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Title: Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants.more » In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.« less
Authors:
ORCiD logo [1] ; ORCiD logo [2] ;  [1] ;  [3] ;  [4] ;  [5] ;  [6] ; ORCiD logo [7] ;  [8]
  1. Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  3. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Science
  4. Magee-Womens Hospital of UPMC, Pittsburgh, PA (United States)
  5. University of Pittsburgh School of Medicine, Pittsburgh, PA (United States). Department of Surgery
  6. University of Pittsburgh School of Medicine, Pittsburgh, PA (United States). Department of Surgery; Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA (United States). Division of Pediatric General and Thoracic Surgery
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
  8. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Science and Department of Environmental Science, Policy, and Management; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 9; Journal Issue: 2; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
OSTI Identifier:
1474619

Brown, Christopher T., Xiong, Weili, Olm, Matthew R., Thomas, Brian C., Baker, Robyn, Firek, Brian, Morowitz, Michael J., Hettich, Robert L., and Banfield, Jillian F.. Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. United States: N. p., Web. doi:10.1128/mBio.00441-18.
Brown, Christopher T., Xiong, Weili, Olm, Matthew R., Thomas, Brian C., Baker, Robyn, Firek, Brian, Morowitz, Michael J., Hettich, Robert L., & Banfield, Jillian F.. Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. United States. doi:10.1128/mBio.00441-18.
Brown, Christopher T., Xiong, Weili, Olm, Matthew R., Thomas, Brian C., Baker, Robyn, Firek, Brian, Morowitz, Michael J., Hettich, Robert L., and Banfield, Jillian F.. 2018. "Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles". United States. doi:10.1128/mBio.00441-18. https://www.osti.gov/servlets/purl/1474619.
@article{osti_1474619,
title = {Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles},
author = {Brown, Christopher T. and Xiong, Weili and Olm, Matthew R. and Thomas, Brian C. and Baker, Robyn and Firek, Brian and Morowitz, Michael J. and Hettich, Robert L. and Banfield, Jillian F.},
abstractNote = {During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.},
doi = {10.1128/mBio.00441-18},
journal = {mBio (Online)},
number = 2,
volume = 9,
place = {United States},
year = {2018},
month = {4}
}

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