Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles
[1];
[2];
[7];
- Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
- Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Science
- Magee-Womens Hospital of UPMC, Pittsburgh, PA (United States)
- University of Pittsburgh School of Medicine, Pittsburgh, PA (United States). Department of Surgery
- 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
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
- 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
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.
- Research Organization:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Organization:
- USDOE
- Grant/Contract Number:
- AC05-00OR22725
- OSTI ID:
- 1474619
- Journal Information:
- mBio (Online), Vol. 9, Issue 2; ISSN 2150-7511
- Publisher:
- American Society for MicrobiologyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
Effects of early life NICU stress on the developing gut microbiome
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journal | January 2019 |
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
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journal | February 2019 |
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Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life
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