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

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https://ir.library.oregonstate.edu/concern/articles/f4752j46d

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  • 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.
  • This is the publisher’s final pdf. The published article is copyrighted by Frontiers Research Foundation and can be found at: http://journal.frontiersin.org/journal/microbiology
  • Keywords: infant gut, colonization, physiology, microbiome, metaproteomics, microbial ecology
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  • 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, 6, 654. doi:10.3389/fmicb.2015.00654
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  • This work was partly funded by NIH grants 1R01-GM-103600 and 5R01-AI-092531, a March of Dimes Foundation grant 5-FY10-103 (MM), and an NSF Graduate Fellowship to BB and stipend support from the Genome Science and Technology program at the University of Tennessee, Knoxville to JY.
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