Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes

  • Lim, SooYeon (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Seo, Jaehyun (Department of Agricultural Science, Korea National Open University) ;
  • Choi, Hyunbong (Department of Agricultural Science, Korea National Open University) ;
  • Yoon, Duhak (Department of Animal Science, Kyungpook National University) ;
  • Nam, Jungrye (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Cho, Seoae (C&K genomics Inc. 514 Main Bldg., Seoul National University Research Park) ;
  • Chang, Jongsoo (Department of Agricultural Science, Korea National Open University)
  • Received : 2013.04.16
  • Accepted : 2013.04.29
  • Published : 2013.08.01
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Abstract

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

Keywords

References

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