Indigenous Microbial Flora (Normal Flora)

This lecture will discuss "the Indigenous Microbial Flora" of human,

which has other terms that are "Indigenous Micro- biota" and "Normal Flora".
"However; the doctor prefers to use the last one "Normal Flora (NF)
Slide No. 2 "References":

The first part of this lecture is taken from our text book (Burton’s
Microbiology for the Health Sciences, 9th Ed,chapter 10)

The other part is taken from (Jawetz, Melnick, & Adelberg's Medical
Microbiology,24th, Chapter 11)

Slide No.3 "introduction":

Ecology: is the systematic study of the relationships that exist between

organisms and their environment.
Microbial ecology: is the study of the relationships between microbes and
the world around them. It includes the relationship between microbes and
other microbes, microbes with humans, animals, soil and water.

It is mentioned earlier in the course that most of the microbes are non-
pathogenic for human or animal , only a small percentage are pathogenic, and
in fact most relationships between humans and microbes are beneficial to
human rather than being harmful.
So all microorganisms whether they are bacteria, fungi, yeast, etc..that
present both on and in our bodies are called indigenous micro flora (normal
flora).

Slide No.4, 5, & 6: "Symbiotic Relationships Involving Microorganisms":

The relationship between two dissimilar organisms basically is an

expression of the word Symbiosis.
Symbiosis: is that two organisms associated with each other, and each of
the two organisms is called symbionts.

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 Symbiosis can exist in 4 forms :
1. Neutralism:
Two organisms live in a compact relationship in which neither of them is
interacting with the other one or affecting its goal, so basically the two
organisms are present in the same place and neither symbionts is affected by
the relationship.

2. Commensalism :
Two organisms live in the same place; one organism is taking benefits of
the other one, while the last is not affected by this relationship.

For example: Many microorganisms that live in your GIT or in your skin are
considered to be commensals ,because the human body provide the
nutrients ,proper temperature and moisture to them; however, they will not
cause any infection to it.

Many human normal flora are considered commensals

3. Mutualism :
Two organisms live together in the same place and both of them take
advantages of the other one.
For example : lichens which referred to algae and fungi live in the same place
,so algae perform photosynthesis and provide energy and nutrition for the
fungi ,while fungi provide a protective environment for the algae .

Also the intestinal bacterium "Escherichia coli" lives in mutualistic

relationship with human, where the intestinal tract provide the nutrients and a
shelter for E.coli which in turn provides the human body with vitamin K.

4. Parasitism:
In this relationship one organism lives in the extent of another organism,
causing a harmful effect for it.

So this relationship is beneficial to one sympiont which is called the

parasite and harmful to the other sympiont which is called the host.

***Many of the protozoal infections are considered parasitic infection.

However it is not necessary that the parasite that infects the host will cause
a clinical disease, sometimes when the parasite numbers are low there will be

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a little harm and no clinical manifestations will appear ,so the disease is
ataxonomic .

**** Important point about all the types of Symbiotic relationships is that:
Any disturbance in the conditions due to the application of alcohol or taking
anti-microbial agents might shift the relationship from Commensalism to
Parasitism relationship, for example, and so on.

So a key point is that any changes in conditions can cause one type of
symbiotic relationship to shift to another type ,that’s why sometime the
component of normal flora which are usually commensals turns to
pathogenic.

A Summary

The 1st symbiont The 2nd symbiont

Neutralism No effect No effect
Commensalism Beneficial Harmless
Mutualism Beneficial Beneficial
Parasitism Beneficial Harmful

Slide No.7" Indigenous Microflora (Normal Flora) of Humans":

Normal flora basically is composed of many species of bacteria, fungi,

Protozoa and viruses that reside on the skin , the upper respiratory tract and
gastro intestinal tract GIT.
There are approximately 500-1000 different species of microbes living on or
within the human body in many tissues and locations.
However, some places of the body are free of pathogens which are:
1- Blood
2- Lymph
3- spinal fluid
4- Most internal tissues and organs are normally free of microorganisms.

But in other parts of the body there is a high risk of infection.

Slide No.8:

The picture shows the areas of the body where most of the indigenous
Micro flora reside.

