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Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments
M. Kim, M. Morrison, Z. Yu,
Language English Country Czech Republic
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Rumen microbiology MeSH
- Bacteria classification genetics isolation & purification MeSH
- Biodiversity MeSH
- Phylogeny MeSH
- Genomic Library MeSH
- Animal Feed microbiology MeSH
- Microbial Consortia genetics MeSH
- Polymorphism, Restriction Fragment Length MeSH
- Ribotyping MeSH
- RNA, Ribosomal, 16S analysis MeSH
- Sequence Analysis, DNA MeSH
- Cattle MeSH
- Animals MeSH
- Check Tag
- Cattle MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Phylogenetic analysis was conducted to examine ruminal bacteria in two ruminal fractions (adherent fraction vs. liquid fraction) collected from cattle fed with two different diets: forage alone vs. forage plus concentrate. One hundred forty-four 16S rRNA gene (rrs) sequences were obtained from clone libraries constructed from the four samples. These rrs sequences were assigned to 116 different operational taxonomic units (OTUs) defined at 0.03 phylogenetic distance. Most of these OTUs could not be assigned to any known genus. The phylum Firmicutes was represented by approximately 70% of all the sequences. By comparing to the OTUs already documented in the rumen, 52 new OTUs were identified. UniFrac, SONS, and denaturing gradient gel electrophoresis analyses revealed difference in diversity between the two fractions and between the two diets. This study showed that rrs sequences recovered from small clone libraries can still help identify novel species-level OTUs.
References provided by Crossref.org
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