Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

Abstract

Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment, yet the factors that govern skin microbial community composition among mammals are poorly understood. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. Skin from the back, torso, and inner thighs of 177 nonhuman mammals was sampled, representing individuals from 38 species and 10 mammalian orders. Animals were sampled from farms, zoos, households, and the wild. The DNA extracts from all skin swabs were amplified by PCR and sequenced, targeting the V3-V4 regions of bacterial and archaeal 16S rRNA genes. Previously published skin microbiome data from 20 human participants, sampled and sequenced using an identical protocol to the nonhuman mammals, were included to make this a comprehensive analysis. Human skin microbial communities were distinct and significantly less diverse than all other sampled mammalian orders. The factor most strongly associated with microbial community data for all samples was whether the host was a human. Within nonhuman samples, host taxonomic order was the most significant factor influencing skin microbiota, followed by the geographic location of the habitat. By comparing the congruence between host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing evidence of phylosymbiosis between skin microbial communities and their hosts.

Keywords: 16S rRNA; coevolution; mammals; phylosymbiosis; skin microbiome.

Fig. 1.

Ordination (PCoA) generated by using the Bray–Curtis dissimilarity metric for each of the three body locations sampled. Samples are colored according to mammalian order. (Inset) Ordination colored according to human and nonhuman samples.

Fig. 2.

Boxplots of diversity indices for 10 mammalian orders and humans, including both number of OTUs (A) and Shannon indices (B).

Fig. 3.

Heatmap summarizing the significant metadata factors correlating with the observed skin microbiota for sampled individuals from mammalian orders. Categories with higher PERMANOVA F statistics have higher variation in community dissimilarity. Gray regions of the heatmap represent categories that do not apply. Samples and categories are clustered according to Bray–Curtis dissimilarities.

Fig. 4.

Barplot of predicted functions based on FAPROTAX database. Stars indicate P < 0.05 among mammalian and human samples after Bonferroni correction was applied. Error bars denote the SD of animal (n = 512) and human (n = 77) samples.

Fig. 5.

Dendrograms for species-specific skin microbiota generated using the Bray–Curtis distance metric and a 99% OTU threshold, compared with the known host phylogenies of Perissodactyla (A), Artiodactyla (B), and Carnivora (C). Congruence was measured using normalized Robinson–Foulds (nRF) scores and normalized matching cluster (nMC) scores. Bootstrap values for all microbiota dendrogram branch points were ≥98% and are not shown. Mammal, bovine, goat, and sheep images courtesy of Tracey Saxby, John C. Fisher, Jane Hawkey, and Tim Carruthers, Integration and Application Network, University of Maryland Center for Environmental Science (ian.umces.edu/imagelibrary/). Alpaca image courtesy of Meaghan Mechler (artist).