A Stoichioproteomic Analysis of Samples from the Human Microbiome Project.

Briana Vecchio-Pagan,Kumar Mainali,William F Fagan,Sharon Bewick,David K Karig

doi:10.3389/fmicb.2017.01119

Abstract

Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates.

Highlights

The study of ecological stoichiometry (Sterner and Elser, 2002) derives from observed commonalities and differences in the elemental compositions of organisms (Elser et al, 1996), populations and communities (Moe et al, 2005)
It is impossible to rule out other forces of selection that might indirectly select for differences in element composition across body sites, our results provide strong preliminary evidence that nutrient limitation may vary across the human body and that this, in turn, may impact the associated structure of the human microbiome
For analysis of minor body sites in the remainder of the paper, we restrict our discussion to the three oral sites with sufficient sampling to obtain statistical significance, noting that further exploration of differences across other body sites would be an interesting extension of the current work

Summary

Introduction

The study of ecological stoichiometry (Sterner and Elser, 2002) derives from observed commonalities and differences in the elemental compositions of organisms (Elser et al, 1996), populations and communities (Moe et al, 2005). Stoichioproteomics of the HMP (Andersen and Hessen, 1991; Hessen and Lyche, 1991; Elser et al, 1996) and systems (Cebrian and Kingsolver, 1999; Elser et al, 2000a) Such variation is important because it provides valuable biological understanding into both the nature of the organisms in a particular ecosystem (Elser et al, 2000a,c; Fagan et al, 2002; Denno and Fagan, 2003), and the environmental conditions that these organisms face (Cebrian and Kingsolver, 1999; Elser et al, 2000a). For instance, are more nutrient rich (lower C:P and C:N ratios) than freshwater autotrophs, which are more nutrient rich than terrestrial autotrophs (Elser and Hassett, 1994; Elser et al, 2000a; Sterner and Elser, 2002), while marine autotrophs exhibit smaller ranges in elemental ratios as compared to autotrophs from terrestrial systems (Elser et al, 2000a, 2006)

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Discussion

Conclusion