GROUP 1

CHAPTER 5
NORMAL MICROBIAL FLORA & PATHOGENIC BACTERIA

DEFINITION OF NORMAL FLORA

-Normal flora are the microorganisms that live on another living organism (human
or animal) or inanimate object without causing disease.
What does flora mean in microbiology?
- Collective bacteria and other microorganisms in a host are historically known as
flora. Flora pertains to the Kingdom Plantae. Microbiota includes Archaea,
Bacteria, Fungi and Protists.
What is Normal Flora and why is it Important?
-This normal flora helps to prevent us becoming colonized with more dangerous
bacteria, which might lead to infection.

Significance of the Normal Flora

The Normal Flora in humans usually develops in an orderly sequence, or
succession, after birth,leading to the stable populations of bacteria that make up the
normal adult flora.
The normal flora influences the anatomy, physiology, susceptibility to pathogens,
and morbidity of the host.

FACTORS INFLUENCING NORMAL FLORA

Factors that determine the composition of the normal flora in a body region include
the following:
1.The nature of the local environment,which is determined by
pH,temperature,redox potential, and oxygen,water, and nutrient levels;and
2. Various non-specific host mechanisms such as peristalsis,saliva,lysosome
secretion and secretion of immunoglobulins.
GROUP 1

BENEFICIAL EFFECTS OF NORMAL FLORA

 They prevent or suppress the colonization/invasion of the body by

pathogens.
 The bacterial flora of the intestinal tract synthesize vitamins, especially K
and several B vitamins.
 Antibodies produced in response to commensals cross-react with pathogens
having related or shared antigens and thus raise the overall immune status of
the host against pathogens.

HARMFUL EFFECTS OF NORMAL FLORA

 They become pathogenic when the host resistance is lowered.

 They may act as pathogens in tissue outside their normal habitat normal
flora of the intestine may cause urinary tract infection.
 The use of broad-spectrum antibiotics affects the normal flora by inhibiting
sensitive bacteria and thereby allowing overgrowth of resistant bacteria.

Where can we find normal flora?

 Skin
 Eye
 Mouth
 Upper Respiratory Tract
 Gastrointestinal Tract
 Urogenital Tract

Normal Flora of Skin

 Skin can acquire any bacteria from the environment but it either get washed
off or die because the skin is dry, has acidic pH, and produce sweat and oil. •
Permanent bacteria present on skin can be in any layer of the skin. Skin
GROUP 1

provides good examples of various microenvironments. The composition of

the dermal microflora varies from site to site according to the character of
the microenvironment. A different bacterial flora characterizes each of three
regions of skin: (1) axilla, perineum, and toe webs; (2) hand, face and trunk;
and (3) upper arms and legs.

RESPECTIVE MICROORGANISM IN NORMAL FLORA OF SKIN

1. Staphylococcus epidermis

>is a major inhabitant of the skin, and in some areas, it makes up more than 90 percent
of the resident aerobic flora.

2. Staphylococcus aureus

> present in the nose and perinium. S. aureus is extremely common (80 to 100 percent)
on the skin of patients with certain dermatologic diseases such as atopic dermatitis, but
the reason for this finding is unclear.

3. Micrococci

>Micrococci are not as common as staphylococci and diphtheroid; however, they are
frequently present on normal skin.

4. Diphtheroid or Coryneforms

>The term diphtheroid denotes a wide range of bacteria belonging to the genus
Corynebacterium. Diphtheroids have been categorized into the following four groups:
lipophilic or nonlipophilic diphtheroids; anaerobic diphtheroids; diphtheroids producing
porphyrins and those that possess some keratinolytic enzymes and are associated with
trichomycosis axillaris. Lipophilic diphtheroids are extremely common in the axilla,
whereas nonlipophilic strains are found more commonly on glabrous skin. Anaerobic
diphtheroids are most common in areas rich in sebaceous glands.
GROUP 1

5. Gram-Negative bacilli

> Gram-negative bacteria make up a small proportion of the skin flora. They are seen in
moist intertriginous areas, such as the toe webs and axilla, and not on dry skin.
Desiccation is the major factor preventing the multiplication of Gram-negative bacteria
on intact skin.

Nail Flora
Similar to skin flora, these dust particles may carry fungi and bacilli. Aspergillus,
Penicillium, Cladosporium, and Mucor are the major types of fungi found under
the nails.

