NORMAL FLORA
Normal flora refers to a diverse population of microorganisms that live on or within the
human body without causing disease or harm under normal physiological conditions. These
microorganisms are found on body surfaces such as the skin and in body sites including the
mouth, gastrointestinal tract, respiratory tract, and urogenital tract.
Normal flora exists in a symbiotic relationship with the host and perform several important
functions. They help protect the body by preventing the colonization of harmful
microorganisms, contribute to metabolic activities such as vitamin production, and play a
significant role in the development and regulation of the immune system.
Although normal flora is generally harmless, they may become opportunistic pathogens and
cause infection if they enter normally sterile areas of the body or when the host’s immune
defences are weakened. In addition, several internal factors, such as age, and external
factors, including geographical location, dietary habits, stress, infections, and the use of
antibiotics, can affect the composition and function of the normal microflora (McFarland,
2000).
THE NORMAL FLORA OF THE SKIN
The skin is a very large organ. It has a slightly acidic and dry environment which is suitable
for some microorganisms. Normal flora of the skin is mostly located on the skin surface, hair
follicles and sweat glands (Jawetz et al,2022). The skin’s normal flora can be located in areas
like the armpit, scalp, chest, back, skin foldings and many others.
Common organisms that form the normal flora of the skin include staphylococcus
epidermidis, staphylococcus aureus, catibacterium acnes and micrococcus species (Murray
et al., 2020). These organisms usually exist in a balance and are non-pathogenic under
normal conditions.
Staphylococcus epidermidis is mostly on the skin surface at moist areas, staphylococcus
aureus is mostly found at hair bearing regions and around wounds and skin folds,
corynobacterium species are mostly found at moist areas and sweat gland-rich regions,
cutibacterium (proioni-bacterium) acnes is found mainly in hair follicles and sebaceous
glands whilst micrococcus species is found at dry areas of the skin and exposed skin areas.
Normal flora of the skin can be aerobic or anaerobic. The anaerobic ones are found in the
deep skin layers whilst the aerobic ones are mostly found in the skin surfaces.
The skin flora prevents the colonization of pathogenic organisms by competing for nutrients
and space. Some also produce antimicrobial substances and help to maintain the pH of the
skin (Tortora et al., 2021). However, under certain conditions such as broken skin, reduced
immunity or invasive medical procedures, some skin flora may become opportunistic
pathogens, particularly staphylococcus aureus.
NEWBORN
A new born baby is sterile while the uterus. Microorganisms colonize the baby at birth and
after birth (continues at the first few days of life) (Jawetz et al.,2022). The sources of
newborn normal flora include the mother’s birth canal, skin, breast milk, care givers and the
environment.
Through physical contact, organisms such as staphylococcus epidermidis, staphylococcus
aureus, and corynebacterium species colonize the baby’s skin.
In the gastrointestinal tract, beneficial bacteria such as bifidobacterium and lactobacillus
become dominant and play an important role in digestion, vitamin K production, and
immune development, especially at the breast-level feeding stage (Tortora et al.,2021).
Also, the oral cavity of the newborn is commonly colonized by streptococcus salivanus and
streptococcus mitis after feeding begins (Jawetz et al.,2022).
NORMAL FLORA OF THE EYES AND EARS
THE NORMAL FLORA OF THE EYE
The normal flora of the eyes plays an important role in maintaining ocular homeostasis by
various mechanisms. They compromise of mainly bacteria which do not cause infection in
normal conditions but can be a main source of infection after ocular surgery, trauma or
immune compromised. The ranges of these microorganisms vary with age, sex and
geographical distribution. Therefore, it is very important for the ophthalmologist to know
the ocular normal flora before giving prophylactic antibiotics and treating infections. This is
to describe the conjunctiva flora of the normal human eye which vary with age,sex ,
geographical distribution, right and left eye.
The diversity of normal ocular flora in different individuals in relation to sex, age and
geography makes it important to have a thorough knowledge about them in order to
prescribe appropriate antibiotics in ocular infections and trauma.
EXAMPLES OF NORMAL FLORA OF THE EYES AND HUMAN ACTIVITIES THAT COMPROMISE
THEM
• STAPHYLOCCUS AUREUS
Close contact in crowded or communal environments like gyms
• ACINETOBACTER
Antibiotics overuse and poor equipment cleaning further enable multi drug-resistant
strains.
• ASPERGILLUS
Cleaning dusty areas without protection.
• CANDIDA SPECIES
Poor sleep, chronic stress, etc.
NORMAL FLORA OF THE EARS
Cerumen or ear wax present in outer ear traps number of microorganisms and
prevent them from entering into the inner ear.
Cerumen also contains antimicrobial compounds which discourage growth of
pathogenic pseudomonas acruginosa and staphylococcus aureus, otherwise outer ear
being moist and warm would have been an ideal place for microbial growth. Despite
cerumen, external ear contains staphylococcus epidermidis, alpha haemolytic
streptococci as normal flora. Internal ear, under normal healthy state of individual is
free from any microorganisms, reason is that it is closed by membranes and filled with
lymph fluid. Middle ear normal flora matches microbes of nasopharynx as nasal
microorganisms can enter middle ear via canal. Ottis media, an infection of middle ear
is caused by haemophilus influenza received from nasopharynx region.
