GAS) infections may take the form of pharyngitis,
scarlet fever, impetigo, or cellulitis. Invasive infections can result in necrotizing fasciitis,
myositis, and streptococcal toxic shock syndrome. Patients infected with Group A Strep may
also develop immune-mediated complications such as acute rheumatic fever and acute
glomerulonephritis.
Adults infected with S. agalactiae (Group B Strep or GBS) may experience vaginitis,
puerperal fever, urinary tract infection, skin infection, and endocarditis. In newborn infants, S.
agalactiae is a common cause of meningitis, neonatal sepsis, and pneumonia.
Members of the Group C Strep are important veterinary pathogens, the most notable
being S. equi which causes a highly contagious respiratory disease in horses called strangles.
Group C Strep are rarely pathogenic to humans.
Members of the Group D Strep, in particular E. faecalis, are commonly associated with
urinary tract and biliary tract infections.
Both Group K Strep (S. salivarius) and the Viridans streptococci (S. mitis and S. mutans)
can cause dental caries and endocarditis.
Members of the Streptococcus genus can be distinguished from Staphylococcus by a
negative catalase test and by the inability of most streptococcal species to grow in the presence
of high salt (NOTE: Enterococcus species can grow in high salt media). Streptococci are
capnophiles, and grow best in the presence of carbon dioxide. Streptococcus species are
distinguished from one another based on colony morphology, hemolytic properties, and
biochemical reactions. Most Streptococcus species produce hemolysins that hydrolyze red
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blood cells, and their hemolytic patterns are classified as alpha, beta, or gamma based on the
degree of hemolysis. In addition to hemolytic patterns, Streptococcus species can be
distinguished from one another by their susceptibility to the antibiotics bacitracin and SXT, the
ability to grow on high-salt media, and the ability to hydrolyze esculin in bile esculin slants.
During todays lab we will be inoculating different Streptococcus species onto mannitol salt
agar, blood agar, and bile esculin agar to examine the different characteristics of each species.
Mannitol Salt Agar:
MSA is both selective and differential. However, it is used solely as a selective medium in the
identification of streptococci. MSA contains 7.5% NaCl, which selects for organisms which are
halotolerant. The only members of the Streptococcus family that are able to grow on MSA are
the Enterococcus species.
Blood Agar:
Blood agar is a differential medium. It is also commonly used as an enriched medium for
growing fastidious bacteria. Some bacteria produce exotoxins called hemolysins that cause lysis
of red blood cells. The degree of the hemolysis is an especially useful tool for differentiation
among Streptococcus species. The three types of hemolysis are:
1. Beta hemolysis, which is the complete lysis of red blood cells and hemoglobin. This
results in complete clearing of the blood around colonies.
2. Alpha hemolysis refers to the partial lysis of red blood cells and hemoglobin. This results
in a greenish-grey discoloration of the blood around the colonies.
3. No hemolysis, sometimes called gamma hemolysis, results in no change in the medium.
The blood agar will also be used to test the susceptibility of the Streptococcus species to the
antibiotics bacitracin and SXT.
Bile esculin agar:
BEA is both a selective and differential medium. It contains bile salts, esculin, ferric ammonium
citrate, and beef and gelatin extracts. The bile salts give BEA its selective property, because
only enteric organisms are able to grow in the presence of bile. The esculin and ferric
ammonium citrate give BEA its differential property, because it distinguishes those organisms
which are able to hydrolyze the carbohydrate esculin. When esculin is hydrolyzed to glucose
and esculetin, the esculetin reacts with ferric ammonium citrate to form a blackish precipitate.
The beef and gelatin extracts provide macromolecules for general growth requirements.
1 Blood agar plate
1 Mannitol salt mini-plates
1 Bile Esculin agar slant
1 0.85% saline tube
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Streptococcus pyogenes
Streptococcus bovis
Streptococcus equi
Streptococcus agalactiae
Streptococcus zooepidemicus
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PROCEDURE:
1. Each student will choose one of the Streptococcus (or Enterococcus) cultures listed
above. Try to ensure that each member in your lab group chooses a different culture.
Make sure to label your plates and slants with your name and the name of the organism.
2. Suspend several loopfuls of the organism into a 0.85% saline tube. The inoculated saline
should be slightly to moderately turbid. Using a sterile swab, dip into the inoculated
saline and completely swab of the blood agar plate, creating a lawn.
3. On the other of the plate do a straight line streak with a sterile loop to see the
hemolysis pattern.
4. Place and seat a Bacitracin disc and an SXT (trimethoprim-sulfamethoxazole) disc
equidistant within the designated area on the swabbed area of the blood plate.
5. Inoculate your Mannitol salt mini-plate with your Streptococcus (or Enterococcus)
organism using a straight-line streak.
6. With a loop, streak a Bile Esculin slant tube with your Streptococcus (or Enterococcus)
organism using a zig-zag motion. Make sure to replace the cap so that it is loose, but
secure.
7. Place the blood agar plate and Mannitol salt agar plate into an Anaeropak box (for an
aerobic environment enriched with carbon dioxide). Incubate at 37 oC for 48 hours.
8. Incubate the Bile Esculin slant tube at 37 oC for 48 hours.
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RESULTS:
Examine Streptococcus cultures for the following:
1. Susceptibility to Bacitracin and SXT (trimethoprim-sulfamethoxazole) on blood plate:
Susceptible organisms will not grow adjacent to the antibiotic discs. Measure the
diameter of the zone of inhibition of the SXT disc in millimeters. If the zone of
inhibition is greater than 20 mm, the organism is susceptible to SXT. If there is ANY
zone of inhibition with the Bacitracin disk, the organism is susceptible.
2. Hemolysis pattern on blood plate is it alpha, beta, or gamma?
3. Growth on Mannitol Salt agar. (Note: The color of the agar does not matter. We are
exclusively looking for growth!)
4. Ability to hydrolyze esculin in Bile Esculin slants, which is indicated by a black
precipitate. Note: Greater than half the media must turn black for the bile esculin test to
be considered positive.
5. Record your results on the data chart below.
Organism
Hemolysis Bile
MSA
SXT
Esculin Growth Diameter /S or R
Bacitracin
Diameter /S or R
STUDY QUESTIONS:
1. Explain the medical significance of Staphylococcus and Streptococcus species. Why is it
important to be able to distinguish between these two genera?
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EXPERIMENT #23: RAPID STREP TEST

The rapid strep test allows for a quick diagnosis of Group A Streptococcus directly from
throat swabs, eliminating the need for 1 or 2 day incubations on blood plates to positively
identify Group A Strep. The rapid test uses a sandwich immunoassay to detect group A
streptococcal antigens. The test cassette contains a membrane strip that has been coated with
anti-Strep A antibodies. If the specimen being tested contains Group A Strep bacteria, the Strep
A antigens extracted from the throat swab will bind to the antibodies. The antigen-antibody
complex then binds with a second antibody that is conjugated with a chromogen, producing a
colored line. Thus, a colored line at the test line region of the cassette indicates the sample is
positive for Group A Strep. However, rapid Strep tests are not foolproof, giving false negative
results approximately 15% of the time. For this reason, most clinical microbiologists
recommended that a traditional throat culture also be performed when rapid Group A Strep test
gives a negative result.
CULTURES NEEDED: (per group of 4)
Polyester swab containing throat specimen
Test Device Cassette in sealed foil pouch
Reagent A
Reagent B
Extraction tube and dropper tip
PROCEDURE:
1. Add 4 drops of Reagent A to the Extraction tube. The solution should be light red.
2. Add 4 drops of Reagent B to the Extraction tube. The solution should turn pale yellow.
3. Place the throat swab in the Extraction tube. Agitate the swab 10 times in the tube.
Leave the swab in the tube for 1 minute.
4. Squeeze the swab firmly against the tube to expel as much liquid as possible from the
swab. Discard the swab in the Biohazard trash.
5. Fit the dropper tip on top of the extraction test tube.
6. Remove BD Directigen EZ Group A test device from its pouch and place on a level
surface. Add 3 full drops of solution into the specimen well.
7. Read results in 5 minutes. Do not read results after 10 minutes. A positive result should
have a red line in both the test and control line regions on the device. A negative result
will only have a red line in the control region. Note: Any line, regardless of intensity,
should be interpreted as a line.
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RESULTS:
Sketch the results displayed on the test device cassette:
Was the sample positive or negative for Group A Strep? ____________

STUDY QUESTIONS:
1. What autoimmune-related complications can result from this infection?
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EXPERIMENT #24: IDENTIFICATION OF STAPHYLOCOCCUS SPECIES