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1-skin: the biggest organ in the human body that has high level of bacteria
2- Gastro intestinal tract (GIT)
3- Upper respiratory tract
4- Urogenital tract
5- Eyes and the external ears
****The lower respiratory tract is usually sterile so the bronchi, the small
bronchioles and the alveoli are usually sterile.
Slide No.9"Constituents of Normal Flora:"

There are two types of population present in normal flora:

1- Resident ( fixed) flora:
A type of microorganism that is present in fixed numbers, but it might
change according to age.
However, if the population is disturbed it will quickly reestablishes itself.
E.g. the normal flora in the skin; if you wash your hand you will remove most
of the bacteria that present there ,that actually come from the sweat glands
and sebaceous gland, then it will re-colonize on the skin.
2 - Transient flora:
A type of microorganism that's obtained from the environment .These
organisms stay in their position for hours, days, or weeks, but can't establish
themselves for longer period of time ,and usually do not produce diseases.
However, they can produce diseases if the resident flora is disturbed.
Slide No.10, 11" Normal Flora":

As mentioned before ,most of the NF are considered commensals (not

essential for human life), but also other NF are beneficial for the human e.g.
E.Coli that can synthesis vitamin K.
And a very important aspect for bacterial NF is Bacterial Interference
which prevents the colonization of skin and mucus membranes by pathogenic
bacteria.

Mechanisms for Bacterial Interference:

 NF Will utilize all available nutrients at the site of colonization.
 It will utilize or bind to all pathogenic binding sites at that location.

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  Also it will produce metabolic or toxic products.
 And it may produce some antibiotics.
**By doing all that it can prevent the binding and the colonization of
pathogenic bacteria.
So the bacterial interference is a very important mechanism to prevent the
human infection.
** Removal or disturbance of NF might lead to problems due to rapid
colonization by other organisms which are called (opportunists pathogens) so
might end up with a disease.
Slide No.12:

If the NF components are introduced into a new site such as blood or deep
tissue it may cause an infection.
For example; Viridans streptococci (that presents in the mouth); if you
extract your tooth it can enter the blood circulation, might attach and colonize
at the heart valve leading to what is called infective endocarditis
Alternatively if the bacteria get into the deep tissue or normal sterile site they
can lead to infection
For example; Bacteroides vragilis (that is found in the large intestine of the
human body) might enter the peritoneal cavity if there is a trauma or an
accident or someone bunches you in the stomach, and some of this bacteria
will enter the peritoneal cavity then it will multiply there very quickly and
cause purulent infection and bacteremia.

Slide No.13 "Normal Flora Examples:"

Only Memorize the UNDERLINED EXAMPLES In the Slide, there are

many other examples but the Doctor doesn’t want us to memorize them 

1. Skin Normal Flora :

2. Staphylococcus epidermidis
3. Staphylococcus aureus
4. Alpha-hemolytic and nonhemolytic Streptococci

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Slide No.14, 15 "Skin NF:"

The skin is not an easy place to colonize by bacteria, because there are
many factors that inhibit bacterial colonization which are:
1. Low pH
2. Fatty acids from sebaceous secretions (some of the fatty acids have anti-
microbial activity)
3. Lysozymes that degrade the cell wall of bacteria.
***So not any microorganism that introduce into the skin can colonize there.
 A key point in skin normal flora is that it differs by different locations
due to:
1- Different anatomical location might have slightly different numbers of
the normal flora according to different moisture secretion that can change the
components of the normal flora.
2- Places of wearing of clothes can change skin components
3- Proximity to mucous membranes (mouth, nose, perineal areas have
components of the normal flora that are derived by the mucous membrane)

As mentioned before washing your hands thoroughly or sweating

extensively can't easily eliminate or significantly modify the components of
the skin NF.
If the skin NF is removed it will be quickly restored due to secretions
from sweat and sebaceous glands.

Slide No.16" Normal Flora:"

Nasopharynx (The area behind the nose and throat):

There are some bacteria that extend from the skin :
 α-hemolytic streptococci
 nonhemolytic streptococci
 Staphylococcus epidermidis
 Diphtheroids
 nonpathogenic Neisseria species.
Slide No.17:

The nose normal flora :

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 Corynebacteria.
 Staphylococci (S. epidermidis, S. aureus)
 Streptococci.

NF of Mouth and upper RT:

Might be involved under certain conditions in many infections:
 Periodontal infections
 Perioral abscesses
 Sinusitis
The upper bronchi usually have very few bacteria where Small bronchi and
alveoli are normally sterile.
Slide No.18"Role of NF in Dental Caries:"

As we are the future dentists , it is important for us to know how the dental
caries are formed.

The tooth consists of enamel layer, dentin, pulp, and cement layer.
The dental caries evolve 2 things:
1. Demineralization of enamel.

2. Digestion of the protein matrix of dentin and cement layers.

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Slide No.19, 20 " Role of NF in Dental Caries:"

The first step in developing dental caries is the Formation of a plaque on

the enamel:
""Plaque is a mixture of bacteria and high molecular weight glucan""
So Streptococcus mutans is a component of the normal flora of the human
mouth, this bacteria will first attach to the tooth enamel and it will start taking
carbohydrates and sugars and convert them to high molecular glucan" bacteria
and the glucan will form plaque on the enamel" ,then the bacteria will
ferment the sugar and carbohydrates to produce a lot of acids so the PH of
enamel will become less than 5, and this low PH will basically lead to
demineralization or destruction of the enamel layer.
Once the enamel is completely destroyed, the bacteria have to deal with the
dentin and the cement layers by proteolytic organisms, including
actinomycetes and bacilli.
Slide No.21" Control of Caries:"

 How can you protect your teeth from caries??