Oral and Upper respiratory tract flora

- the normal flora of the oral cavity and the upper respiratory tract include the
following:
1. General Distribution- Bordetella Parapertussis, Eikenella corrodens.
2. Nose- Cardiobacterium species and Staphylococcus Aureus.
3. Nasopharynx- Acinetobacter species, Campylobacter sputorum, Hemophilus
species, Moraxella species, Neisseria cinerea, Neisseria lactamica, Neisseria
meningitidis, Neisseria mucosa, Neisseria sicca, Selenomonas sputigena,
and Streptobacillus species.
4. Pharynx- Candida albicans, Citrobacter freundii, Hemophilus
parainfluenzae, Hemophilus paraphrophilus, Neisseria elongata,
Peptostreptococcus species, Streptobacillus species, and Viridans
streptococcus.
5. Upper Respiratory Tract- Kingella species, Peptostreptococcus species, and
Streptococcus pyogenes.
6. Respiratory epithelium- Mycoplasma pneumoniae.

Gastrointestinal Tract Flora

GROUP 1

Gastrointestinal Tract – refers to the parts of our body that is related to our

stomach and intestines.

The gastrointestinal tract refers to the parts of our body related to our

stomach and intestines, namely- the mouth, the pharynx (throat), the esophagus,

the stomach, the small intestine, the large intestine, the rectum, and the anus + the

salivary glands, liver, gallbladder, and pancreas.

Flora – Bacteria and other organisms

+ produces vitamins such as biotin and vitamin K. Also known as gut flora,

intestinal microflora, and microflora

What do these bacteria do?

Stomach acidity, intestinal transit, nutritional factors, antibiotic usage, and

bacterial interactions

90% of this flora is composed of anaerobes

Examples of normal flora:

Saliva Lactobacillus Species

Stomach Clostridium Sordelii,

Helicobacter Pylori

Small Intestines Anaerobes

Large Intestines Anaerobes

Rectum and Anus Clostridium Sordelii

GROUP 1

Urogenital Flora

Urogenital Flora - The type of bacterial flora found in the vagina

Types of bacterial flora found in the vagina depending on the

- age, pH, and hormonal levels

These are the most common flora found in the vagina as a woman grows

Infants – Lactobacillus species

Children to Puberty – diphtheroid, staphylococcus epidermis, streptococci

Puberty to Adulthood – Contains Adult Flora

CONJUNCTIVAL FLORA
-The study of normal conjunctival flora by Keshav and Basu found that coagulase-
negative staphylococci (81.5%) and S. aureus (3.7%) are the normal flora
inhabiting the lid margin and conjunctiva of normal populations and are the main
causes of acute postoperative endophthalmitis, this study showed that an increase
in age is related to higher amount of bacteria. They also found that both patients
with lacrimal duct obstruction and immunosuppressed patients are more likely to
be colonized by pathogens that cause postoperative endophthalmitis.

Overview of bacteria and pathogen

GROUP 1

1. Bacteria ( s. bacterium)- are type of biological cell.

Shapes:
 Cocci (s. coccus)- spherical or coccoid shaped bacteria.
 Bacilli ( s. bacillus)- rod-shaped bacteria.
 Sprilli- curved or spiral shaped bacteria.

DIFFERENTIATE GRAM POSITIVE AND GRAM-NEGATIVE

BACTERIA

 Gram-positive bacteria stain blue or violet by Gram staining because they

are able to retain the crystal violet because they are surrounded by layers of
peptidoglycan many times thicker than is found in the Gram-negatives.
Gram negative bacteria do not retain the crystal violet stain such that the
final stain is characterized by a pink or pale red stain.

GRAM POSITIVE BACTERIA CLASSIFICATION

Enterococcus:
Enterococcus is a member of the lactic acid bacteria group, and is characterized by
its ability to grow in high-salt and low-pH environments. These bacteria are
catalase-negative, which means that they do not produce the enzyme catalase,
which is used to break down hydrogen peroxide. They are also facultative
anaerobes, which means that they can survive in both the presence and absence of
oxygen. Enterococcus can be further divided into several species, including
Enterococcus faecalis, Enterococcus faecium, Enterococcus avium, and
Enterococcus casseliflavus, among others.

Staphylococcus:
Staphylococcus is a genus of Gram-positive, cocci-shaped bacteria that are
commonly found on the skin and in the nasal passages of humans and animals.
Staphylococcus aureus is the most clinically significant species, as it can cause a
range of infections, from minor skin infections to life-threatening conditions such
as sepsis and toxic shock syndrome. Methicillin-resistant Staphylococcus aureus
GROUP 1

(MRSA) is a particular concern due to its resistance to many commonly used

antibiotics. Diagnosis of staphylococcal infections typically involves culturing the
bacteria from a wound or other infected site, followed by identification and
antibiotic susceptibility testing.