Members of the genus Staphylococcus are gram-positive cocci of significant clinical
importance. The Staphylococcus genus is classified into two major groups: S. aureus and non-S.
aureus. S. aureus is a leading cause of skin and soft tissue infections (SSTIs), as well as toxic
shock syndrome (TSS) and scalded skin syndrome. S. aureus has also been found to be the
causative agent in such ailments as pneumonia, meningitis, arthritis, and osteomyelitis. It can be
distinguished from other pathogenic species of Staphylococcus by its ability to ferment mannitol
and by a positive result in a coagulase test.
An important subclass of S. aureus are the methicillin-resistant S. aureus (MRSA), which
are resistant not only to the penicillin-derived methicillin, but to other antibiotics as well. MRSA
emerged in hospitals and hospital-like settings in the early 1960s, and has become a significant
threat to public health. Much attention is currently being given to an emerging type of MRSA
called community-acquired MRSA (CA-MRSA), which is not hospital associated, and is causing
serious infections in otherwise healthy people.
Of the non-S. aureus species, S. epidermidis is the most clinically significant. This
bacterium is an opportunistic pathogen which is a normal resident of human skin, and often
infects IV drug users, newborns, elderly, and those using catheters or other artificial appliances.
Members of the Staphylococcus genus can be distinguished from other gram-positive
cocci by two main properties: (1) the ability to grow on high salt media, and (2) the production
of the enzyme catalase. Staphylococcus species are distinguished from one another based on
their ability to ferment mannitol, their susceptibility to the antibiotic Novobiocin, and whether or
not they produce a hydrolytic enzyme called DNase, which degrades DNA. During todays lab
we will be inoculating different Staphylococcus species onto mannitol salt agar, DNase agar, and
Mueller-Hinton agar to examine the different characteristics of each species.
Mannitol Salt Agar:
MSA is both selective and differential. It contains 7.5% NaCl, which selects for organisms
which are halotolerant. The media also contains mannitol and phenol red, which allows
differentiation of organisms based on whether or not they are able to ferment mannitol. If
mannitol is fermented, the acidic fermentation products react with the phenol red pH indicator,
which changes color from red to yellow.
DNase agar:
DNase agar contains an emulsion of DNA, peptides, and methyl green dye. The dye and
polymerized DNA form a complex that gives the agar a blue-green color at pH 7.5. Bacterial
colonies that secrete DNase will hydrolyze the DNA in the medium into smaller fragments
unbound from the methyl green dye. This results in clearing around the bacterial growth.
Mueller-Hinton agar:
M-H agar is a type of nutrient agar standardized for use in antimicrobial testing that allows for
antibiotic diffusion into the agar. In addition, the levels of thymine, thymidine, calcium ions and
magnesium ions are controlled in this medium so as not to interfere with susceptibility testing.
The M-H agar will be used to test susceptibility to the antibiotic Novobiocin.
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MEDIA NEEDED (per student):

1- Staphylococcus tri-plate
Mannitol Salt agar (pink)
DNase agar (bluish-green)
Mueller-Hinton agar (yellowish)
1- 0.85% Saline tube
CULTURES NEEDED:
Staphylococcus aureus
Staphylococcus intermedius
Staphylococcus epidermidis
Staphylococcus saprophyticus
(Your instructor may supply additional Staphylococcus species)
PROCEDURE:
1. Each student will choose one of the Staphylococcus cultures listed above. Try to ensure
that each member in your lab group chooses a different culture. Make sure to label your
plate with your name and the name of the organism.
2. With a sterile loop, inoculate the plate with a straight line streak on the MSA portion
and the DNase agar portion of the tri-plate.
3. Create a liquid suspension of your Staphylococcus species by diluting 2-3 loopfuls of the
organism into a saline tube using a sterile loop. Using a sterile swab, completely cover
the Mueller-Hinton portion of the plate with the suspension to create a bacterial lawn.
Place and seat a Novobiocin disc in the center with sterile forceps.
4. Incubate your tri-plates at 37 oC for 48 hours.
5. Obtain a clean glass slide and perform a Gram stain on your Staphylococcus culture.
(Refer to page 14 for instructions.)
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RESULTS:
1. Record the results of your Gram stain:
Morphology (shape):
Arrangement:
Color:
2. Examine Staphylococcus tri-plates for the following:
a. Growth on Mannitol Salt agar and ability of organism to ferment mannitol,
indicated by a change in color from pink to yellow.
b. Ability of organism to degrade DNA in DNase agar: A positive result is indicated
by a zone of clearing in the blue-green agar.
c. Susceptibility of organism to Novobiocin on Mueller-Hinton agar: Susceptible
organisms will not grow adjacent to the antibiotic disc. Measure the diameter of
the zone of inhibition in millimeters. If the zone of inhibition is greater than 18
mm, the organism is susceptible (S) to Novobiocin. If it is less than 18 mm, the
organism is resistant (R).
3. Record your results on the data chart below:
Organism
MSA
Fermentation
DNase
Novobiocin
Diameter / S or R
STUDY QUESTIONS:
1. What advantages does possessing the enzyme DNase confer on bacteria? How could
DNase aid in the virulence of pathogenic bacteria?
2. What do the acronyms MRSA and CA-MRSA stand for? Why are these organisms
considered to be such a threat to public health?
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EXPERIMENT #25: COAGULASE TEST (DEMO)

The coagulase test allows differentiation of Staphylococcus aureus from other
Staphylococcus strains by the fact that most S. aureus strains produce an enzyme called
coagulase, which acts within host tissue to convert fibrinogen to fibrin. Two versions of the
coagulase test may be used: the tube test or the slide test. To perform the tube test, S. aureus is
inoculated into a tube of citrated plasma and incubated at 37 C for four hours and periodically
examined for fibrin formation or coagulation. If a clot forms within four hours, the test is
positive for the presence of coagulase, and signifies virulent S. aureus. Alternatively, several S.
aureus colonies can be emulsified in a drop of citrated plasma on a glass slide in the slide test
procedure. If coagulase-positive, visible white clumps will appear almost instantly. Although
the slide test is much quicker and more economical, it is considered to be less sensitive than the
tube test. Therefore, isolates which test negative using the slide test are usually re-tested with the
tube test.
A demonstration of a positive coagulase test will be available on the front table during
the results lab session.
NOTES / OBSERVATIONS:
STUDY QUESTIONS:
1. How does coagulase contribute to the virulence of pathogenic Staphylococcus aureus?
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EXPERIMENT #26: RAPID STAPH TEST

The rapid Staphylococcus aureus test is based on the fact that most pathogenic strains of
S. aureus produce a bound coagulase and contain Protein A on their cell surface. [Remember
from lecture that coagulase and Protein A are two of the many virulence factors that S. aureus
has. The coagulase converts fibrinogen to fibrin, producing clots that allow the bacteria to
hide from the immune system. Protein A binds to the Fc region of IgG antibodies, inhibiting
IgGs which have opsonized the bacteria from binding to receptors on phagocytes.] The rapid
Staph test kit contains latex particles coated with human fibrinogen and IgG. These latex
particles will bind with any Staph bacteria that contain bound coagulase and/or Protein A,
resulting in visible clumping or agglutination of the latex particles. A positive result from the
rapid test is conclusive for Staphylococcus aureus, and replaces the need to grow the bacteria on
selective and differential media such as mannitol salt agar and DNase agar.
CULTURES NEEDED: (per group of 4)
Nutrient agar plate containing suspected S. aureus colonies
BBL Staphyloslide Test Latex
BBL Staphyloslide Control Latex
BBL Staphyloslide Latex Reaction Card
PROCEDURE:
1. Make sure card is flat.
2. Dispense 1 drop of Test Latex onto one of the circles on the reaction card.
3. Dispsense 1 drop of Control Latex onto the other circle on the reaction card.
4. Using a sterile loop, pick up and smear 5-10 colonies onto the Test Latex-containing
circle, and spread to cover the circle.
5. Repeat step 4 for the Control Latex.
6. Pick up and hand-rock the card for 20 seconds and observe for agglutination. The
Control Latex should NOT agglutinate.
7. Dispose of the reaction card in the Biohazard waste.
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RESULTS:
Sketch the results displayed on the reaction card:
Was the patient sample positive or negative for Staphylococcus aureus? _____________
STUDY QUESTIONS:
1. Based on the results, the attending physician wants a blood sample taken from the patient
to test for bacteremia. Why do you think this additional test has been ordered?
2. What further tests do you think should be performed on the patient specimen? Why?
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EXPERIMENT #27: IDENTIFICATION OF GRAM-NEGATIVE SPECIES

