The study of the relationships between microorganisms and their

• Among these relationships is the relationship of microbes with

humans, and such include the normal flora (or indigenous flora)
of the human
body.
• Normal flora consists of the group of organisms that inhabit the
body of a normal healthy individual in the community.

- indigenous flora may be non-pathogenic or pathogenic and may at

times behave as opportunistic pathogens
- beneficial to the human body because they can inhibit the growth of
pathogenic organisms by priming the immune system of newborns
- protects the body's organs and systems that are in direct contact
with invasive organisms

The external environment and are therefore subject to the attack of

Two types of flora:

1. Resident flora
-are organisms that are relatively of fixed types and are regularly
found in a given area of the body at a given age
2. Transient flora
-are those that inhabit the skin and mucous membrane temporarily
for hours, days, or weeks and are derived

Normal intestinal flora secrete vitamin K that is needed for the activity
of some clotting factors. Other beneficial effects of normal flora
include the following:

1. Normal flora can prevent pathogenic organisms from attaching to

and penetrating the skin and other tissues by producing mucin which
make it difficult for the pathogenic organisms to attach to the tissues
to produce disease.
2. Normal flora in the intestines aid in the digestion of food by
producing enzymes such as cellulase, galactosidase, and
glucosidase.
3. Intestinal flora also help in the metabolism of steroids.
intestines aid in the digestion of food by producing enzymes such as
cellulase, galactosidase, and glucosidase.
4.Intestinal flora also help in the metabolism of steroids.

FETUS
•The healthy fetus is normally sterile until birth
• the newborn normal flora is derived from the mother's genital tract
during delivery, from the skin and respiratory tract of individuals who
handled the newborn, and from the environment.

Body tissues and fluids that are normally sterile:

BODY FLUIDS
•Cerebrospinal fluid (CSF)
•Synovial fluid
•Blood - there may be low transient bacteremia brought about by
physiologic trauma

STERILE TISSUES
* urinary bladder
* uterus
* fallopian tubes middle ear
* paranasal sinuses

- Presence of bacteria in these tissues and body fluids may lead to

serious infections in these areas.
- For example, bacteria in the CSF can gain entry into the central
nervous system, leading to a potentially fatal encephalitis

- Normal Flora on Different Sites of the Body

- SKIN the part of the human body that is in constant contact
- with the environment, making it the most exposed to
microorganisms
- certain factors that eliminate non-resident flora from the skin,
namely
1. lysozyme in the skin
2. acidic pH of the skin due to sweat
3. free fatty acids in sebaceous secretions
4. the constant sloughing off of the skin

•The normal flora of the skin consists mainly of bacteria and fungi.
• The microorganisms vary depending on the region of the skin.
• The skin may be divided into three regions:
1. axilla, perineum, and toe webs
2. hand, face, and trunk'
3. upper arms and legs

• Skin of the axilla, perineum, and toe webs is characterized b) having

higher moisture levels higher body temperature higher levels of
surface lipids
•These regions have more microorganisms compared to the others
and are predominantly inhabited by gram-negative bacilli.

Skin
• Dry sites have diverse flora because of their exposure to the
environment
-Hands
-Forearms
-Feet legs
• Predominant flora in these areas include Staphylococcus
epidermidis and Staphylococcus hominis.

• Most microorganisms in the skin are found in its superficial layers

(stratum corneum) and hair follicles.
•Anaerobes inhabit the deeper structures and layers of the skin, such
as hair follicles, sebaceous glands, and sweat glands.
Table 5.1 summarizes the various microorganisms that inhabit the
skin.
Organism Remarks
Staphylococcus epidermis Major skin inhabitant, comprising
approximately 90% of resident
aerobic flora
Staphylococcus Most commonly found in nose
and perineum; in the nose,
number varies with age (greater
in newborns than in adults)
Micrococci (Micrococcus luteus) Accounts for 20%-80% of
micrococci. In the skin
Diphtheroids (Coryneforms) Classified into; lipophilic (common
in axilla) or non-lipophilic ( more
common on glabrous or hairless
skin such as palms of hands )

Anaerobic diptheroids
(propionibacterium acne) -areas
rich sebaceous glands
Gram-negaPve bacilli Seen in moist intertriginous areas
(Enterobacter, klebsiella, such as toe webs and axilla
escherichia coli, and proteus spp.
)
Nail flora Similar to that of the skin

Fungi may also be present (

aspergillus, penicillium,
cladosporium, Mucor)
Mouth and Respiratory Tract

• The tongue and buccal mucosa are inhabited mostly by

Streptococcus viridans group, which includes S. mutans, S. miller, S.
salivarius, and S sanguis.
-Although they are part of the normal flora of the mouth, the viridans
streptococci have been implicated in the pathogenesis of dental
caries.

-The gingival crevices and the tonsillar crypts are primarily inhabited
by anaerobic flora

•The normal flora of the pharynx and trachea are similar to those
found in the oral cavity.
-there may be transient carriage in the pharynx of potentially
pathogenic organisms.
- include; Haemophilus and Mycoplasma, influenza, Streptococcus
pneumoniae, Neisseria meningitidis

Upper respiratory tract

• initial colonization by pathogenic organisms may be seen

-include; Neisseria meningitidis, Corynebacterium diphtheriae, and
Bordetella pertussis.

Lower respiratory tract

•usually sterile and organisms that reach this region are usually
destroyed by the defense mechanisms of the body such as the
alveolar macrophages.

