Determining the culturability of the rumen bacterial microbiome

Christopher J. Creevey, William J. Kelly, Gemma Henderson, Sinead C. Leahy

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The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000.

Original languageEnglish
Pages (from-to)467-479
Number of pages13
JournalMicrobial Biotechnology
Issue number5
Early online date01 Jul 2014
Publication statusPublished - 01 Sept 2014


  • Animals
  • Bacteria/classification
  • Cluster Analysis
  • Computational Biology
  • DNA, Bacterial/chemistry
  • DNA, Ribosomal/chemistry
  • Microbiota
  • Phylogeny
  • RNA, Ribosomal, 16S/genetics
  • Rumen/microbiology
  • Ruminants
  • Sequence Analysis, DNA


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