Gram-negative bacteria are distinguished from Gram-positive bacteria by their cell wall
properties. Gram-negative organisms possess a thin layer of peptidoglycan in their cell wall,
plus an outer phospholipid bilayer membrane containing lipopolysaccharide (LPS). Gramnegative bacteria can be found in diverse environments, including soil, fresh water, and salt
water. Gram-negative bacteria are found in abundance as normal flora in the intestinal tracts of
mammals. Gram-negative bacteria also constitute the largest group of human bacterial
pathogens. Almost every Gram-negative bacterium has the capacity to cause morbidity and
mortality in humans under the right conditions. The pathogenesis of gram-negative bacteria is
due in part to the lipid A component of the LPS in the outer membrane. Lipid A, also known as
endotoxin, can trigger symptoms such as fever, vasodilation, inflammation, shock, and blood
clots within blood vessels. Many pathogenic gram-negative bacteria also produce additional
toxins and virulence factors.
In order to distinguish among the gram-negative bacteria, the following tests will be
utilized. Each student will choose ONE of the gram-negative organisms listed below and use
that organism in each of the following tests. Be sure to label all tubes with the name of the
organism, as well as your name and date.
Acinetobacter lwoffii
Alcaligenes faecalis
Citrobacter freundii
Edwardsiella tarda
Enterobacter aerogenes
Enterobacter cloacae
Escherichia coli
Klebsiella oxytoca
Klebsiella pneumoniae
Morganella morganii
Proteus mirabilis
Proteus vulgaris
Pseudomonas aeruginosa
Pseudomonas putida
Providencia alcalifaciens
Salmonella cholerasuis
Salmonella typhimurium
Shigella boydii
(Note: Your lab instructor may not use all the bacteria on this list, and/or may add additional
Gram-negative bacteria to the above list.)
MACCONKEY AGAR
MacConkey Agar is both selective and differential. This media contains crystal violet
and bile salts, which inhibit most gram-positive organisms and select for gram-negative
organisms. It also contains the carbohydrate substrate lactose and the pH indicator neutral red,
which allow differentiation among gram-negative bacteria based on their ability to ferment
lactose. When lactose is fermented by coliforms such as Escherichia coli, acid end-products
lower the pH of the media below 6.8, with the resulting colonial growth turning pinkish-red. If
an organism is unable to ferment lactose, the colonies will be colorless, taking on the color of the
medium.
1 MacConkey plate
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PROCEDURE:
1. Obtain a MacConkey plate and label it with your name and the name of your
microorganism.
2. With a permanent maker, divide the bottom of the plate into four quadrants. With a
sterile loop, perform a 4-way streak. Refer back to page 27 for directions.
3. Invert the plate, and incubate overnight at 37 C.
(Note to instructors: After incubating overnight at 37 C, the plates may be refrigerated
at 4 C until the next lab period. Plates that are incubated at 37 C longer than 24 hours
may give aberrant results.)
RESULTS:
1. Observe your MacConkey plate for growth. Because the agar is selective for Gramnegative bacteria, all Gram-negatives should grow on this agar.
2. Observe the color of the growth on the agar. Growth that is pinkish-red indicates the
organism is able to ferment lactose. Growth that is colorless indicates the organism is
unable to ferment lactose.
3. Record your results.
TRIPLE-SUGAR IRON (TSI) AGAR TEST
TSI agar slants are used to differentiate between various gram-negative bacilli. There are
seven ingredients in a TSI slant: (1) 0.1% glucose (2) 1.0% sucrose (3) 1.0% lactose (4)
peptones (5) phenol red pH indicator (6) sodium thiosulfate and (7) ferrous sulfate. Glucose,
sucrose, and lactose are carbohydrate substrates, and fermentation of these carbohydrates into
acid end-products will result in a yellow color on the slant and/or butt as the acids react with the
phenol red. Results are reported as A for acid or Alk for alkaline. Note: all organisms will
preferentially ferment glucose before fermenting lactose and/or sucrose. Gas production can also
be determined with this test by observing the butt of the tube for gas bubbles or cracks in the
agar. If the microorganism produces hydrogen sulfide, it will utilize the sodium thiosulfate as a
substrate, producing H2S which reacts with the ferrous sulfate (the H2S indicator) to cause a
black precipitate.
1 TSI slant
PROCEDURE:
1. Obtain a TSI slant and label it with your name and the name of your microorganism.
2. Using a sterile loop, inoculate the slant of the tube using a zig-zag streak. Then, use a
sterile needle to stab the butt of the tube 5-10 times to push the organism down into the
butt of the tube.
3. Make sure the cap is loose but secure. Incubate overnight at 37 C.
RESULTS:
1. Observe your TSI slant for the following reactions:
a. Slant: acid (yellow) or alkaline (red, orange, or pink)
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b. Butt: acid (yellow) or alkaline (red, orange, or pink)

c. Gas production: bubbles or cracks throughout the media
d. Hydrogen sulfide production: indicated by black coloration in the tube
Note: Hydrogen sulfide production is always acidic, even though black coloration
masks yellow color of pH indicator.
2. Interpretation:
a. Red (alk) slant and yellow (acid) butt: only glucose fermentation has occurred.
Since glucose is present in a 0.1% concentration, the small amount of acid
produced by glucose fermentation is rapidly oxidized on the slant, resulting in an
alkaline reaction. In the butt, the acid reaction is maintained because of reduced
oxygen tension and slower growth of the organisms.
b. Yellow (acid) slant and yellow (acid) butt: lactose and/or sucrose fermentation
has occurred.
c. Red (alk) slant and red or orange-red (alk) butt: no carbohydrate fermentation has
occurred. Instead, peptones are catabolized resulting in an alkaline pH due to the
production of ammonia.
UREASE TEST
Some microorganisms are able to degrade urea using a hydrolytic enzyme called urease.
Urease breaks the covalent carbon-nitrogen bonds in the compound, hydrolyzing the urea into
ammonia and carbon dioxide. (Water is also produced). Urea broth tubes are used in the lab to
determine if a microorganism is urease-positive or -negative. The tube contains urea as a
substrate and phenol red as a pH indicator. If the bacterium is urease-positive, the ammonia
produced by urea hydrolysis will raise the pH and react with the pH indicator, creating a hot
pink color.
1 Urea broth tube
PROCEDURE:
1. Obtain a urea broth tube and label the tube with your name and the name of your
microorganism.
2. Using a sterile loop, inoculate your tube.
3. Make sure the cap is loose but secure and incubate at 37 C.
RESULTS:
1. Observe your tube for a positive or negative result.
a. Positive is indicated by a hot pink coloration.
b. Negative is indicated by no color change in the media.
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SIM AGAR TEST

