Introduction on the human body are referred to


The collection of gene and their products from all the microbes
living within and on the human body are referred to as the human microbiome. These
microbes can be commensals or opportunistic ones. They can be bacteria, fungi,
protozoans, viruses or some other microscopic organisms.

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The major contributor of human microbiome is the bacterial phylum
that primarily includes Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria

Based upon the anatomical area of human body the microbiome
differs in composition as:-


Skin is the second most common habitat for microbes on human
body. Bacteria are by far the most common skin microbes, although fungi and viruses
are also a part of skin microflora.

Skin being our interface with environment acts as both a
barrier as well as a habitat to these microbes, thus contains the most flexible
microbial composition. As our skin shows variations in physiochemical
properties with various anatomical sites, it can be concluded that skin is a
hub of habitats harboring a vast diversity of microbes. Thus the composition of
our skin microbiota differs considerably with various physiological areas on
the skin like moist areas including underarms and dry area including forearms

Usually, the skin microbiota is similar among different
individuals, although it is never exactly the same. Environment and age, sex,
site, immune system and certain physicochemical factors such as humidity, pH and temperature are
examples of factors that lead to variation. 2

In a study of skin microbiota from different sites on the
body about 19 different phyla dominated by Firmicutes, Actinobacteria,
Bacteroidetes and Proteobacteria were observed 22. As we talk about species diversity
anatomically our skin consists of three type microenvironments that are sebaceous,
moist and dry.

Propionibacterium and Staphylococci species are the main bacterial
species observed in oily or sebaceous sites of the head, neck, and trunk areas
while Corynebacterium
and Staphylococci are major species in moist places of the
skin such as underarm area, the crease of the elbow or between the toes. Phylum
Firmicutes comprise the major
bacterial phyla in the vagina. 22

In dry areas of the skin like the surfaces of the forearms
and legs, a mixture of species is observed dominated by Staphylococcus species,
in particularly, S. epidermidis and
S.hominis 3.

As we talk about fungal flora of
skin Malassezia is abundant
in sebaceous areas 4. The heel, toenail, and toe web are found to have much more fungal
diversity than other skin areas. Skin microbiota also includes some fungi like Candida species and Penicillium species. 5

Other than above mentioned
facts skin microbiota is also affected by various skin related disorders and physical
interactions like antibiotics exposure, sanitation, hygienic practices etc. Moreover
skin microbiota is the primary one to be in direct contact with external
atmosphere thus faces the major impacts of environment also.


Gut is the largest habitat for commensals
inside the human body. It can be divided into upper (stomach and duodenum) and
lower gastro intestinal tracts (jejunum, ileum, caecum, colon, and rectum). The
majorly colonizing phyla’s are Firmicutes, Bacteroidetes, and Proteobacteria 6,
7. Gut microbiota is established after the birth depending upon various
factors and there are compositional changes related to diet, age and diseased
conditions 8. Gut microbiota also varies in composition according to various
anatomical areas of GI tract. Like in stomach major microbial colonies are of
Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria 9. Major genera observed in human stomach are Helicobacter,
Streptococcus, and Prevotella 10. Similarly in small intestine majorly there
are facultative and obligate anaerobes (Streptococcus sp., enterobacteria,
Clostridium sp., Bacteroidetes).

Oral cavity:-

Our oral cavity also acts as a
habitat for microbes, thus a distinct type of oral flora occurs there. Firmicutes has the major population in
the oral cavity along with proteobacteria, bacteroidetes, actinobacteria,
fusobacteria and spirochaetes 11.

Other Body surfaces:-

are also some other body surfaces other than the above mentioned, that act as a
habitat for the microbes. They include vagina, lungs, uterus etc. Like in lungs
some Prevotella, Sphingomonas, Pseudomonas species are observed 12.That much
availability of habitats on a human body facilitates the microbial species to
grow up in count as well as diversity. Thus there is generated a complex
ecosystem containing a blend of genomes and their expressions.


establishment and early colonization

Before birth, we have no
microbes on or inside our body. With increasing time after birth different
species of microbes start to colonize in every possible habitat on our body. With
age we acquire large sized different populations of various microbes in the habitats
around our bodies. With our age, our microbiota continues to change in
composition and diversity.