EXAMPLES OF NORMAL FLORA OF THE EARS AND HUMAN ACTIVITIES THAT
COMPROMISE THEM
• MICROCOCCUS LUTEUS
Poor hand-washing practices by health workers or patients transmitting akin bacteria
during contact.
• ACNES
Smoking and chronic stress elevating oil production and skin sensitivity
• STAPHYLOCOCCUS EPIDERMIDIS
Inserting prosthetics without proper sanitation
• PSEUDOMONAS SPECIES
Failing to maintain water systems like sinks, taps or hot tubs promote bacterial growth
and transmission.
NORMAL FLORA OF THE URT AND THE NAILS
NORMAL FLORA OF THE URT
The upper respiratory tract includes the nasal cavity, nose, oropharynx, nasopharynx
and throat. These are areas that are constantly exposed to air and microorganisms
from the environment. The URT is warm and moist and therefore supports the growth
of normal flora.
The URT is mainly colonized by bacteria. Common normal flora include staphylococcus
aureus in the anterior nares and staphylococcus epidermis.
Streptococcus viridans is normally found in the oropharynx. Corynebacterium
species, also called diphtheroids are frequent inhabitants of the nose and throat.
Non-pathogenic species of Neisseria and Haemophilus are also present.
Anaerobic bacteria such as: Bacteroides, Fusobacterium and Peptostreptococcus are
mainly found in the oropharynx.
IMPORTANCE OF THE NORMAL FLORA OF THE URT
❖ The normal flora of the URT help prevent the growth of harmful pathogens
❖ They compete for nutrients and attachment sites on the mucosal surfaces
❖ Some members of the normal flora may cause disease if host immunity is reduced or
if they enter sterile sites.
NORMAL FLORA OF THE NAILS
Nails, especially the subungual region (which is under the nails) are;
❖ Warm
❖ Moist
❖ Rich in organic debris
These conditions are favourable for microbial growth. Nail flora closely resemble skin
flora.
The normal flora of the nails mainly consist of bacteria that are similar to those found
on the skin.
Staphylococcus epidermidis is the most common organism present under and around
the nails. Other bacteria such as staphylococcus aureus, micrococcus species and
corynebacterium species are also commonly found. Occasionally gram-negative
bacteria like Pseudomonas and Klebsiella may be present when nails are kept too
long or especially hygiene is poor.
Fungi are also part of the normal nail flora. Candida species are commonly found
particularly in individuals who frequently wet their hands. Environmental fungi may
also be present occasionally under the nails.
IMPORTANCE OF NAIL NORMAL FLORA
❖ They act as reservoirs for microorganisms
❖ They are easily transmitted organisms and can be transmitted through; touch, food
handling and medical procedures.
❖ It is a major source of cross-infection in healthcare settings.
❖ It is also the reason for strict handwashing and nail hygiene can cause infections such
as paronychia and onychomycosis.
The upper respiratory tract and nails harbour diverse normal flora that play a
protective role in human health. While those microorganisms are usually harmless,
they can cause infections in host defences when compromised or if they gain access
to sterile body sites.
THE NORMAL FLORA OF THE ORAL CAVITY
Normal flora found in the mouth are extremely variable. The mouth is highly
selective for microorganisms. The diversity in the oral cavity is due to the various
anatomical structures (teeth, tongue, cheek walls, gum, etc) that supports their
different ecological environment. The oral cavity houses the following microbes
1. BACTERIA
They are the dominant microbes in the mouth. They include;
❖ Streptococcus
❖ Lactobacillus
❖ Prevotella
❖ Neisseria: found on the tongue and saliva
❖ Veillonella: found in the gingival crevice
❖ Actinomyces: found on the teeth and in the gingival crevice
2. FUNGI: eg. Candida albicons
3. VIRUS: eg. Herpes simplex virus
ESTABLISHMENT OF ORAL FLORA
The establishment of the oral flora begins at birth during delivery, the new born is exposed
to vaginal flora or caesarian flora depending on the mode of delivery. The first
microorganism to colonize the mouth are bacteria termed as pioneer species. They include;
Staphylococcus, Lactobacillus and streptococcus which are the dominant species. They are
transmitted through birth, feeding and other environmental conditions. This initial
colonization is crucial because it sets the stage for the development of other microbes. As
the infant or newborn starts to grow other microbes begin to develop.
The table below illustrates the establishment of the infant and the flora
AGE BACTERIA LOCATION/HARD SURFACE
Newborn (0-1) Streptococcus salivanus, Tongue, buccal mucosa
Streptococcus mits,
Neisseria
1-7 days Streptococcus, Actinomyces Tongue, buccal mucosa,
palate
1-4 weeks Veillonella, Lactobacillus Tongue, buccal cavity,
gingival crevice
Streptococcus mutons, Teeth sufarces (enamel),
Streptococcus sanguins gingival crevice
1-3 years Actinomyces, Teeth surfaces, gingival
Porphyromonas crevice, tongue
3-6 years Fusobacterium, Prevotella Gingival crevice, subgingival
plaque
Adolescence Porphyromonas gingivalis Gingival crevice, subgingival
plaque
IMPORTANCE OF ORAL FLORA
❖ Digestion: Breakdown of complex food.