A SIM agar deep contains the amino acid tryptophan, as well as peptones, sodium
thiosulfate, and ferrous sulfate. SIM agar deep tubes test for three things: (1) indole production,
(2) hydrogen sulfide production, and (3) motility.
Indole production: If an organism produces an enzyme called tryptophanase, it will
degrade tryptophan into indole, pyruvate, and ammonia. To test for the presence of
tryptophanase, the agar deep is inoculated with a sterile needle and incubated for 24-48 hours.
After incubation, a solution called Kovacs Reagent is added to the tube. Kovacs Reagent
contains HCl, Butanol, and para-dimethyl-amino-benzaldehyde (pdaba). The acidified butanol
extracts any indole that is produced and brings it to the surface of the agar, where it reacts with
the pdaba, turning red.
Hydrogen sulfide production: Organisms which produce the enzyme thiosulfate
reductase can reduce sulfur to hydrogen sulfide gas. In the SIM deep tubes, the source of sulfur
is sodium thiosulfate. If hydrogen sulfide gas is produced, it reacts with ferrous sulfate, giving a
black precipitate.
Motility: Organisms which are motile will exhibit diffuse growth that spreads out from
the initial stab line, whereas organisms which are not motile will only grow where the agar was
initially stabbed.
1 SIM agar deep
PROCEDURE:
1. Obtain a SIM deep tube and label the tube with your name and the name of your
microorganism.
2. Inoculate SIM deep tube with a straightened sterile needle, stabbing the butt all the way
to the bottom a single time.
RESULTS:
1. Retrieve your SIM deep tube inoculated during the previous lab period.
2. Add ____* drops of Kovacs Reagent slowly down the side of the SIM deep tube. If a
cherry red color develops, the result is positive for indole production. (*Your instructor
will tell you how many drops to add.)
3. Observe your SIM tube for a black precipitate, which indicates the production of
hydrogen sulfide gas.
4. Observe the pattern of growth along the stab line. If the growth spreads out from the stab
line, your organism is positive for motility.
MRVP TEST
The MRVP test consists of two separate components, the Methyl Red (MR) test and the Vogues
Proskauer (VP) test. The purpose of these tests is to determine if the organism is able to
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ferment glucose, and if so, what types of fermentation acids are produced. To perform both tests,
the bacteria are initially grown in MRVP broth, which contains peptone, glucose, and phosphate
buffer.
Methyl Red (MR) test:
This test was initially designed to distinguish between Escherichia coli and Enterobacter
aerogenes. During growth in the MRVP broth, E. coli will ferment the glucose in the media to
produce a mixture of fermentation acids lactic, acetic, and formic acids. E. aerogenes will
produce only acetic acid. The acids produced by E. coli are strong enough to overcome the
buffering capacity of the phosphate buffer in the media, thus lowering the pH. The acetic acid
produced by E. aerogenes is not strong enough to overcome the buffering capacity of the
phosphate buffer. After incubation of the organism in the MRVP tube, methyl red is added to
the tube to determine the pH. A red color indicates a positive MR reaction, indicating a pH of
4.4 or lower. Note: Although the test was originally designed to distinguish E. coli from E.
aerogenes, there are other organisms besides E. coli which produce a mixture of fermentation
acids and give a positive methyl red test!
Vogues-Proskauer (VP) test:
The purpose of this test is to detect bacteria which ferment glucose, but only produce one
acid end-product, usually acetic acid. The acetic acid produced initially lowers the pH of the
media, but is quickly converted to acetylmethylcarbinol, which leads to a pH of approximately
6.2. The VP test uses an MRVP broth tube (described above). After incubation of the organism
in the MRVP tube, Barritts Reagent A (-napthol) and B (40% KOH) are added to the media.
The chemicals in the reagents will react with acetylmethylcarbinol, and a positive reaction will
show a dark red band at the top of the broth in the tube which will diffuse over time into the rest
of the media. NOTE: An organism will NEVER be positive for both the MR and VP tests!!
1 MRVP broth tube
PROCEDURE:
1. Obtain an MRVP broth tube and label the tube with your name and the name of your
microorganism.
2. Inoculate the MRVP broth tube with a sterile loop.
RESULTS:
1. Retrieve your MRVP broth tube inoculated during the previous lab period.
2. Transfer 1 ml of your MRVP broth to an empty tube. Add ____* drops of methyl red
color indicator. Mix well and observe for a continuing red color, which indicates a
positive result for the methyl red test. A positive MR result means that the organism has
fermented glucose to produce a mixture of fermentation acids that were able to lower the
pH below 4.4.
3. Transfer another 1 ml of your MRVP broth to an empty tube. Add ____* drops of
Barritts Reagent A, but do not mix. Then add ____* drops of Barritts Reagent B to the
same tube, and mix thoroughly. Incubate at room temperature for a minimum of 25
minutes to allow the reaction to occur. If a dark red band begins to appear at the top of
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the liquid, this indicates a positive result for the Vogues-Proskauer test. A positive VP
results means that the organism has fermented glucose to produce acetic acid only, which
has been converted to acetylmethylcarbinol. (*Your instructor will tell you how many
drops to add.)
CITRATE UTILIZATION TEST
The purpose of this test is to determine if an organism can use citrate as a carbon source.
The citrate agar slant contains sodium citrate, bromthymol blue (pH indicator), sodium, and
water. If the organism is able to utilize citrate, an enzyme called citrase will break the citrate
into oxaloacetic acid and acetic acid. The oxaloacetic acid is then broken down into pyruvate
and the acetic acid is converted to CO2. The CO2 reacts with the water and sodium in the media
to produce alkaline sodium carbonate. The sodium carbonate reacts with the pH indicator to
produce a Prussian blue color.
1 Citrate agar slant
PROCEDURE:
1. Obtain a citrate agar slant and label the tube with your name and the name of your
microorganism.
2. Inoculate the citrate agar slant by streaking the surface of the slant with a sterile loop in a
zig-zag motion. Do not stab the butt!
RESULTS:
1. Retrieve your citrate agar slant inoculated during the previous lab period.
2. Observe your citrate slant for color and bacterial growth. A Prussian blue color
indicates a positive result, which means the organism is able to use citrate as a carbon
source.
NOTE: Historically, the previous three types of media (SIM, MRVP, and Citrate) have been
grouped together in a test called the IMViC test, which stands for Indole, Methyl Red, VoguesProskauer, and Citrate.
NITRATE REDUCTION TEST
Some organisms possess an enzyme called nitrate reducatase which enables them to
anaerobically reduce nitrate into nitrite. Some of these organisms can then further reduce the
nitrite to ammonia or completely to molecular nitrogen. Nitrate broth tubes contain beef extract,
peptone, and nitrate. After incubation of an organism in a nitrate broth tube, reagents are added
to determine if the nitrate has been reduced, and if so, to what extent. Nitrate Reagent A,
containing sulfanilic acid, is added to the test tube, followed by addition of Nitrate Reagent B,
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containing alpha-naphthylamine. Formation of a red color indicates the presence nitrites,

indicating the organism has reduced the nitrate to nitrite and is positive for nitrate reduction. If
no color appears, a pinch of zinc is added to the tube. If a red color appears, the organism is
negative for nitrite reduction, because the zinc has reduced the nitrate to nitrite, causing the red
color. However, if there is still no color change after the addition of zinc, this indicates the
nitrates were reduced beyond nitrites to ammonia or molecular nitrogen, and the organism is
positive for nitrate reduction.

1 Nitrate broth tube
PROCEDURE:
1. Obtain a nitrate broth tube and label the tube with your name and the name of your
microorganism.
2. Inoculate the nitrate broth with a sterile loop.
3. Make sure the cap is on loose but secure and incubate at 37 C.
RESULTS:
1. Retrieve your nitrate broth tube inoculated during the previous lab period.
2. Add ____* drops of Nitrate Reagent A to the broth tube and mix thoroughly. Next, add
____* drops of Nitrate Reagent B and mix. If a red color is produced, this indicates a
positive result for nitrate reduction. This means the organism has reduced the nitrate to
nitrite. *Your instructor will tell you how many drops to add.
3. If no red color is produced, add a pinch of Zinc and mix thoroughly. Allow to sit for
several minutes. If the broth turns red, this indicates that the zinc has reduced the nitrates
and the organism is negative for nitrate reduction.
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4. If the addition of zinc does NOT cause a color reaction, the test is positive. This means
that the organism has reduced the nitrate to nitrites and then reduced the nitrites to
ammonia or molecular nitrogen.
LYSINE IRON AGAR
The purpose of this test is to determine if the organism is able to carry out lysine
decarboxylation, which is an anaerobic process, or lysine deamination, which is an aerobic
reaction. The LIA slant contains lysine, glucose, peptones, bromcresol purple (pH indicator),
sodium thiosulfate and ferric ammonium citrate. Bromcresol purple is a dark purple color at pH
6.8 or higher, and turns yellow when the pH drops below 5.2.
Upon fermentation of glucose, some organisms will synthesize an enzyme called lysine
decarboxylase, which cleaves a carboxyl group from the lysine. This lysine decarboxylation
creates a diamine end-product called cadaverine, which raises the pH above 6.8 and reacts with
the pH indicator to give a dark purple color in the butt of the tube. Other organisms may ferment
glucose but are unable to synthesize lysine decarboxylase. These bacteria will produce acid endproducts that lower the pH, resulting in a yellow color in the butt of the tube.
If the organism has the ability to deaminate lysine, the ammonia produced will react with
the ferric ammonium citrate to produce -ketocarboxylic acid, which produces a dark red color
on the slant of the tube. Deamination requires oxygen, so it never occurs in the butt of the tube.
Lysine iron agar also tests for hydrogen sulfide production. Organisms which produce
the enzyme thiosulfate reductase can reduce sulfur to hydrogen sulfide gas. In LIA tubes, the
source of sulfur is sodium thiosulfate. If hydrogen sulfide gas is produced, it reacts with ferric
ammonium citrate, giving a black precipitate.
1 Lysine Iron Agar (LIA) slant
PROCEDURE:
1. Obtain a LIA slant and label the tube with your name and the name of your
microorganism.
2. Using a sterile loop, inoculate the slant of the tube using a zig-zag streak. Then, use a
sterile needle to stab the butt of the tube 5-10 times to push the organism down into the
butt of the tube. Do not stab into the slant, only into the butt!
3. Make sure the caps are loose but secure, and incubate at 37 C.
RESULTS:
1. Retrieve your Lysine Iron Agar slant inoculated during the previous lab period.
2. Observe the color of the slant of the media. A PURPLE color indicates a negative
deamination reaction and a RED color indicates a positive deamination reaction. If
unsure of red vs. purple, use a light source such as an overhead projector.
3. Observe the color of the butt of the media. A PURPLE color indicates a positive
decarboxylation reaction, and a YELLOW color indicates a negative decarboxylation
reaction.
4. Note: If you have a red slant, you will nearly always have a yellow butt!
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5. Observe your LIA slant for a black precipitate, which indicates the organism is positive
for hydrogen sulfide production.
Butt Decarboxylation
Slant
Deamination
Nitrate
VP
Lysine Iron
Agar
MR
H2S
Citrate
Urease
H2S
Gas
Butt
Indole
SIM
Triple Sugar Iron

Agar
Slant
Lactose
Fermentation
RESULTS TABLE:
Gram Negative MacConkey
Agar
Organism
SIM: Motility ______

