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Title: Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association

Abstract

It has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. For this study, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated withmore » herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.« less

Authors:
 [1];  [2];  [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Dept. of Bacteriology
  2. Leibniz Inst. German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig (Germany)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1463886
Grant/Contract Number:  
SC0008104
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Microbial Genomics
Additional Journal Information:
Journal Volume: 2; Journal Issue: 12; Journal ID: ISSN 2057-5858
Publisher:
Society for General Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; phylogeny; 16S rRNA; host diet; Ruminococcus; host range; phylogenomics

Citation Formats

La Reau, Alex J., Meier-Kolthoff, Jan P., and Suen, Garret. Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. United States: N. p., 2016. Web. doi:10.1099/mgen.0.000099.
La Reau, Alex J., Meier-Kolthoff, Jan P., & Suen, Garret. Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. United States. doi:10.1099/mgen.0.000099.
La Reau, Alex J., Meier-Kolthoff, Jan P., and Suen, Garret. Thu . "Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association". United States. doi:10.1099/mgen.0.000099. https://www.osti.gov/servlets/purl/1463886.
@article{osti_1463886,
title = {Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association},
author = {La Reau, Alex J. and Meier-Kolthoff, Jan P. and Suen, Garret},
abstractNote = {It has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. For this study, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated with herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.},
doi = {10.1099/mgen.0.000099},
journal = {Microbial Genomics},
number = 12,
volume = 2,
place = {United States},
year = {Thu Dec 01 00:00:00 EST 2016},
month = {Thu Dec 01 00:00:00 EST 2016}
}

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Cited by: 8 works
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Works referenced in this record:

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009

  • Schloss, P. D.; Westcott, S. L.; Ryabin, T.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
  • DOI: 10.1128/AEM.01541-09

MrBayes 3: Bayesian phylogenetic inference under mixed models
journal, August 2003