Streptococcus:
Streptococcus is a genus of Gram-positive, cocci-shaped bacteria that are
commonly found on
the skin and in the respiratory tract of humans and animals. Streptococcus
pyogenes, also
known as Group A Streptococcus, is a common pathogen that can cause a range of
infections,
including pharyngitis (strep throat), impetigo, and cellulitis. More severe
infections, such as
necrotizing fasciitis and toxic shock syndrome, can also occur. Diagnosis of
streptococcal
infections usually involves culturing the bacteria from a throat swab or other
infected site,
followed by identification and antibiotic susceptibility testing.

Peptostreptococcus
Peptostreptococci (formerly Peptococcus) are anerobic cocci that are normal
residents of the mouth,GI tract,genital tract,and skin.These organisms produce
mixed anaerobic infections.The tiny, spherical cells might appear individually, in
pairs, or in short chains. Typically, they use cilia to move. Peptostreptococcus are
slow-growing bacteria that are becoming more and more resistant to antibiotics.
Peptostreptococcus is a typical resident of a healthy woman's lower reproductive
tract.

Rod (Anaerobe)
 Clostridium – are rod-shapes genus of anaerobic, Gram positive bacteria.

Aerobic
A. Bacillus
-species are aerobic, sporulating, rod-shaped bacteria that are ubiquitous in nature.
As secondary invader, Bacillus species may exacerbate preexisting infections by
GROUP 1

producing either tissue-damaging toxins or metabolites such as penicillinase that

interfere with treatment.

B. Corynebacterium
-Corynebacteria are rod-shaped, aerobic or facultative anaerobic, non-spore-
forming, and non-motile bacteria that are straight or slightly curved. Its most
important specie C diphtheriae, causes diphtheria. Diphtheria is the most
commonly an infection of the upper respiratory tract and causes fever, sore throat,
and malaise.

C. Listeria
-are rod-shaped bacteria commonly found in soil, stream water, sewage, plants, and
food. Listeria monocytogenes is the causative organism of listeriosis, a rare but
potentially deadly food-borne infection manifested as meningitis in newborns and
sepsis.

GRAM NEGATIVE BACTERIA CLASSIFICATION

NEISSERIA
The family Neisseria comprises the genera Neisseria, Moraxella, Kingella, and
Acinetobacter. The only significant human pathogens are N. gonorrhoeae, the
agent of gonorrhea, and N. meningitidis, an agent of acute bacterial meningitis.
Neisseria are gram-negative bacteria that have diplococcus arrangement.Probably
it is the only pathogenic bacteria that have this arrangement.

2 main important species:

•Neisseria Gonorrhea
•Neisseria Meningitidis

RODS
(Aerobic Rods Definition)
GROUP 1

-A group of gram-negative bacteria consisting of rod- and coccus-shaped cells.

They are both aerobic (able to grow under an air atmosphere) and microaerophilic
(grow better in low concentrations of oxygen) under nitrogen-fixing conditions but,
when supplied with a source of fixed nitrogen, they grow as aerobes.

PSEUDOMONAS
-Pseudomonas aeruginosa had been considered as an obligately aerobic bacterium
previously, but it is now recognized to be highly adapted to anaerobic conditions.
Because the P. aeruginosa-infected mucus in the CF airway is depleted of oxygen,
the anaerobic physiology of P. aeruginosa is believed to be important for its
pathogenesis
(Microaerophilic)
A. Campylobacter
-are spiral, motile and microaerophilic bacteria that are oxidase positive. The main
specie, Campylobacter jejuni, is one of the main causes of bacterial food
poisoning. Other species include C coli and C fetus as an opportunistic infection in
humans.

B. Helicobacter
-is a group of microaerophilic bacteria that lives in the lining of the upper Gi tract
and has been implicated in the development of peptic ulcers, chronic gastritis,
duodenitis, and gastric cancer. Helicobacter pylori is the type specie of genus.

BACTEROIDES
The human colon possesses the largest population of bacteria in the body, and the
majority of these organisms are anaerobes , Anaerobes are the bacteria that do not
require oxygen to live , and about 25 percent of these are species of Bacteroides.
Bacteroides fragilis is a pleomorphic bacterium commonly found in the human
gastrointestinal tract as normal flora. It can cause infections like sepsis, abscesses,
and peritonitis when there is a disruption of the mucosal surface, either by trauma
or surgery, leading to the spread of the bacterium to the bloodstream or
surrounding tissues.
Now, a little bit more about this microbe , Bacteroides fragilis is Gram-negative,
which means that it has a thin peptidoglycan cell wall that can't readily retain
purple dye when Gram stained.Additionally, it can be either motile or non-motile
GROUP 1

bacteria.It's also an obligate anaerobe, meaning that it can only live without
oxygen.

RODS (Facultative anaerobes)

1. Escherichia

> Escherichia is non-spore-forming, rod-shaped and facultatively anaerobic genus

with species that inhabit the human intestine. Most species of Escherichia are
nonpathogenic commensals. Other species cause enteritis or urinary tract
infections.