LIA: H2S _______
STUDY QUESTIONS:
1. Why are the TSI and LIA slants inoculated with both a streak and a stab?
2. The nitrate test requires the addition of several reagents to the culture after incubating the
culture for 48 hours. Explain why the absence of a red color after the addition of
Reagents A and B and zinc signifies a positive result.
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3. Name the three different types of media used to test for hydrogen sulfide production
during this weeks lab exercises. What is the substrate available for H2S production in
each type of media?
4. Explain why an organism will never be positive for both the MR and the VP test.
5. Organisms that secrete the enzyme urease are able to change the pH in their local microenvironment. Would the change be an increase or a decrease in pH? Explain.
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EXPERIMENT #28: EPIDEMIOLOGY INVESTIGATION

One of the jobs of an epidemiologist is to investigate outbreaks of infectious diseases.
When a suspected outbreak occurs in a community, epidemiologists gather data to first determine
the cause of the disease and its the route of transmission, and also to trace the pattern of
transmission with the goal of identifying the original carrier, often termed patient 0. Once the
patients involved in the outbreak have been identified, steps can be taken to prevent the outbreak
from spreading further.
This laboratory exercise simulates an outbreak of a disease transmitted via body fluids,
and students will assume the role of an epidemiologist to trace the pattern of transmission and
identify the original carrier of the disease.
CULTURES NEEDED:
None
MATERIALS NEEDED:
Test tube containing Body fluids 1 per student
Phenol red indicator solution
Plastic pipettes
PROCEDURE:
1. Select numbered Body fluid test tube from the rack and record your number. ______
Note: one of the test tubes contains the diseased body fluid. The remainder of the
tubes contain uninfected body fluids.
2. Using your plastic pipette, draw up about half of the solution from your test tube. Then
do the following:
a. Choose someone at random in the class. Note: it should NOT be someone who
sits at your lab table!
b. Dispense the contents of your pipette into your contacts test tube as he/she
dispenses the contents of their pipette into your test tube.
c. Using your pipette, mix the solution in your tube.
d. Record your contacts name and tube number: ____________________________
IMPORTANT: Wait until everyone in the class completes this step before proceeding to
the next step!
3. Repeat Step 2 twice more (Rounds 2 and 3), each time with a different contact. Again, it
is imperative that you wait until everyone in the class completes Round 2 before moving
on to Round 3.
Round 2 contacts name and tube number: _______________________________
Round 3 contacts name and tube number: _______________________________
4.
Once you have completed Rounds 1-3, add 1 drop of phenol red to your test tube. If the
solution turns red, that indicates your tube is positive for the disease. If the solution
turns yellow, your tube is negative for the disease.
5. Using the results from the entire class, complete the class data table.
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RESULTS:
1. Review the data in the class data table, and indicate which students tested positive at the
end of round 3 by putting an asterisk next to their name.
2. Then, trace the transmission of the disease to each student testing positive, and determine
the identity of the original carrier.
Outbreak Data Table
Student Name / Number
Round 1 Contact
Round 2 Contact
Round 3 Contact
Adapted from Germ Scene Investigation, healthcareers.sd.gov.
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EXPERIMENT #29: ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) TESTING

The enzyme-linked immunosorbent assay, or ELISA (sometimes called EIA, or enzyme
immunoassay), is a commonly used tool in diagnostic medicine. It is used to test for many
diseases and conditions, including HIV infection, Lyme disease, pregnancy, thyroid deficiencies,
and lupus. The test is a type of immunoassay based on specific antigen-antibody binding.
ELISA can directly test for a particular antigen, such as in a pregnancy or Lyme disease test, or,
it can test for specific antibodies, such as in an HIV or lupus
test.
For this lab exercise, we will be using the BioRad
ELISA Immuno Explorer Kit to conduct an HIV test on
simulated patient samples. In this kit, the test strips contain
wells that will be coated with HIV antigens. Samples
containing patient serum are then added to the wells. If the
patients serum contains antibodies to HIV, those antibodies
will bind to the antigen in the wells. At this point, the wells are
washed with a buffer to remove any unbound antibody. In
order to detect the antibody-antigen complexes in the wells, a
second antibody is then added, which will bind to the first
antibody. Again, the wells are washed with a buffer to remove
any unbound antibody. The secondary antibody is conjugated
with a chromogenic enzyme, which will elicit a color change in
the sample when a detection reagent containing the substrate is added. The more intense the
color, the more antibody is present in that sample. The overall procedure is outlined in the
diagram below.
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MATERIALS NEEDED: (per table)

Test Samples A and B (Yellow tubes)
(+) Positive control (Violet tube)
(-) Negative control (Blue tube)
(AG) Purified antigen (Green tube)
(SA) Secondary antibody (Orange tube)
(SUB) Enzyme substrate (Brown tube)
12-well microplate strip
Micropipetter
Yellow tips
Disposable plastic transfer pipette
Wash buffer
Paper towels
PROCEDURE:
1. Identify the yellow tubes labeled Sample A and Sample B that contain the
samples being tested.
2. Label your 12-well strip. On each strip label the first 3 wells with a + for the
positive controls and the next 3 wells with a for the negative controls. Label the
remaining wells to identify the samples being tested (3 wells each).
3. Use a fresh pipette tip to transfer 50 l of purified antigen (AG) into all 12 wells of the
microplate strip.
4. Wait 5 minutes for the antigen to bind to the plastic wells.
5. WASH:
a. Tip the microplate strip upside down onto the paper towels, and gently tap the
strip a few times upside down. Make sure to avoid splashing sample back into
wells.
b. Discard the top paper towel.
c. Use your transfer pipette to fill each well with wash buffer, taking care not to
spill over into neighboring wells. Note: the same transfer pipette is used for all
washing steps.
d. Tip the microplate strip upside down onto the paper towels and tap.
e. Discard the top 23 paper towels.
6. Repeat wash step 5.
7. Use a fresh pipette tip to transfer 50 l of the positive control (+) into the three +
wells.
8. Use a fresh pipette tip to transfer 50 l of the negative control () into the three
wells.
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9. Use a fresh pipette tip to transfer 50 l of Sample A into the appropriately labeled three
wells.
10. Use a fresh pipette tip to transfer 50 l of Sample B into the appropriately labeled
three wells.
11. Wait 5 minutes for the antibodies to bind to their targets.
12. Wash the unbound primary antibody out of the wells by repeating all of wash step 5
two times.
13. Use a fresh pipet tip to transfer 50 l of secondary antibody (SA) into all 12 wells of
the microplate strip.
14. Wait 5 minutes for the antibodies to bind to their targets.
15. Wash the unbound secondary antibody out of the wells by repeating wash step 5 three
times.
16. Use a fresh pipet tip to transfer 50 l of enzyme substrate (SUB) into all 12 wells of
the microplate strip.
17. Wait 5 minutes. Observe and record the results.
RESULTS:
Record your results in the table below:
+ Control
-- Control
Sample A
Sample B
Color
Positive/Negative
Do all of the wells that show a color change have the same color intensity?
Explain the significance of some wells having a darker color than others.
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STUDY QUESTIONS:
1. In a clinical setting, a positive ELISA is typically repeated to confirm the results, and
additional samples are sent to a certified laboratory to re-confirm the results via other
methods. Why is this important? What types of tests would be used to reconfirm the
results?
2. The ELISA test is the most commonly used tool for diagnosing HIV infections.
However, it can give a false negative result if a patient was only recently infected (i.e.
less than 3 months prior). Explain how a patient can be infected with HIV but still have a
negative result in this test.
3. The assay used in this lab exercise employed an indirect ELISA because we were testing
patient samples for the presence of specific antibodies to a particular antigen, which is
what is illustrated in the diagram on page 95. Other diagnostic tests use a direct ELISA,
which tests for the presence of the antigen itself, using wells that are coated with
antibodies to capture the targeted antigen. A secondary antibody is subsequently used to
detect any bound antigen. In the space below, draw the sandwich that would result in a
direct ELISA test.
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EXPERIMENT #30: YOGURT PRODUCTION