Conjunctiva

•The normal flora in the conjunctive are very scanty because they are
held in check by the flow of tears that contain lysozyme.
•lysozyme may interfere with the cell wall synthesis of organisms
•some bacteria may transiently colonize the conjunctiva including
Neisseria, Moraxella, and Corynebacterium, Staphylococci and
streptococci may also be present.

Digestive Tract
* The esophagus contains transient mouth flora.
* Minimal bacteria may be found in the
• stomach due to the relatively hostile environment in the stomach.
• Bacteria that may be found in the stomach are those that may be
swallowed with the food or those that are dislodged from the mouth.
* The acidity in the environment of the stomach is further increased
after meals because of the release of gastric acid.
• there are certain bacteria that are able to survive in the acidic
environment of the stomach-Helicobacter pylori, the most common
cause of duodenal ulcer
* This organism produces urease that causes alkalinization of gastric
acid thereby enabling it to colonize the stomach

Small Intestine

* scanty flora may be found due to the constant peristaltic movement

of the intestines.
* Most of the bacteria cultured in the small intestine include
streptococci, lactobacilli, and Bacteroides which are all transient.

Large Intestine

* The number of bacterial flora in the large intestine is far greater than
in the small intestine.
* The colon is inhabited predominantly by anaerobes (95%-99%)
whichincludes:
- Bacteroides fraglis (most common).
- Bifidobacterium/Lactobacillus bifidum (predominant in breast-fed
infants)
- Eubacterium, Peptostreptococcus
- Clostridium
* In bottle-fed infants, the predominant intestinal flora is
Lactobacillusacidophilus
* About 1% 4% of the flora of the colon are facultative
aerobes,predominantly Escherichia coli and other
Enterobacteriaceae.

• Intestinal flora play important roles in the body, namely:

1. synthesis of vitamin B complex and vitamin K
2. conversion of bile into bile acids
3. competition with transient flora for nutrients
4 prevention of colonization of the intestines by transient flora
5. production of potentially pathogenic end

Genitourinary Tract

* The urinary tract is sterile above the distal 1 cm of the urethra.

* In the anterior urethra, the predominant flora isolated are S.
epidermidis, enterococci, and diphtheroids.
* In both males and females, Mycobacterium smegmatis may be
found as normal commensals in their secretions.
* Gardnerella vaginalis, bacteroides, and alpha streptococci may be
found in penile urethra
* The female urethra is either sterile or contains, Staphylococcus
epidermidis.

Vaginal flora

* varies depending on the age, hormonal levels, and vaginal pH of the

host
* In female infants, the predominant vaginal flora is Lactobacillus spp
* From 1 month of age until puberty, there is cessation of glycogen
secretion making the vaginal pH higher (around 7.0)
-The microorganisms that may inhabit the vagina at this time include
Staphylococcus epidermidis, Streptococci, diphtheroids, and
Escherichia coli.
* At the onset of puberty, there is resumption of glycogen secretion
making the vaginal pH acidic.
-Predominant flora include Lactobacillus acidophilus, corynebacteria,
peptostreptococci, streptococci, Bacteroides, and staphylococci.
* Lactobacillus plays a crucial role in preventing gonococcal infection
by producing lactic acid that adds to the acidity of the vagina.

* varies depending on the age, hormonal levels, and vaginal pH of the

host
* In female infants, the predominant vaginal flora is Lactobacillus spp
* From 1 month of age until puberty, there is cessation of glycogen
secretion making the vaginal pH higher (around 7.0)
- The microorganisms that may inhabit the vagina at this time include
Staphylococcus epidermidis, Streptococci, diphtheroids, and
Escherichia coli.
* At the onset of puberty, there is resumption of glycogen secretion
making the vaginal pH acidic.
- Predominant flora include Lactobacillus acidophilus, corynebacteria,
peptostreptococci, streptococci, Bacteroides, and staphylococci.
* Lactobacillus plays a crucial role in preventing gonococcal infection
by producing lactic acid that adds to the acidity of the vagina.
* Young girls are more prone to the development of gonococcal
infection compared to adult women because the normal acidic pH of
the vagina as well as the normal vaginal flora are not yet fully
developed.

* After menopause, the vaginal pH increases once more due to the

lessened production of glycogen.
- Normal flora that predominate during this period are similar to those
found during pre-puberty.
- Most of these flora are derived from the skin and from the colon.
Fungi such as Torulopsis and Candida may also be found (10%-
30%).
- Conditions that will allow the overgrowth of these fungi (e.g., Intake
of antibiotics) can lead to vaginal infections such as vaginitis.

Bacterial flora in normal Bacterial flora in normal

person in the community persons in hospital or long-
term facilities
• Staphylococcus • Staphylococcus
• Streptoccus • Anaerobes
- Streptoccus pneumonia • Enterobacteriaceae
- Viridans streptococcus -escherichia coli
• Haemophilus -kiebsiella
• Anaerobes • Candida
• pseudomonas
• staphylococcus • staphylococcus
• coryneform bacteria or • Enterobacteriaceae
“diptheroids” - Escherichia coli
• priopionibacterium - kiebsiella
• anaerobes • Anaerobes
• enterococcus • Enterococcus
• Enterobacteriaceae • Enterobacteriaceae
- Escherichia coli - Escherichia
- Kiebsiella - Kiebsiella
• Streptococcus • Candida
- Streptococcus anginosus • Pseudomonas
(milleri) group
• Lactobacillus
• Candida

• Lactobacillus • candida
• Streptococcus
- Streptococcus algalactiae