1- Frequent cleaning otherwise plaque will develop on the enamel layer.
2- Physical removal of plaque by professional healing .
3- The application of fluoride either by that in the toothpaste or by
drinking water .Fluoride will increase the resistance of the enamel layer
toward bacteria.
4- Limitation of sucrose and carbohydrates intake.
5- Good nutrition with adequate protein intake to make dentin healthier
and stronger.
Slide No. 22:

1Normal Flora of the Esophagus:

The esophagus usually contains bacteria that are derived from saliva and
food, although it is not a good place for infections.
Once the food enters the stomach most of the bacteria will be destroyed
due to very low PH and high acidity.
If you want to count the number of bacteria in the stomach you will find
only 1000 to 100000 gram of bacteria per food content.

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***Once the food get to the stomach not many organisms can withstand its
high acidity (pH=2).
Slide No. 23" Normal Flora of the Intestines:"

Once the food exit from the stomach it will mix with the bile in the small
intestine that will drive the PH to increase slightly, so now bacteria can grow
and multiply much more quickly.
In the Duodenum (the first part of the small intestine) you can find 103-106
bacteria per gram of contents.
As the food gets down in the small or the large intestine the number of
bacteria will increase very quickly.

So in Jejunum and ileum there are 105-108 bacteria per gram of content.
In the cecum and transverse colon 108-1010 bacteria per gram of content.

And finally Sigmoid colon and rectum contains almost 1011 bacteria per
gram of content.

It is estimated that10-30% and according to some text books about 50% of

the fecal mass is actually made up by bacteria .
That’s mean that there is a huge amount of bacteria in the stole.
Slide No. 24, 25:

GIT has various numbers of normal flora; the most important is a group
of bacteria that is called Enterobacteriaceae.
Some members of Enterobacteriaceae are not present in the normal flora and
are only present if you have an infection with these bacteria; so Salmonella,
Shigella, Yersinia are members of Enterobacteriaceae but they aren’t
members of the normal flora that present in the healthy gastro intestinal tract,
but they present in case of infection.
So these Enterobacteriaceae are facultative anaerobic: they can use the
oxygen if present and can live without oxygen ,also there are anaerobic
bacteria in the small and large intestine and these are in extremely high
numbers.
There are 1000 time more anaerobic bacteria than the facultative
anaerobic bacteria. The most important example about anaerobic bacteria that
the Dr wants us to memorize is Bacteroides fragilis.
Another example is Clostridum perfringens, which is the main cause of
gas gangrene in human, so if these bacteria introduce to a deep tissue it can
cause gangrene.

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Slide No. 26" Normal Flora of the Intestines:"

If you take Oral antimicrobial agents randomly without proper guidance

and for a very long time there is a chance that you might disturb the NF
components in your GIT.
So if you take Neomycin & Erythromycin you can suppress aerobic
bacteria, and if you take Metronidazole you can suppresses anaerobic
bacteria.

Normal Flora of the Urethra:

Urethra basically has NF derived from the skin and the perineum.
So if you do a cultural for normal urine you will probably find some bacteria
there which is very normal you will find a 100 – 10000 gram of bacteria per
ml of urine and this is considered normal, only if the bacterial count is more
than 100000/ml the urine it will considered to be infected or the urethra to be
infected.
Slide No. 27 "Normal Flora of the Vagina:"

Vaginal NF is varying according to age:

Before puberty and after menopause it is composed of multiple types of
bacteria, but at the time of puberty it will have mainly Lactobacilli and
other bacteria. The most important example is group B streptococci like
streptococcal agalaci which is present in 25% of women.
So Lactobacilli are very important because they ferment
carbohydrates(mainly glycogen) which are basically in the form of nitrogen
that is secreted from the vaginal mucosa, and they will produce acids and
decrease the PH. So Low vaginal pH will prevent the colonization by other
harmful bacteria.
*** Lactobacilli basically protect females from vaginal infections.
Slide No. 28:

Group B streptococci are very important because they are the cause of
neonatal infection.
If a women carry this bacterium gives birth to a baby, the bacteria will
spread to the baby and will cause a very severe infection that will lead to
neonatal sepsis and meningitis which is highly mutant.

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  Normal Flora of the Conjunctiva(‫)ملتحمة العين‬:

The eye has few bacteria in it, usually it has Diphtheroids,

Staphylococcus epidermidis and so on .However; it has lysozyme that can kill
bacteria which colonize there, and also it has tears that will wash away many
of the bacteria.

The End
Done By: Enas Salameh

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