Yogurt is one of many types of fermented milk products that is consumed around the
world. Commercial yogurt is made in North America from cows milk and prepared under
precisely controlled conditions in order to favor the metabolism and growth of different types of
lactic acid bacteria. These bacteria ferment the milk to produce the distinct taste of yogurt. To
produce yogurt, milk is first brought almost to the point of boiling to kill any bacteria present in
the milk. It is then cooled so that when the lactic acid bacteria are added, they are not destroyed.
When the milk has cooled sufficiently, two of the active cultures are added: Streptococcus
thermophilus and Lactobacillus bulgaricus.
The first step of yogurt making is to incubate the mixture at 45C, which encourages the
growth of Streptococcus thermophilus, allowing the bacteria to rapidly ferment the lactose in the
milk to lactic acid. This causes the pH of the milk to decrease. Cows milk has a natural pH of
about 6.6. At this pH, the casein (milk protein) exists as a colloidal suspension of a calcium salt
called calcium caseinate which gives milk its white color and turbid appearance. When lactic
acid is produced during lactose fermentation, the calcium caseinate is converted to calcium
lactate and free (soluble) casein. As the pH drops to 4.6, the casein will denature to form
smooth, semi-solid curds. This first step is continued only until the coagulated milk has the
proper texture. If the step continues too long, too much lactic acid will be produced and the
yogurt will be too sour.
After the proper texture has been achieved, the second step involves cooling the yogurt.
The lower temperature prevents further growth of S. thermophilus and promotes growth of
Lactobacillus bulgaricus. L. bulgaricus will ferment the remaining lactose in the milk.
Lactobacillus is a more acid-tolerant bacterium and can withstand the already-present lactic acid.
The second step continues until the temperature drops below the temperature range of L.
bulgaricus, which halts the production of lactic acid and other minor fermentation products. The
low pH will inhibit the growth of most other types of bacteria.
~700 ml of milk
Yogurt starter (container of plain Dannon yogurt with active bacteria)
Hot plate
Beaker in which to stir the milk
Glass stirring rod and/or magnetic stir bar
Thermometer
Plastic spoon (1 per student)
Styrofoam cup (1 per student)
Plastic wrap
Aluminum foil
PROCEDURE:
1. Use pH paper to measure the pH of the milk
2. Heat the milk in the beaker on medium-high to high heat, stirring constantly. Do not scorch!
When the milk just begins to boil, turn off the heat. Cover with plastic wrap, allowing the plastic
to touch the milk to prevent a film from developing on the milk.
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3. Allow the milk to cool to 55C. Note: An ice water bath may be used to cool the milk more
rapidly.
4. Remove the plastic wrap and stir the milk. Pour the milk into 4 Styrofoam cups (one for each
student in the group).
5. Add one teaspoon of the starter yogurt culture to each cup of milk. Stir carefully, but
thoroughly, to distribute the starter throughout the milk.
6. Cover the cup with plastic wrap and cover the plastic wrap with the cup lid or aluminum foil.
Incubate the yogurt cups at 45C for at least 6 hours (overnight is fine).
7. Remove the cups, and check to see that the milk is solid. Refrigerate.
8. Use pH paper to measure the pH of the yogurt.
RESULTS:
Record your observations of the milk/yogurt before and after fermentation:
pH
Texture
Appearance
Color
Milk
Yogurt
STUDY QUESTIONS:
1. Many people are unable to consume dairy products such as milk and cheese because they
are lactose-intolerant. However, these same people often have no trouble eating yogurt.
Based on your knowledge of the yogurt-making process, why do you think this is
possible?
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EXPERIMENT #31: WATER MICROBIOLOGY

Contaminated water is a major route of transmission of infectious disease. When a body
of water becomes contaminated with organic waste materials, it becomes a breeding ground for
microorganisms, both infectious and non-infectious. Testing water for the presence of bacteria
typically involves testing for the presence of fecal coliforms, which are considered indicator
organisms. The presence of fecal coliforms indicates the water has been contaminated with
human or animal feces. The presence of fecal coliforms correlates with presence of enteric
bacterial pathogens such as Vibrio cholerae, Escherichia coli, and Salmonella and Shigella
species; and enteric viral pathogens such as enterovirus, rotavirus, and Norwalk virus. Three
tests are used to determine if a water sample is contaminated with coliform bacteria: a
presumptive test, a confirmed test, and a completed test.
In the presumptive test a series of tubes of phenol red lactose broth are inoculated with
measured amounts of water to see if the water contains any lactose-fermenting bacteria that
produce gas. If, after incubation, fermentation plus gas is seen in the lactose broth, it is
presumed that coliforms are present in the water sample. By counting the number of tubes
positive for gas production at each dilution, the most probable number (MPN) of coliforms is
statistically determined using a standardized chart. Based on MPN results, the EPA sets specific
limits on the number of fecal coliforms for different types of water, such as drinking water and
recreational water, to determine the threshold for contamination. Positive presumptive tests
require follow-up with the confirmed and completed tests.
Confirmed tests involve plating the bacteria from the lactose broth tube onto differential
media such as EMB or MacConkey to confirm the presence of fecal coliforms. Completed tests
involve testing for various biochemical properties (MRVP, citrate, urease, indole, etc.) to
determine the genus and species of the coliforms present. In todays lab exercise, we will be
performing a modified version of the presumptive test with samples from tap water, an
aquarium, and sewage water.
MEDIA NEEDED (per group of 4):
Single Strength Lactose broth with Durham tubes (6)
Double Strength Lactose broth with Durham tubes (3)
CULTURES NEEDED:
250 ml bottle Tap Water
250 ml bottle Aquarium or Pond Water
250 ml bottle Sewage Water
PROCEDURE:
1. Each group will select one water sample to test for the presence of fecal coliforms.
Coordinate with other groups so that all 3 water samples are tested.
2. Label each tube with the water sample source and the amount of sample to be added to
the tube (i.e. 10 ml, 1 ml, or 0.1 ml).
3. Using a sterile pipette, add 10 ml of the water sample to 3 double-strength Lactose broth
tubes.
4. Using a sterile pipette, add 1 ml of the water sample to 3 single-strength Lactose broth
tubes.
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5. Using a sterile pipette, add 0.1 ml of the water sample to the other 3 single-strength
Lactose broth tubes.
6. Make sure all caps are on loosely. (Hint: completely tighten, then un-screw half a turn.)
7. Incubate all tubes at 37 C.
RESULTS:
1. Observe the tubes for the presence of gas in the Durham tube. Even a few tiny bubbles in the
Durham tube is considered positive for gas.
2. Count the number of single-strength and double-strength lactose broth tubes which contain
gas, and refer to the attached chart to determine the MPN.
3. Results:
Sample
# DS-lactose w/
gas (10 ml water)
# SS-lactose w/
gas (1 ml water)
# SS-lactose w/
gas (0.1 ml water)
MPN
Tap Water
Aquarium Water or
Pond Water
Sewage Water
MPN Determination from Multiple Tube Test: (EPA, 2003)

Number of Tubes Giving Positive
MPN Index
95% Confidence Limits
Reactions Out Of
per 100 ml
3 of 10 ml each 3 of 1 ml each 3 of 0.1 ml each
Lower
Upper
0
0
0
0
0
0
0
0
1
3
<0.5
9
0
1
0
3
<0.5
13
1
0
0
4
<0.5
20
1
0
1
7
1
21
1
1
0
7
1
23
1
1
1
11
3
36
1
2
0
11
3
36
2
0
0
9
1
36
2
0
1
14
3
37
2
1
0
15
3
44
2
1
1
20
7
89
2
2
0
21
4
47
2
2
1
28
10
150
3
0
0
23
4
120
3
0
1
39
7
130
3
0
2
64
15
380
3
1
0
43
7
210
3
1
1
75
14
230
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3
3
3
3
3
3
3
3
1
2
2
2
3
3
3
3
2
0
1
2
0
1
2
3
120
93
150
210
240
460
1100
>1100
30
15
30
35
36
71
150
n/a
380
380
440
470
1300
2400
4800
n/a
STUDY QUESTIONS:
1. Why are fecal coliforms considered indicator organisms?
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EXPERIMENT #32: FOOD MICROBIOLOGY

Contaminated food is another major route of transmission of infectious disease. Meat
products such as beef, pork, and chicken often become contaminated during the slaughtering
process, and individuals become infected when the meat is not properly cooked. Some of the
primary bacterial pathogens associated with contaminated meat include Escherichia coli and
other fecal coliforms, Campylobacter, Salmonella and Shigella. In todays lab, we will be
testing chicken and ground meat from the supermarket for the presence of gram-negative
bacterial contaminants using Salmonella-Shigella agar plates.
Salmonella-Shigella agar plates contain lactose, bile salts, ferric citrate, and neutral red.
The bile salts in agar make the media selective for gram-negative enteric bacteria by inhibiting
the growth of gram-positive organisms. The lactose in the media is a carbohydrate substrate
which allows the differentiation between lactose fermentors and non-lactose fermentors. If
lactose is fermented, the acid end-products will react with the neutral red pH indicator, giving the
bacterial growth a pinkish-red color. The ferric citrate in the media acts as an indicator of
hydrogen sulfide production, producing a black precipitate when H2S is present.
MEDIA NEEDED: (per group of four)
Salmonella-Shigella agar plates (SS plates)
CULTURES NEEDED:
Chicken parts
Sausage or ground beef
PROCEDURE:
1. With a permanent marker, divide the SS plate in half. On one half write chicken and
on the other half write sausage or ground beef. (Also label with your groups
name/initials, lab period, and date.)
2. Swab over the chicken with a sterile cotton-tipped swab and rub over the chicken half
of the SS plate.
3. Swab over the sausage with a sterile cotton-tipped swab and rub over the sausage half
of the SS plate.
4. Incubate the plates at 37 oC.
RESULTS:
1. Observe SS plates for bacterial growth. Determine which bacteria are growing on the plate
using the following criteria:
Escherichia and other fecal coliforms such as K. pneumoniae: ferment lactose and produce
reddish pink colonies on the agar.
Salmonella: do not ferment lactose, but do produce hydrogen sulfide. Colonies will either be
black, or clear with a black dot in the center.
Shigella: do not ferment lactose, and do not produce hydrogen sulfide. Colonies will be clear.
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2. Record results in the table below.

