|Wells, James - Jim|
|KIM, M - Former ARS Employee|
Submitted to: Current Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2015
Publication Date: 1/15/2016
Publication URL: http://handle.nal.usda.gov/10113/61798
Citation: Wells, J., Kim, M. 2016. A meta-analysis of bacterial diversity in the feces of cattle. Current Microbiology. 72:145-15. doi:10.1007/s00284-015-0931-6.
Interpretive Summary: Bacteria in the intestinal tract have a symbiotic relationship with the host. Different species of bacteria can digest and ferment complex foodstuffs, can affect the host immune system, and can compete and exclude pathogens. The composition of the intestinal microbiota can be complex, and the presence of numerous bacterial species has been demonstrated by molecular sequencing. However, the potential role and function of these bacteria is often ignored. An in-depth analysis of the known bacterial sequences has provided a clearer understanding of the bacteria present and proposed possible functions for the known bacterial types identified in bovine feces.
Technical Abstract: In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13447 sequences were assigned to 10 phyla, 17 classes, 28 orders, 59 families and 110 genera while the remaining 216 sequences could not be assigned to a known phylum. About 41% of the total sequences could not be assigned to a known genus. The total sequences were assigned to 2360 OTUs at 97% sequence similarity, and Firmicutes and Bacteroidetes were represented by 52% and 36% of the 2360 OTUs, respectively. A small number of OTUs shared among datasets indicates that fecal bacterial communities of cattle are greatly affected by various factors, specifically diet. The rarefaction estimate showed that a meta-analysis of the collective sequences explained 69% coverage. This study may guide future studies to further analyze fecal bacterial communities of cattle.