title: Sequence-based analysis of the genusRuminococcusresolves 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 genusRuminococcus. 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. Here, 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 genusRuminococcus, 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.
authors.affiliation: 1​Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA.
authors.forename: Alex J
authors.initials: AJ
authors.lastname: La Reau
authors.affiliation: 2​Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: 1​Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA.
authors.forename: Garret
authors.initials: G
authors.lastname: Suen
mesh_terms: D000818:Animals; D054884:Host-Pathogen Interactions; D006801:Humans; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D045857:Ruminococcus / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; Ruminococcus; host diet; host range; phylogenomics; phylogeny