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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Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand.
Watsawan Sangkaew,Akechai Kongprajug,Natcha Chyerochana,Warish Ahmed,Surapong Rattanakul,Thammanitchpol Denpetkul,Skorn Mongkolsuk,Kwanrawee Sirikanchana +7 more
TL;DR: The importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox is underlined.
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Grazing accelerates labile and recalcitrant soil carbon loss driving by rare microbial taxa in a desert steppe
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Variation of Bacterial Communities with Water Quality in an Urban Tropical Catchment
Jean Pierre Nshimyimana,Adam J. E. Freedman,Adam J. E. Freedman,Peter Shanahan,Peter Shanahan,Lloyd Hc Chua,Janelle R. Thompson,Janelle R. Thompson +7 more
TL;DR: This study suggests that measurements of E. coli concentration could be useful in predicting samples enriched in sewage-associated and pathogen-like bacteria in tropical environments despite the potential for nonconservative behavior.
Journal ArticleDOI
Microbial interaction-driven community differences as revealed by network analysis.
TL;DR: In this article, the Shiga toxin 2 gene (stx2) was not expressed (defined as Stx2− group) in the bacteria, and those with stx2 expressed ( defined as St x2+ group) were used to explore whether microbial networks affect gut microbiota and foodborne pathogen virulence in cattle.
Journal ArticleDOI
Age-Related Shifts in the Density and Distribution of Genetic Marker Water Quality Indicators in Cow and Calf Feces
Orin C. Shanks,Catherine A. Kelty,Lindsay Peed,Mano Sivaganesan,Thomas Mooney,Michael B. Jenkins +5 more
TL;DR: It is suggested that currently available PCR-based water quality indicator technologies can under- or overestimate fecal pollution originating from calves and identify a need for novel calf-associated source identification methods.
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