Abstract
The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.
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Acknowledgements
We thank Dr David Tabb and the Yates Proteomics Laboratory at Scripps Research Institute for DTASelect/Contrast software, the Institute for Systems Biology for proteome bioinformatics tools used in the analysis of the MS data, and M Land of the ORNL Genome Analysis and System Modeling Group for computational resources for proteomic analysis. We thank Patricia Carey (ORNL) for computational assistance with proteome informatics. Becky R Maggard (ORNL) is thanked for secretarial assistance in the preparation of this paper. The ORNL part of this research was sponsored in part by US Department of Energy under contract DE-AC05-00OR22725 with Oak Ridge National Laboratory, managed and operated by UT-Battelle, LLC. The SLU research was sponsored by the SLU Faculty for Natural Resources and Landscape Management, by the MICPROF grant funded by Uppsala Bio-X (www.uppsalabio.se/) and in part by US Department of Energy contract DE-AC02-05CH11231 with Lawrence Berkeley National Laboratory. The Burnham Institute for Medical Research (BIMR) was sponsored in part by the NIH Grant P20 GM076221. The human sampling was sponsored by Örebro University Hospital Research Foundation and the Örebro County Research Foundation. Alison L Russell was funded by the Genome Science and Technology Program at the University of Tennessee and by Oak Ridge National Laboratory.
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Supplementary Information accompanies the paper on The ISME Journal website (http://www.nature.com/ismej)
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Verberkmoes, N., Russell, A., Shah, M. et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J 3, 179–189 (2009). https://doi.org/10.1038/ismej.2008.108
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DOI: https://doi.org/10.1038/ismej.2008.108
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