Community structures of fecal bacteria in cattle from different animal feeding operations.
Orin C. Shanks,Catherine A. Kelty,S. L. Archibeque,Michael B. Jenkins,Ryan J. Newton,Sandra L. McLellan,Susan M. Huse,Mitchell L. Sogin +7 more
TLDR
Network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels.Abstract:
The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria 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 cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (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 in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.read more
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Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene disalicylate treatment and scours
G. Xie,G. Xie,Glenn C Duff,L. W. Hall,J.D. Allen,C. D. Burrows,J. C. Bernal-Rigoli,Scot E. Dowd,Vincent Guerriero,Carl J. Yeoman +9 more
TL;DR: It is shown that BMD has the ability to alter the composition of the fecal microbiome but failed to improve performance in Holstein bull calves.
Journal ArticleDOI
Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed
Xiang Li,Mano Sivaganesan,Catherine A. Kelty,Amity G. Zimmer-Faust,Pat Clinton,Jay R. Reichman,York Johnson,William Matthews,Stephanie A. Bailey,Orin C. Shanks +9 more
TL;DR: Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed.
Journal ArticleDOI
Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers.
TL;DR: D diets supplemented with EML and SMFP have little influence on the fecal bacterial community composition in finishing steers, and the different diets did not significantly influence most selected species.
Journal ArticleDOI
Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue.
Ryan S. Mote,Nicholas S. Hill,Joseph H. Skarlupka,Zachary B. Turner,Zachary P. Sanders,Dean P. Jones,Garret Suen,Nikolay M. Filipov +7 more
TL;DR: In this paper, the authors used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n'='6) or nontoxic (Max-Q; n´=`6) tall fescue before and 1, 2, 14, and 28'days after pasture assignment.
Journal ArticleDOI
Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1
Margaret D. Weinroth,Jennifer N. Martin,Enrique Doster,Ifigenia Geornaras,Jennifer K. Parker,Clay R Carlson,Jessica L. Metcalf,Paul S. Morley,Keith E. Belk +8 more
TL;DR: Comparing the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in three geographical regions with differing liver abscess prevalences suggests location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.
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