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ISME J. 2016 May;10(5):1170-81. doi: 10.1038/ismej.2015.187. Epub 2015 Nov 17.

The effect of microbial colonization on the host proteome varies by gastrointestinal location.

Author information

1
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
2
Department of Computer Science, Stanford University, Stanford, CA, USA.
3
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
4
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
5
Department of Bioengineering, Stanford University, Stanford, CA, USA.
6
The Climate Corporation, San Francisco, CA, USA.
7
Digital Productivity Flagship, Commonwealth Scientific and Industrial Research Organization, Dutton Park, Queensland, Australia.

Abstract

Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum and proximal colon under three colonization states: germ-free (GF), monocolonized with Bacteroides thetaiotaomicron and conventionally raised (CR). Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal (GI) tract. Unsupervised clustering showed that host protein abundance primarily depended on GI location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between CR mice relative to GF and monocolonized mice. Finally, comparison with fecal proteomic data sets suggested that the identities of stool proteins are not biased to any region of the GI tract, but are substantially impacted by the microbiota in the distal colon.

PMID:
26574685
PMCID:
PMC5029216
DOI:
10.1038/ismej.2015.187
[Indexed for MEDLINE]
Free PMC Article

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