Original Research ARTICLE
A Stoichioproteomic Analysis of Samples from the Human Microbiome Project
- 1Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, United States
- 2Biology, University of Maryland, College Park, United States
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.
Keywords: Human Microbiome Project (HMP), stoichioproteomics, gut microbiome, oral microbiome, Skin microbiome, vaginal microbiome, nasal microbiome, CN ratio, G+c content
Received: 02 Feb 2017;
Accepted: 01 Jun 2017.
Edited by:James J. Elser, Flathead Lake Biological Station, University of Montana, United States
Reviewed by:Jay T. Lennon, Indiana University Bloomington, United States
Claudia Acquisti, Universität Münster, Germany
Peggy Baudouin-Cornu, CEA, France
Copyright: © 2017 Vecchio-Pagan, Bewick, Mainali, Karig and Fagan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Sharon Bewick, University of Maryland, College Park, Biology, College Park, 20742, MD, United States, firstname.lastname@example.org