Acquisition and Development of the Human Mucosal and Skin Microbiome

Objectives: The human body hosts complex microbial communities on the skin as well as on several mucosal surfaces including the oral cavity, gut and genito-urinary tract. The purpose of this study was to characterize the development of the skin, oral, rectal and urogenital microbiomes and to examine their shifts at key stages of life from infancy to puberty.

Methods: 38 systemically healthy female subjects were recruited from the following age groups: newborn, 6 months, 1-3 years and 9-12 years old. Samples of the mucosal and skin microbiomes were collected from oral, perivaginal, perirectal and auricular sites, 16S pyrotag sequencing targeting the V1-V3 and V6-V9 regions was preformed generating 24 million chimera-depleted high-quality sequences. Filtered sequences were compared to the Human Oral Microbiome Database (HOMD) using the QIIME pipeline for bacterial level identification and characterization. The habitat-specific core microbiome for each dentition state was calculated by identifying all species detected in 75% of the population and compared between groups.

Results: Linear Discriminant analysis revealed significant (p=0.007, permanova) clustering of the peri-vaginal microbiomes of newborns and 6-month olds, however the microbiomes of toddlers and prepubescent children diverged significantly from the younger age group and from each other. The peri-rectal microbiomes of the newborns and 6-month olds demonstrated significant (p=0.001, permanova) differences while the toddlers and prepubescent children grouped together. The epidermal sites were microbially distinct among all the groups. The oral microbiomes exhibited a significant clustering between newborn and 6-months old, which is uniquely different from the clustering between toddlers and prepubescent children.
Conclusions: Mucosal and epidermal microbiomes shift distinctly with age. Site-specific unique patterns were observed in these microbial shifts.