Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Name
journal.pone.0223680.pdf
Description
Published version
Size
2.94 MB
Format
Adobe PDF
Checksum (MD5)
a3ba1ea0782530500cd46f2db67cfbc4
Author(s)
Jiang, Xiaofang
Hall, Andrew Brantley
Xavier, Ramnik J.
Alm, Eric J.
Date Issued
December 12, 2019
Journal
PLoS one
Publisher
Public Library of Science (PLoS)
Citation
Jiang, Xiaofang et al. "Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools." PLoS one 14 (2019):e0223680 © 2019 The Author(s)
Version
Final published version
Abstract
Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.
Subjects
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
General Medicine
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1371/journal.pone.0223680
