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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Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies
TL;DR: The effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome are reported.
Journal ArticleDOI
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming.
Kyle Hartman,Marcel G. A. van der Heijden,Marcel G. A. van der Heijden,Raphaël Wittwer,Samiran Banerjee,Jean Claude Walser,Klaus Schlaeppi +6 more
TL;DR: It is found that about 10% of variation in microbial communities was explained by the tested cropping practices, which presents the basis towards developing microbiota management strategies for smart farming.
Journal ArticleDOI
Seasonal variability in bacterial and fungal diversity of the near-surface atmosphere.
Robert M. Bowers,Nicholas Clements,Joanne B. Emerson,Christine Wiedinmyer,Michael P. Hannigan,Noah Fierer +5 more
TL;DR: A comprehensive analysis of airborne microbes across two aerosol size fractions at urban and rural sites in the Colorado Front Range over a 14-month period suggests that a complex set of environmental factors act to control the composition of microbial bioaerosols in rural and urban environments.
Journal ArticleDOI
Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing.
Todd R. Callaway,Scot E. Dowd,Tom S. Edrington,Robin C. Anderson,Nathan A. Krueger,N. Bauer,Paul J. Kononoff,David J. Nisbet +7 more
TL;DR: In this article, a new molecular method, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was used to perform diversity analyses of gastrointestinal bacterial populations.
Journal ArticleDOI
Rumen microbiome from steers differing in feed efficiency.
TL;DR: The involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level is suggested to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.
References
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A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
Jian Xu,Magnus K. Bjursell,Jason Himrod,Su Deng,Lynn K. Carmichael,Herbert C. Chiang,Lora V. Hooper,Jeffrey I. Gordon +7 more
TL;DR: The complete genome sequence of the Gram-negative anaerobeBacteroides thetaiotaomicron, a dominant member of the authors' normal distal intestinal microbiota, is presented and expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in their intestine.
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