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United States Department of Agriculture

Agricultural Research Service

Research Project: SURVIVAL AND TRANSPORT OF PATHOGENS FROM ANIMAL PRODUCTION SYSTEMS WITHIN LANDSCAPES OF THE SOUTHEASTERN USA Title: Diversity and population structure of bovine fecal-derived microorganisms from different animal feeding operations

Authors
item Shanks, O -
item Kelty, C -
item Archibeque, S -
item Jenkins, Michael
item Huse, S -
item Sogin, M -

Submitted to: American Society for Microbiology Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: March 10, 2010
Publication Date: May 19, 2010
Citation: Shanks, O.C., Kelty, C.A., Archibeque, S., Jenkins, M., Huse, S.M., Sogin, M.L. 2010. Diversity and population structure of bovine fecal-derived microorganisms from different animal feeding operations [abstract]. American Society for Microbiology Annual Meeting. CDROM.

Technical Abstract: The fecal microbiome of cattle plays a critical role not only in animal health and productivity, but in odor emissions, agricultural land nutrient loading, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, our understanding of the specific changes in fecal bacterial community structure that occur within and across cattle populations is limited because most work to date has focused on either surveying a small number of samples in detail or a large number with techniques that provided insufficient detail. Using massively parallel 454 pyrosequencing of a hypervariable region of the rRNA gene, we profiled the microbial communities of six different animal feeding operations where animals were under the influence of the same feeding practice for a minimum of six months. We obtained a total of 620,611 high quality sequences from 30 adult beef cattle fecal samples (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. In addition, UPGMA trees show the bacterial communities clustered by feed type: predominately forage, processed grains, or unprocessed grains. Overall bacterial community composition correlated significantly with fecal starch concentrations, largely driven by changes in Bacteroidetes, Proteobacteria, and Firmicutes subpopulations. Together, these results suggest that the structure of bovine fecal bacterial communities can dramatically change between different animal feeding operations, even at the phylum and class taxonomic levels, and that feeding operation is a more important determinant of cattle microbiome than is geographic location of the feed lot.

Last Modified: 8/22/2014
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