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Title: The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes

item WU, S - University Of California
item Baldwin, Ransom - Randy
item LI, W - University Of California
item Li, Congjun - Cj
item Connor, Erin
item Li, Robert

Submitted to: Metagenomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2012
Publication Date: 4/30/2012
Citation: Wu, S., Baldwin, R.L., Li, W., Li, C., Connor, E.E., Li, R.W. 2012. The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Metagenomics. 1:11. DOI:10.4303/mg/235571.

Interpretive Summary: Ruminants have been a key part of sustainable agriculture throughout human civilization. Microbial fermentation of plant fibers occurs within the rumen, thereby synthesizing various small molecules used to produce meat, milk, and wool. Understanding of microbial interactions in the rumen microbial ecosystem provides a scientific basis for successful manipulation of ruminal fermentation for optimal outcomes. In this study, we surveyed the rumen bacterial composition of calves, dairy cows, and beef steers using next-generation sequencing technologies and bioinformatics. Our results demonstrate that the rumen of different developmental stages and breeds displayed distinct microbial compositional profiles. Our findings should guide efforts in formulating strategies for optimal rumen manipulation, which will be beneficial to both cattle farmers and consumers who desire for cheaper and safer meat and dairy products.

Technical Abstract: The rumen as a complex microbial ecosystem plays a critical role in sustainable agriculture. Rumen microorganisms perform important biochemical conversions, including the fermentation of plant fiber to small molecules such as short-chain fatty acids for meat and dairy production. In this study, we surveyed the rumen bacterial community composition of both pre-ruminant dairy calves (the developing rumen) and cows and beef steers (the mature rumen) using pyrosequencing of the 16S rRNA gene. The number of 16S rRNA gene sequences generated per sample was 37,004.6 ± 6,612.4 (mean ± sd). The sequences were analyzed using both taxonomy-dependent and –independent clustering methods. Collectively, the 16S sequences were positively assigned to 21 phyla, 31 classes, 93 families, 219 genera, and at least 1,079 Operational Taxonomic Units (OTUs) at a 3% distance cutoff. The core rumen microbiome, regardless of the rumen developmental status or breeds, consisted of 8 phyla, 11 classes, 15 families, and 17 genera, which may represent the basic components of the rumen microbial community. Principal component analysis and clustering suggested that the bacterial communities in the rumen of pre-ruminant dairy calves, dairy cows, and beef steers were clearly distinguishable. Approximately 66% of phyla, 61% of classes, and 41% of OTUs in a typical rumen bacterial community displayed a significant difference in their relative abundance between the developing and mature rumen while as many as 42 genera and 345 OTUs showed a significant difference in the rumen between beef and dairy cattle (P<0.05). The significantly greater abundance of Fibrobacteraceae and Ruminococaceae in the rumen of beef steers may be associated with diet and likely reflected enhanced fiber-digesting capacity in beef cattle. Our results should facilitate understanding of the structural and functional relationships in the rumen microbial ecosystem.