Selective colonization ability of human fecal microbes in different mouse gut environments
- 15 November 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 13 (3), 805-823
- https://doi.org/10.1038/s41396-018-0312-9
Abstract
Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.Keywords
Funding Information
- U.S. Department of Health & Human Services | National Institutes of Health (1 DP2 GM126893-01)
- American Cancer Society (ACS-RSG-16-255-01-MPC)
- U.S. Department of Health & Human Services | National Institutes of Health (1 DP2 GM126893-01)
- American Cancer Society (ACS-RSG-16-255-01-MPC)
This publication has 86 references indexed in Scilit:
- Pathview: an R/Bioconductor package for pathway-based data integration and visualizationBioinformatics, 2013
- Metagenomic microbial community profiling using unique clade-specific marker genesNature Methods, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011
- FLASH: fast length adjustment of short reads to improve genome assembliesBioinformatics, 2011
- Bayesian community-wide culture-independent microbial source trackingNature Methods, 2011
- Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factorsProceedings of the National Academy of Sciences of the United States of America, 2010
- Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficileProceedings of the National Academy of Sciences of the United States of America, 2010
- Bacterial competition: surviving and thriving in the microbial jungleNature Reviews Microbiology, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009