The mammalian skin microbiome
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Date
2017-08-23
Authors
Ross, Ashley Anne
Journal Title
Journal ISSN
Volume Title
Publisher
University of Waterloo
Abstract
Skin constitutes the primary physical barrier between mammals and their external environment. Characterization of the microorganisms on skin is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins of potential zoonoses that affect humans.
Distinct microbial communities inhabit individuals as part of the human skin microbiome, which are continually shed to the surrounding environment. Microbial communities from 17 skin sites of 10 sexually active cohabiting couples (20 individuals) were sampled to test whether cohabitation impacts an individual’s skin microbiome, leading to shared skin microbiota among partner pairs. Amplified 16S rRNA genes of bacteria and archaea from a total of 340 skin swabs were analyzed by high-throughput sequencing and the results demonstrated that cohabitation was significantly associated with microbial community composition, although this association was greatly exceeded by characteristics of body location and individuality. Random forest modeling demonstrated that partners could be predicted 86% of the time (p < 0.001) based on their skin microbiome profiles, which was always greater than combinations of incorrectly matched partners. Cohabiting couples had the most similar overall microbial skin communities on their feet, according to Bray-Curtis distances. In contrast, thigh microbial communities were strongly associated with biological sex rather than cohabiting partner. Additional factors that were associated with the skin microbiome of specific body locations included the use of skin care products, pet ownership, allergies, and alcohol consumption. These baseline data identified links between the skin microbiome and daily interactions among cohabiting individuals, adding to known factors that shape the human microbiome and, by extension, its relation to human health.
Although many studies have characterized the human microbiome, far less is known about the skin microbiome of non-human mammals. The objective of this research was to create a baseline skin microbiome dataset for the Mammalia class, testing the effects of species, location, hygiene, body region, and biological sex. The back, torso, and inner thigh regions of 177 non-human mammals and 20 human participants were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). Human skin was significantly less diverse than all other mammalian orders according to Shannon indices (6.54 versus 3.96, p < 0.001). The factor most strongly associated with community variation for all samples was whether the host was a human (PERMANOVA, F = 37.8, p < 0.001). By analyzing all samples together, random forest modelling identified that human and animal samples could be distinguished correctly 98.51.2% of the time. This study represents the largest non-human mammalian skin microbiome project to date and is the first study to elucidate the skin microbiota for 32 unique species. Additionally, these findings are the first to demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Baseline data on the mammalian skin microbiome is crucial for making informed decisions for veterinarian research and conservation strategies, as well as providing implications for mammalian evolutionary history.
Description
Keywords
Skin microbiome, Cohabitation, High-throughput sequencing, Microbiology, Mammal