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
Citations
More filters
Journal ArticleDOI
Soil Bacterial Communities Under Different Long-Term Fertilization Regimes in Three Locations Across the Black Soil Region of Northeast China
Xiaojing Hu,Junjie Liu,Dan Wei,Ping Zhu,Xi’an Cui,Baoku Zhou,Xueli Chen,Jian Jin,Xiaobing Liu,Guanghua Wang +9 more
TL;DR: The results highlighted that geographical separation was a more dominant factor affecting bacterial communities than fertilization, and that long-term similar fertilization regimes did not induce consistent changes in bacterial community composition in the black soil region.
Journal ArticleDOI
Effects of Paper Mulberry Silage on the Milk Production, Apparent Digestibility, Antioxidant Capacity, and Fecal Bacteria Composition in Holstein Dairy Cows.
Yangyi Hao,Shuai Huang,Jingfang Si,Jun Zhang,Naren Gaowa,Xiaoge Sun,Jiaying Lv,Gaokun Liu,Yaqin He,Wei Wang,Yajing Wang,Shengli Li +11 more
TL;DR: The results showed that the PM silage had no significant influence on the milk yield, apparent digestibility, and fecal bacteria composition of dairy cows, however, diets with PMsilage can enhance the antioxidant and immune capacity of Dairy cows, mainly due to the bioactive substance in PM.
Journal ArticleDOI
Combining Edge and Cloud computing for low-power, cost-effective metagenomics analysis
TL;DR: How it is possible to couple Edge and Cloud computing in order to manage the full analysis pipeline and a proper scheduling of the computational services between the data center and smart devices equipped with low-power processors represents an effective solution.
Journal ArticleDOI
Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers.
TL;DR: The findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing, and provide a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C.
Patent
Methods, apparatuses, and systems for analyzing microorganism strains from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon
Karsten Zengler,Mallory Embree +1 more
TL;DR: In this paper, methods, apparatuses, and systems for screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and synthesizing microbial ensembles based thereon are disclosed.
References
More filters
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh,Micah Hamady,Tanya Yatsunenko,Brandi L. Cantarel,Alexis E. Duncan,Ruth E. Ley,Mitchell L. Sogin,William J. Jones,Bruce A. Roe,Jason P. Affourtit,Michael Egholm,Bernard Henrissat,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +14 more
TL;DR: The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Journal ArticleDOI
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse,Christian Quast,Katrin Knittel,Bernhard M. Fuchs,Wolfgang Ludwig,Jörg Peplies,Frank Oliver Glöckner +6 more
TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Journal Article
Nonparametric estimation of the number of classes in a population
TL;DR: On applique la methode d'Efron (1981, 1982) a la construction d'intervalles de confiance bases sur des distributions du bootstrap as discussed by the authors.
Related Papers (5)
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more