Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

Miller, Margret E. Berg; Antonopoulos, Dionysios A.; Rincón, Marco T.; Band, Mark; Bari, Albert; Akraiko, Tatsiana V.; Hernández, Álvaro Gonzalez; Thimmapuram, Jyothi; Henrissat, Bernard; Coutinho, Pedro M.; Borovok, Ilya; Jindou, Sadanari; Lamed, Raphael; Flint, Harry J.; Bayer, Edward A.; White, Bryan A.

doi:10.1371/journal.pone.0006650

Cited by 114 publications

(125 citation statements)

References 75 publications

(113 reference statements)

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“…However, most studies identified Prevotella as an important, if not the predominant, genus in the community. These studies also confirm that the cultivated cellulolytic bacterial genera Ruminococcus and Fibrobacter are not among the most abundant members of the community, but detected instead the presence of various other fibredegrading genera (Brulc et al, 2009;Pitta et al, 2010).…”

Section: Rumen Microbial Diversitysupporting

confidence: 68%

“…As in other mammalian gastrointestinal microbiomes (Ley et al, 2008b), the predominant phyla are the Bacteroidetes and the Firmicutes (Brulc et al, 2009;Callaway et al, 2010;Durso et al, 2010). The microbial diversity in the gastrointestinal tract of ruminants is estimated to be higher than that of humans (Eckburg et al, 2005;Brulc et al, 2009;Durso et al, 2010), with a few predominant genera (20 to 25), representing up to 90% of the total number of sequences (Callaway et al, 2010;Durso et al, 2010). Depending on the anatomical site, rumen or caecum, and probably also on the technical approach, the relative proportion of genera may change.…”

Section: Rumen Microbial Diversitymentioning

confidence: 82%

“…Rumen communities associated with bermudagrass diets, rich in structural carbohydrates and secondary compounds, were more diverse than those associated with growing wheat forage (Pitta et al, 2010), and the presence of highly degradable carbohydrates in the diet such as starch decreased bacterial diversity in faeces (Shanks et al, 2011). As in other mammalian gastrointestinal microbiomes (Ley et al, 2008b), the predominant phyla are the Bacteroidetes and the Firmicutes (Brulc et al, 2009;Callaway et al, 2010;Durso et al, 2010). The microbial diversity in the gastrointestinal tract of ruminants is estimated to be higher than that of humans (Eckburg et al, 2005;Brulc et al, 2009;Durso et al, 2010), with a few predominant genera (20 to 25), representing up to 90% of the total number of sequences (Callaway et al, 2010;Durso et al, 2010).…”

Section: Rumen Microbial Diversitymentioning

confidence: 94%

“…F. succinogenes, R. flavefaciens and R. albus have been found to account for a mere 1% to 3% of the total bacteria in the rumen (Stevenson and Weimer, 2007;Mosoni et al, 2011). The primers used for quantification could be too specific to detect all members of these genera ; however, recent evidence also suggest that microbes attached to plant substrates and the glycosyl hydrolases associated with them belong largely to bacteria that are phylogenetically distinct from these three species (Brulc et al, 2009;Hess et al, 2011).…”

Section: The Ruminant Superorganismmentioning

confidence: 99%

“…The metabolism of complex carbohydrates and pathways leading to hydrogen disposal are two salient characteristics that have been identified in gut microbiomes (Brulc et al, 2009;Qin et al, 2010;Arumugam et al, 2011;Hess et al, 2011;Muegge et al, 2011). These two activities are linked as the use of plant structural carbohydrates and the removal of hydrogen are both significant elements in the efficient use of forage feed resources and the optimisation of fermentation in the anaerobic conditions of the rumen (Wolin et al, 1997).…”

Section: The Ruminant Superorganismmentioning

confidence: 99%

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Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

196

163

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Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.

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Section: Rumen Microbial Diversitysupporting

confidence: 68%

Section: Rumen Microbial Diversitymentioning

confidence: 82%

Section: Rumen Microbial Diversitymentioning

confidence: 94%

Section: The Ruminant Superorganismmentioning

confidence: 99%

Section: The Ruminant Superorganismmentioning

confidence: 99%

See 3 more Smart Citations

Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

196

163

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Insights into a type III cohesin–dockerin recognition interface from the cellulose‐degrading bacterium Ruminococcus flavefaciens

Weinstein

Slutzki

Karpol

et al. 2015

J of Molecular Recognition

Self Cite

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Cellulosomes are large multicomponent cellulose-degrading assemblies found on the surfaces of cellulolytic microorganisms. Often containing hundreds of components, the self-assembly of cellulosomes is mediated by the ultra-high-affinity cohesin-dockerin interaction, which allows them to adopt the complex architectures necessary for degrading recalcitrant cellulose. Better understanding of how the cellulosome assembles and functions and what kinds of structures it adopts will further effort to develop industrial applications of cellulosome components, including their use in bioenergy production. Ruminococcus flavefaciens is a well-studied anaerobic cellulolytic bacteria found in the intestinal tracts of ruminants and other herbivores. Key to cellulosomal self-assembly in this bacterium is the dockerin ScaADoc, found on the non-catalytic structural subunit scaffoldin ScaA, which is responsible for assembling arrays of cellulose-degrading enzymes. This work expands on previous efforts by conducting a series of binding studies on ScaADoc constructs that contain mutations in their cohesin recognition interface, in order to identify which residues play important roles in binding. Molecular dynamics simulations were employed to gain insight into the structural basis for our findings. A specific residue pair in the first helix of ScaADoc, as well as a glutamate near the C-terminus, was identified to be essential for cohesin binding. By advancing our understanding of the cohesin binding of ScaADoc, this study serves as a foundation for future work to more fully understand the structural basis of cellulosome assembly in R. flavefaciens.

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