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Title: Community structure of cattle fecal bacteria from different animal feeding operations

Author
item SHANKS, ORIN - Us Environmental Protection Agency (EPA)
item KELTY, CATHERINE - Us Environmental Protection Agency (EPA)
item ARCHIBEQUE, SHAWN - Colorado State University
item Jenkins, Michael
item NEWTON, RYAN - University Of Wisconsin
item MCLELLAN, SANDRA - University Of Wisconsin
item HUSE, SUSAN - Woods Hole Marine Biological Laboratory
item SOGIN, MITCHELL - Woods Hole Marine Biological Laboratory

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2011
Publication Date: 5/1/2011
Citation: Shanks, O., Kelty, C., Archibeque, S., Jenkins, M., Newton, R., Mclellan, S., Huse, S., Sogin, M. 2011. Community structure of cattle fecal bacteria from different animal feeding operations. Applied and Environmental Microbiology. 77:2992-3001.

Interpretive Summary: Characterizing the microbiome (the total microbial community structure) of cattle feces can lead to improved understanding of pathogen shedding, its connection to food safety, and improved performance of fecal pollution detection methods. Scientists at USDA-ARS J. Phil Campbell, Sr., Natural Resource Conservation Center, in collaboration with scientists at USEPA, Cincinnati, Colorado State University, University of Wisconsin, Milwaukee, and the Marine Biological Laboratory at Woods Hole, MA, applied DNA sequencing methodology to profile the fecal microbial community of cattle from six different feeding operations. Animals under each feeding operation were under the influence of a single management practice for a minimum of six months. Results of taxonomic analyses indicated less variability within a population of cattle than between populations. Bacterial community composition correlated significantly with fecal starch concentration. Further bioinformatic analysis of the profiles indicated that profiles could be differentiated by management practice. The differences between profiles appeared to indicate that the bovine microbiome can change between animal feeding operations and that feeding operations are a more important determinant than geographic location of a feedlot. This is new information that will aid in the development of methods of fecal pollution identification and understanding the prevalence of pathogen shedding animal feeding operations.

Technical Abstract: The fecal microbiome of cattle plays a critical role not only in animal health and productivity, but also in methane emissions, food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about specific changes in fecal bacterial community structure within and across cattle populations Using massively-parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where animals were under the influence of a single management 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. Overall bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes to the Bacteroidetes, Proteobacteria, and Firmicutes subpopulations. In addition, network analysis of annotated sequences clustered by management practice and fecal starch concentration suggesting that the structure of bovine fecal bacterial communities can dramatically change between different animal feeding operations, even at the phylum and family taxonomic levels, and that feeding operation is a more important determinant of cattle microbiome than is geographic location of the feedlot.