Introduction the anatomical area of human body
IntroductionThe collection of gene and their products from all the microbesliving within and on the human body are referred to as the human microbiome. Thesemicrobes 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 phylumthat primarily includes Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria1.
Based upon the anatomical area of human body the microbiomediffers in composition as:-Skin:- Skin is the second most common habitat for microbes on humanbody. Bacteria are by far the most common skin microbes, although fungi and virusesare also a part of skin microflora.Skin being our interface with environment acts as both abarrier as well as a habitat to these microbes, thus contains the most flexiblemicrobial composition. As our skin shows variations in physiochemicalproperties with various anatomical sites, it can be concluded that skin is ahub of habitats harboring a vast diversity of microbes. Thus the composition ofour skin microbiota differs considerably with various physiological areas onthe skin like moist areas including underarms and dry area including forearmsskin. Usually, the skin microbiota is similar among differentindividuals, although it is never exactly the same.
Environment and age, sex,site, immune system and certain physicochemical factors such as humidity, pH and temperature areexamples of factors that lead to variation. 2 In a study of skin microbiota from different sites on thebody about 19 different phyla dominated by Firmicutes, Actinobacteria,Bacteroidetes and Proteobacteria were observed 22. As we talk about species diversityanatomically our skin consists of three type microenvironments that are sebaceous,moist and dry. Propionibacterium and Staphylococci species are the main bacterialspecies observed in oily or sebaceous sites of the head, neck, and trunk areaswhile Corynebacteriumand Staphylococci are major species in moist places of theskin such as underarm area, the crease of the elbow or between the toes. PhylumFirmicutes comprise the majorbacterial phyla in the vagina. 22 In dry areas of the skin like the surfaces of the forearmsand legs, a mixture of species is observed dominated by Staphylococcus species,in particularly, S.
epidermidis andS.hominis 3.As we talk about fungal flora ofskin Malassezia is abundantin sebaceous areas 4. The heel, toenail, and toe web are found to have much more fungaldiversity than other skin areas.
Skin microbiota also includes some fungi like Candida species and Penicillium species. 5Other than above mentionedfacts skin microbiota is also affected by various skin related disorders and physicalinteractions like antibiotics exposure, sanitation, hygienic practices etc. Moreoverskin microbiota is the primary one to be in direct contact with externalatmosphere thus faces the major impacts of environment also.Gut:-Gut is the largest habitat for commensalsinside the human body. It can be divided into upper (stomach and duodenum) andlower gastro intestinal tracts (jejunum, ileum, caecum, colon, and rectum). Themajorly colonizing phyla’s are Firmicutes, Bacteroidetes, and Proteobacteria 6,7. Gut microbiota is established after the birth depending upon variousfactors and there are compositional changes related to diet, age and diseasedconditions 8. Gut microbiota also varies in composition according to variousanatomical areas of GI tract.
Like in stomach major microbial colonies are ofProteobacteria, Firmicutes, Bacteroidetes and Actinobacteria 9. Major genera observed in human stomach are Helicobacter,Streptococcus, and Prevotella 10. Similarly in small intestine majorly thereare facultative and obligate anaerobes (Streptococcus sp.
, enterobacteria,Clostridium sp., Bacteroidetes).Oral cavity:-Our oral cavity also acts as ahabitat for microbes, thus a distinct type of oral flora occurs there. Firmicutes has the major population inthe oral cavity along with proteobacteria, bacteroidetes, actinobacteria,fusobacteria and spirochaetes 11.Other Body surfaces:-Thereare also some other body surfaces other than the above mentioned, that act as ahabitat for the microbes. They include vagina, lungs, uterus etc.
Like in lungssome Prevotella, Sphingomonas, Pseudomonas species are observed 12.That muchavailability of habitats on a human body facilitates the microbial species togrow up in count as well as diversity. Thus there is generated a complexecosystem containing a blend of genomes and their expressions. Microbiomeestablishment and early colonizationBefore birth, we have nomicrobes on or inside our body.