❖ Immunity: Fighting of pathogens.
❖ Protection: occupying space to prevent the growth of pathogens
FACTORS AFFECTING NORMAL FLORA
1. Diet: A high diet in sugars and acid can cause imbalance of oral flora.
2. Oral hygiene: Poor hygiene can lead to an overgrowth of pathogenic
microorganisms.
3. Hormonal change: Hormonal fluctuations such as oestrogen increase during
pregnancy or menopause can alter the oral flora.
4. The use of antibiotics and medications .
CONSEQUENCES OF IMBALANCE
1. Dental carries: An overgrowth of acid producing bacteria can lead to tooth
decay. eg. Streptococcus mutans
2. Periodontal disease: An imbalance of oral flora can contribute to gum disease
and potential tooth [Link]. Porphyromonas, Gingivalis, Achinomyces, etc.
3. Oral candidiasis: An overgrow of candida can cause oral [Link]. Candida
albicans
4. Halitosis: Bad breath
NORMAL FLORA OF THE GASTROINTESTINAL TRACT
Understanding the environment of the gastrointestinal tract can help predict the classes of
bacteria that inhabit it.
The gastrointestinal tract is acidic in the stomach which implies indicates that
acidophiles/acidotolerant bacteria will be present.
The normal intestinal flora which is anaerobic bacteria is divided into 6 phyla:
• Firmicutes (Lactobacillus, Enterococcus, Clostridium)
• Bacteroidetes
• Proteobacteria (Enterobacteria)
• Actinobacteria (Bifidobacterium)
• Fusobacteria
• Verrucomicrobia
The first four phyla account for 98% of the total intestinal flora with percentages 64%, 23%,
3% and 8% respectively.
The developing gut biome starts from natal contact of the child to its mother. Some bacteria
such as Rummococcus albus and Rummococcus flavefaciens breaksown the cellulolytic plant
material of animal food as they mutualistic in the gut.
These gut microbiota are our first internal line of defence against pathogens and toxins
protecting the body against disease in tandem with the host immune system. These gut
bacteria are compromised when their natural balance is disrupted, a state known as
dysbiosis which involves a decrease in beneficial bacteria and an increase in harmful
pathogens. Some human activities that cause dysbiosis are
• Antibiotic overuse, when the intake of antibiotics increase they kill some useful
bacteria as they do not the difference between beneficial gut bacteria and harmful
pathogens. This results in the reduction of overall microbial diversity.
• Chronic stress, psychological and physical stress can compromise the integrity of
useful gut flora (like Lactobacillus) and promote the growth of harmful pathogens like
Clostridium.
• Lack of sleep
NORMAL FLORA OF SMALL INTESTINE
The small intestine compromises of three main parts; duodenum (first part), jejunum
(middle part) and ileum (the last) which connects to the large intestine. The number of
bacteria in the small intestine increases from duodenum to ileum.
In the duodenum, Lactobacillus species and streptococcus are mainly found there and are
mostly non-resident flora or temporary organisms from the stomach and oral cavity.
Jejunum has slightly higher bacterial count than the duodenum. Lactobacillus species and
streptococcus species found in the duodenum. These organisms are mostly aerobic and
facultative anaerobes. Ileum has the highest bacterial population in the small intestine.
Organisms there resemble those of the colon but in lower numbers. Escherichia coli,
Bacteroides species, Clostridium species and Enterococcus species are the flora found in the
ileum. More anaerobes are found here.
NB:
Aerobes: Streptococcus species, Lactobacillus species
Anaerobes: Bacteroides species, Clostridium species
Facultative aerobes: Escherichia coli, Enterococcus species
GUT MICROBIAL DEFECTS
1. CLOSTRIDIUM DEFICILE INFECTION
Clostridium deficile is a spore forming, gram positive anaerobe, producing toxins A and
B; the latter is responsible for colonic inflammation and the development of
pseudomembranous colitis.
2. INFLAMMATORY BOWEL
Dysbiosis is present in patients with inflammatory bowel disease (IBD) characterized by a
higher ratio of pathogenic to commensal bacteria, reduced bacterial counts in areas of
active inflammation and areas of bacterial mucosal invasion which is rarely ever seen in
healthy individuals.
EXAMPLES OF NORMAL FLORA IN THE GUT/STOMACH
1. Bacteroides fragilis
2. Bifidobacterium
3. Escherichia coli- bacteria produce essential vitamins: Vitamins K and B complex
4. Lactobacillus- produce lactic acid which breakdown food, eases digestive discomfort
and can accelerate the transit of intestinal contents to help with conditions like
constipation
IN SMALL INTESTINES
1. Candida albicans(yeast) – releases a cytolytic peptide toxin called candidalysin which
damages mucosal surfaces and triggers immune responses.
2. Streptococcus
3. Escherichia coli, in some cases
IN LARGE INTESTINES
1. Bifidobacterium
2. Enterococcus faeculis
3. Lactobacillus
4. Clostridium