title: Identification of metabolically active proteobacterial and archaeal communities in the rumen by DNA- and RNA-derived 16S rRNA gene.
abstract: OBJECTIVE
  To gain new insights into the metabolic contribution of bacterial group in the rumen.
  
  
  RESULTS
  Both DNA- and RNA-derived bacterial 16S ribosomal materials from bovine rumen contents were used as the template for bacterial community and analyse microbiota by three methods namely custom phylogenetic microarray, quantitative real-time PCR and denaturing gradient gel electrophoresis techniques. Bacterial analysis showed that genera affiliating with the Proteobacteria apparently made a greater metabolic contribution to rumen function than their population sizes indicated. Analysis of another rumen microbial group, the methanogens, using clone libraries for the expressed methyl coenzyme reductase subunit A (mcrA) revealed that an uncultivated methanogen clade contributes one-third of RNA-derived mcrA sequences based on a limited number of clones analysed. These uncultivated methanogen species were not observed in the mcrA gene library based on the DNA-derived sequences.
  
  
  CONCLUSIONS
  The comparison of results obtained from DNA- and RNA-derived materials suggests that some of the Proteobacteria and novel methanogen species appeared to be low in abundance in the rumen maintained on grain-based diets might play a greater role in rumen metabolism.
  
  
  CONCLUSIONS
  These studies provide the first report to compare high-throughput analysis of bacterial 16S rRNA genes from DNA- and RNA-derived materials to indicate differences that species make to community structure and metabolic activity.
authors.affiliation: CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Brisbane, Qld, Australia. Seungha.kang@csiro.au
authors.forename: S H
authors.initials: SH
authors.lastname: Kang
authors.forename: P
authors.initials: P
authors.lastname: Evans
authors.forename: M
authors.initials: M
authors.lastname: Morrison
authors.forename: C
authors.initials: C
authors.lastname: McSweeney
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D002417:Cattle; D058645:Denaturing Gradient Gel Electrophoresis; D020459:Genes, rRNA; D020411:Oligonucleotide Array Sequence Analysis; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D012417:Rumen / Q000378:metabolism / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases
keywords: 16S rRNA gene; RNA; mcrA; metabolic activity; methanogen; rumen