Microorganism
Escherichia / coliforms
Chicken
Sausage / Ground Beef
Salmonella
Shigella
STUDY QUESTIONS:
1. Will swabbing and streaking on SS plates identify all bacteria which could be chicken
contaminants? Why or why not? Name at least one organism which commonly
contaminates chicken which cannot be identified by this test. Hint: Refer to lecture
notes if you get stuck!
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Appendix A:
Unknowns
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UNKNOWN INSTRUCTIONS
DAY 1:
Today you will be given a broth tube containing two unknown microorganisms: a gram-positive
coccus and a gram-negative rod. Your ultimate task will be to separate the two organisms and
determine the identity of each organism by performing various biochemical tests previously
learned in this lab course. During the whole unknown project, you will be able to refer to your
notes and consult your classmates for assistance. (However, remember that this is an individual
project a student should not rely completely on another student to tell them what to do!) You
will also get to ask your instructor 5 free questions without any adverse effect on your grade.
For TODAY you will be doing 4 things:
1. Streaking out the broth culture onto a Nutrient Agar plate using a 4-way isolation streak.
2. Streaking out the broth culture onto a MacConkey agar plate using a 4-way isolation
streak.
3. Streaking out the broth culture onto a C-CNA agar plate using a 4-way isolation streak.
4. Performing a gram stain on the culture to verify the presence of both a gram-positive
coccus and a gram-negative rod.
**Incubate all plates at 37C. There will be a GasPak jar or Aneropak on the front table if
you wish to incubate one of your plates in an aerobic environment enriched with CO2.
Helpful hints:
Think . . . why are we using 3 different kinds of plates to separate and isolate the two unknown
organisms?
Label, label, label! Label the type of media, your unknown #, your name and class period, etc.
Be sure you write down your unknown number!!
One of your gram stains will be graded, so if youre happy with the results on this one, its a
good idea to get this hurdle out of the way!
Your 4-way streaks will also be graded, so make sure your lab instructor can identify which
plates belong to you!
DAY 2:
Today you will be doing the following:
1. Examining your streak plates from the previous lab period for the presence of isolated
colonies.
2. Using a sterile needle, pick part of one putative gram-positive colony and perform a
gram-stain to confirm its identity.
3. Once youve confirmed the organism is a gram-positive coccus, transfer the remainder of
the above colony to a nutrient agar slant. This is going to be your working stock culture
from which to inoculate the rest of your gram-positive tests. Make sure you label this
slant with your unknown # AND with gram+ so you dont get it mixed up with your
gram-negative!
4. Using a sterile needle, pick part of one putative gram-negative colony and perform a
gram-stain to confirm its identity.
5. Once youve confirmed the organism is a gram-negative rod, transfer the remainder of
the above colony to a nutrient agar slant. This is going to be your working stock culture
from which to inoculate the rest of your gram-negative tests. Make sure you label this
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slant with your unknown # AND with gram- so you dont get it mixed up with your
gram-positive!
6. Incubate all nutrient agar slants at 37C.
Helpful hints:
Label, label, label!
If you didnt have your gram stain graded during the previous lab period, select one of your gram
stains from today to be graded.
DAY 3
Today you will be inoculating your isolated gram-negative and gram-positive unknowns onto the
appropriate microbiological media in order to determine their identity.
1. Perform a Gram stain on bacterial growth from each nutrient agar slant to confirm that
your cultures are pure.
2. Determine which genus your gram-positive isolate belongs to: is it Staphylococcus or
Streptococcus?
3. Once you determine the genus, inoculate your gram-positive isolate onto either the Staph
ID media or the Strep ID media. DO NOT INOCULATE BOTH!!
4. Inoculate your gram-negative isolate onto the 7 pieces of Gram-negative ID media.
Helpful hints:
Label, label, label!
Antibiotic disks (Novobiocin, SXT, Bacitracin) are available on the front cart.
A Gas-Pak jar or Anaeropak box is available at the front table if you wish to incubate anything
aerobically in the presence of CO2.
DAY 4
Today you will be reading the results of the tests you inoculated during the previous lab period.
Once you have read all of the tests, confirm your results with your instructor before you discard
anything.
Helpful hints:
Dont forget that some gram-negative tests require you to add additional reagents Read your
notes!
Rulers are available on the front cart.
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Name:___________________________________________
Unknown #:____________
Record the results of your unknown tests on this worksheet. Be sure to include this worksheet
in your unknown report!
Gram Stain of Mixed Culture: (Observations)
Isolation Streaks:
Media used for
Observations
Isolation
Gram Stain Results

(if applicable)
Nutrient Agar
MacConkey
Columbia CNA
Agar
Gram Positive Identification:
Catalase Result: ______________
MSA fermentation
DNase
Novobiocin
Result
_______
_______
_______
Hemolysis
Bacitracin
SXT
Bile esculin
MSA growth
Result
_______
_______
_______
_______
_______
Gram Negative Identification:

MacConkey: Fermentation ________
TSI: Slant _______ Butt______ Gas ______ H2S ______
Urease:
________
Citrate: _______
SIM: Indole _______ H2S ______
MR/VP: MR _______
VP _______
Nitrate: + or LIA: Deamination________
Decarboxylation ______
Gram-positive and Gram-negative results confirmed with Instructor? ________ (Initials)
(Note: Instructors will confirm that your test results are correct, but they will not confirm the
identity of your unknowns!)
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Name________________________ Unknown #__________

Unknown Deductions
You will be deducted points for the following:
Ded.
Pts
Instr.
Initial
1. Incorrect 4-way streak procedure (5 pts)

