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. 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 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.

Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk

“…The Clostridium XIVa cluster and Ruminococcaceae are also reduced in those with inflammatory bowel disease (IBD) compared to those without disease, 39,47 which agrees with their protective role in the gut inflammation and an anti‐inflammatory effect of aspirin on the gut microbiome. Moreover, members of the family Ruminococcaceae degrade several types of polysaccharides in the lower gastrointestinal tract and facilitate the production of protective short‐chain fatty acids 47,48 . In contrast, one of the Ruminococcaceae family members, Ruminococcocus gnavus, was shown to be increased in IBD, 48 which could explain an increased abundance of the Ruminococcocus genus in the aspirin vs placebo arm observed in our study.…”

“…For instance, bacteria in the Clostridium XIVa cluster participate in maintaining gastrointestinal functions by producing short‐chain fatty acids and inducing colonic regulatory T (Treg) cells, both of which are known to be protective in inflammation and CRC development and progression 39,46 . The Clostridium XIVa cluster and Ruminococcaceae are also reduced in those with inflammatory bowel disease (IBD) compared to those without disease, 39,47 which agrees with their protective role in the gut inflammation and an anti‐inflammatory effect of aspirin on the gut microbiome. Moreover, members of the family Ruminococcaceae degrade several types of polysaccharides in the lower gastrointestinal tract and facilitate the production of protective short‐chain fatty acids 47,48 .…”

Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue

“…The relative abundances of the Lachnospiraceae OTUs increased up to 8-fold in Eϩ steers, whereas the number of significantly increased Ruminococcaceae OTUs in Eϩ steers increased with time. Both families include cellulose-and hemicellulose-degrading bacteria and members contributing to butyrate production (53)(54)(55). Butyrate, an important energy source for ruminants, has been shown to influence energy expenditure (56,57), modulate nuclear receptor activity, and interact with free fatty acid receptors via the sympathetic nervous system to increase glucagon-like peptide 1 (GLP-1) and peptide YY (PYY) secretion from enteric L cells (58)(59)(60).…”

Gut microbiomes and their metabolites shape human and animal health

“…In this special issue, Dr. Suen's group focus on the Ruminococcus genus, which is commonly found in the rumen of animals, but is also present in non-ruminant animals, including humans (La Reau and Suen, 2018). In herbivorous ruminants, the gut microbiota including Ruminococcus genus is very important to degrade dietary cellulosic biomass into nutritive short-chain fatty acids.…”

“…Ruminococcus species are consistently present in the healthy human gut; therefore, possible roles in maintaining a healthy human gut environment are suggested. Large-scale genomic analysis for the taxonomic classification of Ruminococcus species led to the bacterial genus called "Blautia," formerly assigned to Rumi-nococcus genus, being reclassified (La Reau et al, 2016). This Blautia species occupies up to 16% of the microbiota of the human gastrointestinal tract and a significant reduction of Blautia species was observed in the elderly or patients with colorectal cancer.…”