With increasing time after birth differentspecies of microbes start to colonize in every possible habitat on our body. Withage we acquire large sized different populations of various microbes in the habitatsaround our bodies. With our age, our microbiota continues to change incomposition and diversity.With time our microbiomeincrease in count and adapt according to the changes in environment of theirhabitat.
For example, the foods we eat, theamount of microbes we’re exposed to on a daily basis and the level of stress welive with, all these factors alters the state and structure of our microbiome. Microbial introduction andpersistence is a random process influenced by many factors that leads toformation a much complex microbiome.Major factors influencingthe establishment and development of human microbiome are as follows:-Ø Mode Of DeliveryØ Host’s Age Ø Host Lifestyleo Dietary factorso Sanitation and otherso Day routine activities and interactionso Visited places (Hospitals etc.).Ø Host’s Genetic make up Ø Environmental FactorsØ Geography Ø DemographyØ Health Fluctuationso Medical conditions( Diseased, Pregnancy)o Antibacterial courseso Medicinal courses with various drugso Septic conditions (injuries)o Operations.Modeof Birth (delivery) Species diversity is found tobe low in infants but it is observed to be increased with time and exposure toenvironment.
It is obvious that this exposure differs by mode of delivery andplace of birth. Massive bacterial colonization occurs at birth upon exposure ofthe newborn to vaginal, fecal, and skin microbiota. Deliverymode can affect this early-life establishment of microbiota and its composition13. Babies delivered vaginally are covered by a film of microbialcolonies as they pass through the birth canal.
Thus their primary microbiotacontains 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 15Duringcaesarian delivery, the direct contact with maternal vaginal and intestinalflora is absent, and non-maternally derived environmental microbes play animportant role in primary colonization. Thus babies delivered by cesareansection are colonized mainly by skin microbes (e.
g., Staphylococcus,Corynebacterium, Propionibacterium spp.) composing of a very different set ofspecies than the babies born vaginally.
Caesareansection introduces opportunistic microbial species, including Enterobactercancerogenus/E. hormaechei, Haemophilusspp. and Staphylococcus 16. AgeAge is a major factors effecting microbial composition of ourmicrobiome. From birth, as the age increases the microbial diversity alsoincreases and converges toward an adult like microbiota by 3 to 5 years ofbirth, with a quite differing set of microbial colonies in comparison to those foundin an infant’s microbiota. Various factors like mode of delivery, diet,genetics etc. play a role in primary establishment of the microbiota, onceestablished the adult microbiota is comparatively stable in compositionthroughout the life.
After birth, gut microbiota closely resembles that of themother within the first year of life 17.Primary colonizers of infant gut arethe facultative anaerobes that create an environment that promotes the growth ofstrict anaerobes like Clostridium, and Bifidobacterium spp. The gut microbiotaof infants is of low diversity and majority of the phyla Proteobacteria andActinobacteria are observed. The microbiota increases in diversity with theintroduction of Firmicutes and Bacteroidetes as the time after birth increases 18,19. Variouscharacteristics of the skin like thickness, capability to hold moisture and toproduce sebum, oiliness, hair cover, etc.
changes considerably with aging, whichnaturally affects the microenvironments on skin habitats supporting differentmicrobes. Inteenagers, puberty associated changes in the skin physiology, are the reasonsbehind changes in the skin microbial community composition and diversity. Overallthere is an increase in diversity of skin microbiota during the first eightyears of life along with a reduction in abundance of the Order Lactobacillales(mainly Streptococcus) and relatively increase in other taxa also takes place. Inpuberty there is reduction in diversity due to increase in population of Actinobacteriaspecies (such as Propionibacterium acnes) 20.
Lipophilic bacteria likePropionibacterium tend to increase in abundance between the ages of 25-30 yearsdue high production of sebum by the skin 21.