With time our microbiome
increase in count and adapt according to the changes in environment of their
habitat. For example, the foods we eat, the
amount of microbes we’re exposed to on a daily basis and the level of stress we
live with, all these factors alters the state and structure of our microbiome.

Microbial introduction and
persistence is a random process influenced by many factors that leads to
formation a much complex microbiome.

Major factors influencing
the establishment and development of human microbiome are as follows:-

Ø  Mode Of Delivery

Ø  Host’s Age

Ø  Host 

o   Dietary factors

o   Sanitation and others

o   Day routine activities and interactions

o   Visited places (Hospitals etc.).

Ø  Host’s Genetic make up

Ø  Environmental Factors

Ø  Geography

Ø  Demography

Ø  Health Fluctuations

o   Medical conditions( Diseased, Pregnancy)

o   Antibacterial courses

o   Medicinal courses with various drugs

o   Septic conditions (injuries)

o   Operations.

of Birth (delivery)                                                                                      

Species diversity is found to
be low in infants but it is observed to be increased with time and exposure to
environment. It is obvious that this exposure differs by mode of delivery and
place of birth. Massive bacterial colonization occurs at birth upon exposure of
the newborn to vaginal, fecal, and skin microbiota. Delivery
mode can affect this early-life establishment of microbiota and its composition

Babies delivered vaginally are covered by a film of microbial
colonies as they pass through the birth canal. Thus their primary microbiota
contains microbial species from the vaginal and intestinal flora of the mother.
They are colonized primarily by Lactobacillus sp., Prevotella and Sneathia spp.
14. During vaginal delivery, facultative anaerobic species such as E.coli,
Staphylococcus, and Streptococcus also colonize the infant gut 15

caesarian delivery, the direct contact with maternal vaginal and intestinal
flora is absent, and non-maternally derived environmental microbes play an
important role in primary colonization. Thus babies delivered by cesarean
section are colonized mainly by skin microbes (e.g., Staphylococcus,
Corynebacterium, Propionibacterium spp.) composing of a very different set of
species than the babies born vaginally. Caesarean
section introduces opportunistic microbial species, including Enterobacter
cancerogenus/E. hormaechei, Haemophilus
spp. and Staphylococcus 16.



Age is a major factors effecting microbial composition of our
microbiome. From birth, as the age increases the microbial diversity also
increases and converges toward an adult like microbiota by 3 to 5 years of
birth, with a quite differing set of microbial colonies in comparison to those found
in an infant’s microbiota. Various factors like mode of delivery, diet,
genetics etc. play a role in primary establishment of the microbiota, once
established the adult microbiota is comparatively stable in composition
throughout the life.

After birth, gut microbiota closely resembles that of the
mother within the first year of life 17.Primary colonizers of infant gut are
the facultative anaerobes that create an environment that promotes the growth of
strict anaerobes like Clostridium, and Bifidobacterium spp. The gut microbiota
of infants is of low diversity and majority of the phyla Proteobacteria and
Actinobacteria are observed. The microbiota increases in diversity with the
introduction of Firmicutes and Bacteroidetes as the time after birth increases 18,

characteristics of the skin like thickness, capability to hold moisture and to
produce sebum, oiliness, hair cover, etc. changes considerably with aging, which
naturally affects the microenvironments on skin habitats supporting different


teenagers, puberty associated changes in the skin physiology, are the reasons
behind changes in the skin microbial community composition and diversity.


there is an increase in diversity of skin microbiota during the first eight
years of life along with a reduction in abundance of the Order Lactobacillales
(mainly Streptococcus) and relatively increase in other taxa also takes place. In
puberty there is reduction in diversity due to increase in population of Actinobacteria
species (such as Propionibacterium acnes) 20. Lipophilic bacteria like
Propionibacterium tend to increase in abundance between the ages of 25-30 years
due high production of sebum by the skin 21.