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
Dynamic Variations in Fecal Bacterial Community and Fermentation Profile of Holstein Steers in Response to Three Stepwise Density Diets
Qinghua Qiu,Yangxiang Zhu,Xinjun Qiu,Chaoyu Gao,Jingjing Wang,Haibo Wang,Yang He,Muhammad Aziz Ur Rahman,Binghai Cao,Huawei Su +9 more
TL;DR: It was found that fecal bacterial diversity decreased as dietary density increased and as the fattening phase continued, and time-dependent variations of fecal fermentation profile and microbiota composition exist in the long-term fattened of steers in addition to diet stimulation.
Journal ArticleDOI
The composition and stability of the faecal microbiota of Merino sheep.
M. A. A. Mamun,M. A. A. Mamun,M. A. A. Mamun,Mark Sandeman,P Rayment,P Brook-Carter,Emily Scholes,N Kasinadhuni,David Piedrafita,David Piedrafita,Andrew R. Greenhill,Andrew R. Greenhill +11 more
TL;DR: To determine the composition and temporal stability of the gut (faecal) microbiota of sheep (Ovis aries), a large number of animals were slaughtered and the gut microbiota of these animals were studied using a simple, straightforward, and straightforward procedure.
Journal ArticleDOI
Feeding Pasteurized Waste Milk to Preweaned Dairy Calves Changes Fecal and Upper Respiratory Tract Microbiota.
TL;DR: Differences in relative abundances of bacterial taxa in gut microbiota were only observed at the phylum level, suggesting that antimicrobial residues present in waste milk have a non-specific influence at a lower taxonomical level.
Journal ArticleDOI
Effect of dietary concentrate to forage ratios on ruminal bacterial and anaerobic fungal populations of cashmere goats
TL;DR: It was found that dietary C:F ratio has a significant impact on the composition of the ruminal bacteria and anaerobic fungal populations of Shaanbei white-cashmere (SWC) goats that were reared under different dietary C-F ratios.
Journal ArticleDOI
Effect of Dietary Supplementation of Moringa Oleifera on the Production Performance and Fecal Methanogenic Community of Lactating Dairy Cows.
TL;DR: The study’s main results suggest that inclusion of Moringa oleifera improved milk fat content and changed the composition and diversity of methanogenic community in lactating cows, and indicates that secondary metabolites from Moreda olifera may regulate fermentation conditions and associations between some methanogens and other microbes.
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