2. Pasteurella

> Pasteurella is one of the facultative anaerobic, non-motile, and pleomorphic

bacteria, most of which are catalase- and oxidase- positive. Pasteurella multocida is
the most common cause of soft tissue infection in humans following bites or
scratches from dogs and cats.

3. Salmonella

> Salmonella is a non-spore-forming, facultatively-anaerobic, genus of rod-shaped

Gram-negative bacteria of the family Enterobacteriaceae. These organism produce
typhoid fever, paratyphoid fever, and other food-borne illnesses.

4. Shigella
-are non-spore-forming, rod-shaped bacteria that are related to Escherichia and
Salmonella. This is the primary cause of bacillary dysentery which is severe
diarrhea containing mucus and/or blood and inflammatory cells. The dysenteric
stool is often scant.

5. Vibrio
GROUP 1

-are curved, rod-shaped, motile, and facultatively-anaerobic bacteria associated

with eating undercooked or raw seafood as the organism is typically found in
saltwater. Cholera is a life-threatening secretory diarrhea induced by an enterotoxin
secreted by V cholerae.

6. Yersinia
-are rod-shaped, facultatively anaerobic, and facultative intracellular parasitic
bacteria that is the causative agent of the plague. Rats are the natural reservoirs of
Yersinia pestis and may be transmitted through the blood or by ingestion of food
products such as vegetables, milk products, and meat that have been contaminated
with yersinia-infected urine or feces.

OTHER BACTERIA PATHOGENIC TO MAN

BORRELIA
Borrelia is a spirochete that causes a zoonotic , vector borne disease. Borrelia
species are responsible for the Relapsing fevers and Lyme disease. The organisms
are transmitted to humans primarily by lice or ticks.
Relapsing fevers are acute recurrent illnesses characterized by febrile episodes
that recede spontaneously but generally reappear with decreasing intensity and
duration.
Lyme disease is another tick-borne illness and is caused by B burgdorferi. The
disease occurs in the north temperate zone.

LEPTOSPIRA
Leptospira is a type of bacteria that has a unique flexuous motility and is
characterized as a thin, tightly coiled, and obligate aerobic spirochete. The primary
hosts of this disease are wild and domestic animals, and it is a significant cause of
economic loss in the meat and dairy industry.

MYCOBATERIUM
GROUP 1

Mycobacterium is a group of rod-shaped , aerobic, and non-motile bacteria that are

acid-fast and are the main cause of tuberculosis and leprosy.

Mycobacterium tuberculosis complex

The pathogens that cause tuberculosis are mycobacteria that belong to the M.
tuberculosis complex. This complex comprises the following species:

•M. tuberculosis
•M. bovis
•M. africanum
•M. canettii
•M. microti
•M. pinnipedii

Mycoplasma:
Mycoplasma is a genus of bacteria that are known for their unique characteristics,
including their small size and lack of a cell wall. These bacteria are capable of
infecting a wide range of hosts, including humans, animals, and plants.
Mycoplasma infections can cause a range of symptoms, including respiratory tract
infections, urinary tract infections, and pneumonia.
One of the most notable mycoplasma infections is Mycoplasma pneumoniae,
which is a common cause of respiratory infections in humans. This bacteria is
known to cause atypical pneumonia, which can be difficult to diagnose due to its
non-specific symptoms. Other notable Mycoplasma species include M. hominis,
which can cause urogenital infections, and M. genitalium, which is a sexually
transmitted infection that can cause urethritis and cervicitis.

Nocardia:
GROUP 1

Nocardia is a genus of bacteria that are found in soil and water. These bacteria are
known for their ability to form filaments, which can make them difficult to treat
with antibiotics. Nocardia infections can cause a range of symptoms, including
skin infections, pneumonia, and brain abscesses. Nocardia infections are most
commonly seen in people with weakened immune systems, such as those with
HIV/AIDS or cancer. Treatment of nocardiosis typically involves a combination of
antibiotics, as these bacteria are often resistant to single-drug therapy.

Spirillum:
Spirillum is a genus of bacteria that are characterized by their spiral shape. These
bacteria are typically found in freshwater environments, and some species are
known to cause infections in humans. One of the most notable Spirillum species is
S. minus, which is known to cause rat-bite fever. This bacteria is typically
transmitted to humans through bites or scratches from infected rodents. Symptoms
of rat-bite fever can include fever, rash, and joint pain.

Treponema:
Treponema is a genus of bacteria that are known for their ability to cause syphilis,
a sexually transmitted infection that can cause a range of symptoms, including skin
rashes, fever, and neurological symptoms.