Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota
Abstract
We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs. disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gutmore »
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1237607
- Grant/Contract Number:
- AC05-00OR22725; 1R01-GM-103600
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proteomics (Online)
- Additional Journal Information:
- Journal Name: Proteomics (Online); Journal Volume: 15; Journal Issue: 20; Journal ID: ISSN 1615-9861
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Human gut microbiome; Metaproteomics; Shotgun proteomics; Systems biology
Citation Formats
Xiong, Weili, Abraham, Paul E., Li, Zhou, Pan, Chongle, and Robert L. Hettich. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota. United States: N. p., 2015.
Web. doi:10.1002/pmic.201400571.
Xiong, Weili, Abraham, Paul E., Li, Zhou, Pan, Chongle, & Robert L. Hettich. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota. United States. https://doi.org/10.1002/pmic.201400571
Xiong, Weili, Abraham, Paul E., Li, Zhou, Pan, Chongle, and Robert L. Hettich. Fri .
"Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota". United States. https://doi.org/10.1002/pmic.201400571. https://www.osti.gov/servlets/purl/1237607.
@article{osti_1237607,
title = {Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota},
author = {Xiong, Weili and Abraham, Paul E. and Li, Zhou and Pan, Chongle and Robert L. Hettich},
abstractNote = {We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs. disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.},
doi = {10.1002/pmic.201400571},
journal = {Proteomics (Online)},
number = 20,
volume = 15,
place = {United States},
year = {Fri Apr 24 00:00:00 EDT 2015},
month = {Fri Apr 24 00:00:00 EDT 2015}
}
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