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Brooks B, Mueller RS, Young JC, et al. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol. 2015;6:654doi: 10.3389/fmicb.2015.00654.
Brooks, B., Mueller, R. S., Young, J. C., Morowitz, M. J., Hettich, R. L., & Banfield, J. F. (2015). Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in microbiology, 6654. https://doi.org/10.3389/fmicb.2015.00654
Brooks, Brandon, et al. "Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant." Frontiers in microbiology vol. 6 (2015): 654. doi: https://doi.org/10.3389/fmicb.2015.00654
Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol. 2015 Jul 01;6:654. doi: 10.3389/fmicb.2015.00654. eCollection 2015. PMID: 26191049; PMCID: PMC4487087.
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Front Microbiol. 2015 Jul 01;6:654. doi: 10.3389/fmicb.2015.00654. eCollection 2015.

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.

Frontiers in microbiology

Brandon Brooks, Ryan S Mueller, Jacque C Young, Michael J Morowitz, Robert L Hettich, Jillian F Banfield

Affiliations

  1. Department of Earth and Planetary Sciences, University of California, Berkeley Berkeley, CA, USA.
  2. Department of Earth and Planetary Sciences, University of California, Berkeley Berkeley, CA, USA ; Department of Microbiology, Oregon State University Corvallis, OR, USA.
  3. Department of Genome Sciences and Technology, The University of Tennessee, Knoxville Knoxville, TN, USA ; Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
  4. Department of Surgery, University of Pittsburgh School of Medicine Pittsburgh, PA, USA.

PMID: 26191049 PMCID: PMC4487087 DOI: 10.3389/fmicb.2015.00654

Abstract

While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.

Keywords: colonization; infant gut; metaproteomics; microbial ecology; microbiome; physiology

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