Skin Microbiome and its Interplay with the Environment

Abstract

Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.

Fig. 1

Bacterial composition and richness of Avène Thermal Spring Water. Sample composition and diversity are the average of samples taken between December 2014 and September 2018, with four samples taken per year. Bubble plots represent the bacterial composition (for simplicity, only major phyla shown). Each phylum is represented by a different color. The size of the bubble represents the relative abundance, as indicated in the legend. The y-axis for the bubble plots is on the left. The boxplot represents the bacterial Chao1 richness, with the y-axis on the right. Data adapted from Bourrain et al. [11]

Fig. 2

Human bacterial composition across an urbanization gradient in the Amazon in South America. Sites ranged from a remote village isolated in the Amazon rainforest (Checherta), to a rural village (Puerto Almendra), a large town (Iquitos), and the lower and middle socioeconomic class of a metropolis city (Manaus). Samples presented per skin sample site: right hand (top panel), right foot (bottom panel). Bubble plots, with the y-axis on the left, represent the bacterial composition (for simplicity, only the major taxa are shown). The size of the bubble represents the relative abundance. Boxplots, with the y-axis on the right, represent the bacterial Chao1 richness. Firmicutes are depicted in purple, Actinobacteria in blue, Proteobacteria in green, and Bacteroides in yellow. Data adapted from McCall et al. [37]