Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria
Abstract
Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.
- Authors:
-
[1];
[3];
[4];
[5]
- Univ. of California, Berkeley, CA (United States)
- Univ. of Pittsburgh School of Medicine, PA (United States)
- Univ. of Pittsburgh Medical Center Magee Womens Hospital, PA (United States)
- Univ. of California, Berkeley, CA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States)
- Chan Zuckerberg Biohub, San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH); Alfred P. Sloan Foundation; National Science Foundation (NSF)
- OSTI Identifier:
- 1591850
- Grant/Contract Number:
- AC02-05CH11231; RAI092531A; R01-GM109454; APSF-2012-10-05; DGE 1106400
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Science Advances
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 12; Journal ID: ISSN 2375-2548
- Publisher:
- AAAS
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Olm, Matthew R., Bhattacharya, Nicholas, Crits-Christoph, Alexander, Firek, Brian A., Baker, Robyn, Song, Yun S., Morowitz, Michael J., and Banfield, Jillian F. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria. United States: N. p., 2019.
Web. doi:10.1126/sciadv.aax5727.
Olm, Matthew R., Bhattacharya, Nicholas, Crits-Christoph, Alexander, Firek, Brian A., Baker, Robyn, Song, Yun S., Morowitz, Michael J., & Banfield, Jillian F. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria. United States. doi:https://doi.org/10.1126/sciadv.aax5727
Olm, Matthew R., Bhattacharya, Nicholas, Crits-Christoph, Alexander, Firek, Brian A., Baker, Robyn, Song, Yun S., Morowitz, Michael J., and Banfield, Jillian F. Wed .
"Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria". United States. doi:https://doi.org/10.1126/sciadv.aax5727. https://www.osti.gov/servlets/purl/1591850.
@article{osti_1591850,
title = {Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria},
author = {Olm, Matthew R. and Bhattacharya, Nicholas and Crits-Christoph, Alexander and Firek, Brian A. and Baker, Robyn and Song, Yun S. and Morowitz, Michael J. and Banfield, Jillian F.},
abstractNote = {Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.},
doi = {10.1126/sciadv.aax5727},
journal = {Science Advances},
number = 12,
volume = 5,
place = {United States},
year = {2019},
month = {12}
}
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