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.
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 being our interface with environment acts as both a
barrier as well as a habitat to microbes, thus contains the most flexible
microbiota composition. As our skin shows physiochemical variations with various
anatomical sites thus it can be concluded as a hub of habitats harboring a vast
diversity of microbes.Also the composition of our skin microbiota differs considerably
with various physiological areas of the skin like moist areas including
underarms and dry area including forearms skin. Propionibacteria and Staphylococci species are the main bacterial species
found in sebaceous
area while Corynebacteria and Staphylococci are major species in moist places of the
skin. In dry areas of the skin a mixture of species is observed dominated by b-Proteobacteria
and Flavobacteriales 2. Such as the phylum
Firmicutes comprise the major phylum in the vagina while Malassezia is abundant in atopic
dermatitis 3. Skin
microbiota also includes some fungi like Candida species and Penicillium species. 4
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 5, 6. Gut microbiota is established after the birth
depending upon various factors and there are compositional changes related to
diet, age and diseased conditions 7. 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 8. Major genera
observed in human stomach are Helicobacter, Streptococcus, and Prevotella 9.
Similarly in small intestine majorly there are facultative and obligate
anaerobes (Streptococcus sp., enterobacteria, Clostridium sp., Bacteroidetes).
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 10.
Other Body surfaces:-
There 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 11.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
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.
introduction and persistence is a random process influenced by many factors that
leads to formation a much complex microbiome.
factors influencing the establishment and development of human microbiome are
Mode Of Delivery
Sanitation and others
Day routine activities and interactions
Visited places (Hospitals etc.).
Host’s Genetic make up
Medical conditions( Diseased, Pregnancy)
Medicinal courses with various drugs
Septic conditions (injuries)
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.
13. During vaginal delivery, facultative anaerobic species such as E.coli,
Staphylococcus, and Streptococcus also colonize the infant gut 14
During 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
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 16.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 17,
Various 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 microbes.
In teenagers, puberty associated changes in the skin
physiology, are the reasons behind changes in the skin microbial community
composition and diversity.
Overall 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) 19. Lipophilic bacteria like Propionibacterium tend
to increase in abundance between the ages of 25-30 years due high production of
sebum by the skin 20.