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

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

The Supplementary Material for this article can be found online at:  http://journal.frontiersin.org/article/10.3389/fmicb.2015.00654

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. 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

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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.
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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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  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2015-08-20T16:48:35Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) Mueller RyanMicrobiologyStrain-RresolvedMicrobial.pdf: 2005342 bytes, checksum: 4172536c79765b150ea75d3f0d9ff732 (MD5)
  • description.provenance : Made available in DSpace on 2015-08-20T16:48:35Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) Mueller RyanMicrobiologyStrain-RresolvedMicrobial.pdf: 2005342 bytes, checksum: 4172536c79765b150ea75d3f0d9ff732 (MD5) Previous issue date: 2015-07-01
  • description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2015-08-20T16:48:01Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) Mueller RyanMicrobiologyStrain-RresolvedMicrobial.pdf: 2005342 bytes, checksum: 4172536c79765b150ea75d3f0d9ff732 (MD5)

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