Shotgun metaproteomics of the human distal gut microbiota View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-02

AUTHORS

Nathan C Verberkmoes, Alison L Russell, Manesh Shah, Adam Godzik, Magnus Rosenquist, Jonas Halfvarson, Mark G Lefsrud, Juha Apajalahti, Curt Tysk, Robert L Hettich, Janet K Jansson

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. More... »

PAGES

ismej2008108

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ismej.2008.108

DOI

http://dx.doi.org/10.1038/ismej.2008.108

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1001388414

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18971961


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Turtle is a human-readable linked data format.

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RDF/XML is a standard XML format for linked data.

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