The effect of microbial colonization on the host proteome varies by gastrointestinal location
Open accessAbstract
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.
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The majority of human and mouse research uses stool samples, which only partly reflect conditions along the digestive tract.
“The majority of studies in humans and mice rely on faecal samples, which provide some representation of what is occurring throughout the digestive tract”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [119]
Stool sampling can hide features of the microbiota and host response that are unique to the small intestine.
“aspects of microbial communities and host responses that are specific to the small intestine might be obscured by faecal sampling119,120.”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [119]
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- Authors
- Lichtman, J. S., Alsentzer, E., Jaffe, M., Sprockett, D., Masutani, E., Ikwa, E., Fragiadakis, G. K., Clifford, D., Huang, B. E., Sonnenburg, J. L., Huang, K. C., & Elias, J. E.
- Affiliations
- Stanford Medicine (US)
- Stanford University (US)
- The Climate Corporation , San Francisco, CA, USA
- Commonwealth Scientific and Industrial Research Organisation (AU)
- Corresponding author
- Sonnenburg, Justin L
- Huang, Kerwyn Casey
- Elias, Joshua E
- ORCID
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-17
- Volume
- 10
- Issue
- 5
- Pages
- 1170-1181
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC5029216
- OpenAlex
- W2203497377
- Cited by
- 32
- References
- 39
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 3 · 2022: 3 · 2021: 1 · 2020: 4 · 2019: 6 · 2018: 3 · 2017: 5 · 2016: 5
- FWCI
- 1.88
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The ISME Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation
- National Institutes of Health (DGE-114747, GM107615)
- National Institute of General Medical Sciences (P50GM107615)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK085025)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- gut microbiota, host proteome, germ-free mice, Bacteroides thetaiotaomicron, host-microbe interactions, protein abundance, cecum, colon, stomach, jejunum, ileum
- MeSH terms
- Gastrointestinal Microbiome, Animals, Cecum, Feces, Ileum, Jejunum, Mass Spectrometry, Stomach, Cluster Analysis, Proteome, Gastrointestinal Tract, Mice
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