The Ruminococci: key symbionts of the gut ecosystem

@article{LaReau2018TheRK,
  title={The Ruminococci: key symbionts of the gut ecosystem},
  author={Alex La Reau and Garret Suen},
  journal={Journal of Microbiology},
  year={2018},
  volume={56},
  pages={199-208}
}
Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown… 
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References

SHOWING 1-10 OF 108 REFERENCES
Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association
TLDR
Evidence that ruminococci are predominantly associated with herbivores and omnivores is presented, and the hypothesis that very few ruminitisci are found consistently in non-host-associated environments is supported, to help resolve the phylogeny of this important genus.
Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
TLDR
There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific, and could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens.
Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon
TLDR
It is argued strongly that R. bromii has a pivotal role in fermentation of RS3 in the human large intestine, and that variation in the occurrence of this species and its close relatives may be a primary cause of variable energy recovery from this important component of the diet.
Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota.
TLDR
On the basis of phylogenetic analysis, and morphological and physiological data, strain 18P13(T) can be differentiated from other members of the genus Ruminococcus with validly published names.
Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent
TLDR
It is shown that although both strains could assimilate mucin monosaccharides, only R. gnavus ATCC 29149 was able to grow on mucin as a sole carbon source, and a novel pathway by which R.gnavusATCC29149 utilises sialic acid from sialylated substrates is uncovered, advancing understanding of the role of gut commensals in health and disease.
Ruminococcal cellulosome systems from rumen to human.
TLDR
A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced, revealing two large tandem scaffoldin-coding genes that form part of a gene cluster.
Ruminococcus faecis sp. nov., isolated from human faeces
TLDR
It is proposed that this novel strain isolated from human faeces be assigned to the genus Ruminococcus and be named Ruminitis faecis sp.
Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains
TLDR
This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.
Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis
TLDR
Comparative genomics, fermentation analyses, and transcriptomics are used to further clarify the cellulolytic and fermentative potential of R. albus 7 and contribute to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.
Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation
TLDR
The results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.
...
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