title: Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen.
abstract: BACKGROUND
  The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.
  
  
  RESULTS
  As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.
  
  
  CONCLUSIONS
  The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population.
authors: Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America.
authors: Jennifer M
authors: JM
authors: Brulc
authors: Carl J
authors: CJ
authors: Yeoman
authors: Melissa K
authors: MK
authors: Wilson
authors: Margret E
authors: ME
authors: Berg Miller
authors: Patricio
authors: P
authors: Jeraldo
authors: Sadanari
authors: S
authors: Jindou
authors: Nigel
authors: N
authors: Goldenfeld
authors: Harry J
authors: HJ
authors: Flint
authors: Raphael
authors: R
authors: Lamed
authors: Ilya
authors: I
authors: Borovok
authors: Maša
authors: M
authors: Vodovnik
authors: Karen E
authors: KE
authors: Nelson
authors: Edward A
authors: EA
authors: Bayer
authors: Bryan A
authors: BA
authors: White
mesh_terms: D000818:Animals; D044822:Biodiversity; D002417:Cattle; D002482:Cellulose / Q000235:genetics / Q000378:metabolism*; D004032:Diet; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D054892:Metagenome; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D012417:Rumen / Q000382:microbiology*; D045857:Ruminococcus / Q000235:genetics / Q000302:isolation & purification; D013045:Species Specificity
chemical_list: D012336:RNA, Ribosomal, 16S; D002482:Cellulose