2. Gram stain (0-5 pts)
3. Microscopy (5 pts) cant focus microscope
4. Using the wrong media ______________ (10 pts)
5. Using extra media b/c of inoculation errors (8 pts)
6. Omitting or using the wrong disc on Staph or Strep ID (5 pts)
7. Not labeling tubes and plates correctly (1 pt per piece)
8. Incorrect ID of microbe (10 pts)
9. Each additional question after your 5 permitted (2 pts each)
10. Forgetting your Unknown Work sheet (5 pts)
11. Not bringing your instructions (5 pts)
12. Picking up extra media without instructors permission (5 pts)
13. Viewing organism under wrong objective (5 pts)
14. Not cleaning oil off of microscope objectives (5 pts)
15. Not cleaning table at the end of the lab period (5 pts)
16. Failing to invert agar plates during incubation (5 pts)
17. Incorrectly interpreting results _____________ (__ pts)
18. Incorrectly inoculating media ______________(3 pts each)
19.
20.
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
______
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
_____
NOTES TO REMEMBER:
1. Each student is allowed to ask 5 questions throughout the Unknown Identification process,
whether you ask a lab instructor or a lab assistant. After that, for every question asked, you are
penalized 2 pts.
2. You must refer to your notes for directions and procedures. You may also ask your fellow
students if you have questions. Be sure to bring your protocols to each class.
3. You are also required to bring this Unknown Identification Work Sheet each time you come to
lab. Points will be deducted if you do not.
4. You must be able to independently find your microbes under the microscope.
5. You can and should ask your instructor to confirm your results when you have completed all
of the tests. However, instructors will NOT interpret results for you or tell you the identity of
your unknowns. It is your responsibility to correctly interpret the results of each test and to
determine the identity of each unknown once you have confirmed your test results.
NOTES:
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Appendix B:
Unknown Reports
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GENERAL:
Unknown reports in microbiology are written in scientific format. Scientific writing is different
from other types of writing in that the results of the exercise or experiment are being showcased,
not the writing. The purpose of scientific writing is not to entertain, but to inform. The writing
should be simple and easy to understand. There is a specific style that must be followed when
writing scientific reports. Scientific writing is typically written in the passive voice. The
pronouns "I", "We" and "They" are not used. For example, instead of writing "I used a TSA agar
plate to isolate my unknown," it is customary to write, "A trypticase soy agar (TSA) plate was
used to isolate the unknown." It is also customary to write in the past tense for most of the report.
This includes the introduction, the summary, the description of the materials and methods, and
the results. The present tense is reserved for the conclusions about the results.
Microbial nomenclature: The name of the bacterium should be written out and spelled
correctly. The name should be italicized, e.g. Staphylococcus aureus. The genus is capitalized
but the species is not. After the full genus name is given in the paper, it can be abbreviated as S.
aureus, but it is still italicized. This is as long as there is no other genus in the paper that starts
with the same letter. (For example, if you have a Staphylococcus species and a Salmonella
species as your unknowns, you cannot abbreviate!)
MECHANICS: The lab report should be typed using a 12 point normal font such as Times New
Roman or Arial, and should be single-spaced. The lab report should be presented bound in a
report folder. Reports will be graded on content as well as spelling, grammar, punctuation, and
organization.
SECTIONS OF THE UNKNOWN LAB REPORT:
(Note: Other than the title page, the pages of the report must be numbered)
TITLE PAGE
The title page should include the following information:
UNKNOWN NUMBER
YOUR NAME
DATE (the due date)
LAB INSTRUCTOR'S NAME
COURSE NAME / SECTION NUMBER
SEMESTER / YEAR
INTRODUCTION
This section introduces the reader to the study and why the study was done. This should only be
a few sentences long. Example: "There are many reasons for knowing the identity of
microorganisms. The reasons range from . . .[explain 2-3 reasons why you may want to identify
an unknown bacterium]. This study was done by applying all of the methods that have been
learned in the microbiology laboratory class for the identification of an unknown bacterium."
MATERIALS & METHODS
This is where the details of the study are listed. The materials and methods section should
contain three paragraphs: (1) a description of how the two unknowns were separated and
isolated (2) a description of the identification of the gram-positive isolate and (3) a description of
the identification of the gram-negative isolate.
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Be specific, but concise: do not rewrite the lab manual! The most common way is to mention the
names of the materials used and why they were used, and reference the lab manual for the
procedure or method. See example 1.
Example 1: "An unknown labeled number 37 was selected. The methods that have been learned
in microbiology laboratory were applied to identify this unknown. Procedures were followed as
stated in the course laboratory manual (Cain et al, 2013) unless otherwise noted. The first
procedure that was performed was streaking the unknown out on a nutrient agar plate, using the
T streak method described in the lab manual. This was done in order to . . . [explain why]. After
the plates were incubated and grown, the morphology was observed and recorded and a Gram
stain was performed. After determining the Gram reaction, specific biochemical tests were
performed. The biochemical tests were chosen from the lab manual. Since unknown 37 was
determined to be a Gram positive rod, an endospore stain was also performed. The following
types of media were inoculated with unknown 37: starch, lipid, and casein agars, mannitol salt
agar, a gelatin deep, a bile esculin agar slant, and a nitrate broth. Table 1 lists the test, purpose,
reagents and media components, and results.
RESULTS
This is where the results are summarized. The results should be presented in 2 tables, using a
separate table for each unknown, i.e. one table for your gram-positive, and another table for your
gram-negative (see example below). This is also where the flow charts showing how you arrived
at your answers are presented. The flow charts included in the report should trace the route you
followed on your flow chart to identify your unknown. A short paragraph explaining how the
results are presented should also be included. Example: Unknown 37 appeared as a large,
mucoid, cream-colored colony on the nutrient agar plate. A gram stain revealed that the
organism was a Gram-positive rod, and an endospore stain demonstrated the presence of
subterminal endospores. A stock of unknown 37 was grown on a nutrient agar slant and used to
inoculate the tests listed in Table 1. The results of all tests are presented in Table 1 and shown in
flow chart form.
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Table 1: Gram-positive Identification

Test
Purpose
Gram
Stain
Determine cell
wall properties
Endospore Determine if
Stain
spore producer
Starch
Lipid
Gelatin
Determine if
organism can
hydrolyze
starch
Determine if
organism can
hydrolyze
lipids
Determine if
organism can
hydrolyze
gelatin
Cain et al
Media
Components
/Reagents
Crystal violet,
iodine, alcohol,
safranin
Malachite green,
safranin
Starch in plates
Added iodine after
incubation
Observations
Results
Interpretations
Purple rods
Grampositive
rods
Positive
for spore
formation
Organism has thick

peptidoglycan layer, no
outer membrane
Organism produces
endospores
Positive
Organism has enzymes

maltase and amylase
needed to hydrolyze
starch
Organism does not
possess lipases and
cannot hydrolyze lipids
Pink rods with

small green
endospores
between the center
and the end
Zone of clearing
Tributyrin in plates
No zone of
clearing
Gelatin in tubes
Tube was still solid Negative

after incubating
115
Negative
Organism does not

produce gelatinase
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FLOWCHART: UNKNOWN #37 (GRAM-POSITIVE)

Gram Stain
Gram-positive rod
Endospore stain (positive)
MSA Growth (negative)
Negative
Positive
B. cereus
B. coagulans
B. megaterium
B. subtilis
B. brevis
B. licheniformis
B. polymyxa
B. sphaericus
Casein (positive)
Positive
B. brevis
B. lichniformis
B. polymyxa
Negative
B. sphaericus
Bile Esculin (positive)

Negative
B. brevis
Positive
B. lichniformis
B. polymyxa
Starch (positive)
Positive
B. polymyxa
Negative
B. lichniformis
Nitrate (positive)
B. polymyxa
Lipid (positive)
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Unknown #37 = Bacillus

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polymyxa
DISCUSSION / CONCLUSION
This section interprets the meaning of the results. Again, you should have a separate paragraph
for each identified isolate. The following questions should be answered here:
How did the test results lead to identification? What problems were encountered, if any? In this
section, you should also include 1-2 paragraphs of background information on each bacterium
you identified, including its characteristics and significance.
Example of a discussion: After several differential tests, it was concluded that the gram-positive
organism in unknown 37 was Bacillus polymyxa. After performing the Gram stain, it was
determined that the unknown was a Gram-positive rod. The results of the endospore stain
showed that the organism produced subterminal endospores, indicating it belongs in the genus
Bacillus. The organism was grown on a TSA slant for use in inoculating the rest of the
biochemical tests. All of the biochemical tests worked well except for the test for gelatin
hydrolysis. It gave a false negative result at first, which was inconsistent with the rest of the
results. Using the Bacillus identification dichotomous key, it was concluded that the unknown
was Bacillus polymyxa.
Bacillus polymyxa is a gram-positive endospore-forming bacillus (Bauman, 2006). It is a
motile bacterium, and possesses peritrichous flagella (Todar, 2005). B. polymyxa can be found
in a wide range of environmental habitats, including acidic environments. It is commonly found
in soil, water, and decaying vegetables (Stedman, 2006). Because it can grow in both moderate
and cold temperatures, B. polymyxa is classified as a psychrotroph. B. polymyxa produces a
thick polysaccharide capsule, and is also a facultative anaerobe (Todar, 2005). Although B.
polymyxa does not cause disease in animals or humans, it is of medical significance because it
produces the antibiotics polymyxin and colistin (Madigan and Martinko, 2006).
REFERENCES:
Note: the minimum number of references is three, which can include the lab manual and the
textbook. You may not use wikis (such as Wikipedia or MicrobeWiki) as sources! References
should be listed in APA format, and parenthetical in-text citations must be used where
appropriate. Note: Any information presented that is not your original idea or your own data
must be credited with an in-text citation!
Use this format to cite the lab manual on your reference page:
Cain, D., Hanks, H., Weis, M., Bottoms, C., and Lawson, J. (2013) Microbiology Laboratory
Manual. Collin County Community College District, McKinney, TX.
The corresponding in-text citation would be (Cain et al., 2013).
UNKNOWN WORKSHEET
Attach your completed unknown worksheet.
Modified from: http://www.sci.sdsu.edu/classes/biology/bio210/lab/demers/Howtowriteanunknownlabrepor.pdf
Cain et al
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What are biosafety guidelines and why are they important in a microbiology lab?

What are biosafety guidelines and why are they important in a microbiology lab?

What techniques are described for identifying unknown bacterial specimens?

What techniques are described for identifying unknown bacterial specimens?

W ritten by:

Donna Cain, Hershell Hanks, Mary Weis, Carroll Bottoms , and

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Tutorial Website for

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a) inform your instructor immediately

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MICROORGANISMS / BIOSAFETY LEVEL:

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EXPERIMENT #1: MICROSCOPY

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STAINING OF BACTERIAL SPECIMENS

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PROCEDURE FOR PREPARING A BACTERIAL SMEAR

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EXPERIMENT #2: GRAM STAIN

Gram-positive cell wall

Gram-negative cell wall

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EXPERIMENT #3: CAPSULE STAIN

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8. Dispose of staining waste in designated waste receptacle. Dispose of slides in red

2. Explain the clinical significance of a bacterial capsule.

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EXPERIMENT #4: ACID-FAST STAIN

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running off the slide.

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EXPERIMENT #5: ENDOSPORE STAIN

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EXPERIMENT #6 CULTURE TRANSFER TECHNIQUES

Make sure all caps are loose, but secure.

6. Incubate at 30 C for 48 hours.

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EXPERIMENT #7 ISOLATION OF PURE CULTURES

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Draw the distribution of the growth and colonies on the plate.

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EXPERIMENT #8: VIABLE PLATE COUNTS

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MEDIA NEEDED: (per group of four)

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Number of CFU/ml of original broth culture