A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed

(2017) Goor Sasson et al.   mBio

The ruminal microbiome associated with methane emissions from ruminant livestock

(2017) Ilma Tapio et al.   Journal of Animal Science and Biotechnology

Non-invasive individual methane measurement in dairy cows

(2016) E. Negussie et al.   Animal

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle1

(2016) B. J. Hayes et al.   JOURNAL OF ANIMAL SCIENCE

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

(2016) Rainer Roehe et al.   PLoS Genetics

The rumen microbial metagenome associated with high methane production in cattle

(2015) R. John Wallace et al.   BMC GENOMICS

Comparison of methods to determine methane emissions from dairy cows in farm conditions

(2015) P. Huhtanen et al.   JOURNAL OF DAIRY SCIENCE

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

(2015) Gemma Henderson et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

The Role of Ciliate Protozoa in the Rumen

(2015) Charles J. Newbold et al.   Frontiers in Microbiology

Manipulating rumen microbiome and fermentation through interventions during early life: a review

(2015) David R. Yáñez-Ruiz et al.   Frontiers in Microbiology

Rumen microbial communities influence metabolic phenotypes in lambs

(2015) Diego P. Morgavi et al.   Frontiers in Microbiology

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Rumen Microbiome from Steers Differing in Feed Efficiency

(2015) Phillip R. Myer et al.   PLoS One

Oral Administration of Faecalibacterium prausnitzii Decreased the Incidence of Severe Diarrhea and Related Mortality Rate and Increased Weight Gain in Preweaned Dairy Heifers

(2015) Carla Foditsch et al.   PLoS One

Hydrogen and methane emissions from beef cattle and their rumen microbial community vary with diet, time after feeding and genotype

(2014) John A. Rooke et al.   BRITISH JOURNAL OF NUTRITION

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Anaerobic fungi (phylumNeocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential

(2014) Robert J. Gruninger et al.   FEMS MICROBIOLOGY ECOLOGY

Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

(2014) Christian Koetschan et al.   PLoS One

Estimation of dry matter intake by n-alkanes in dairy cows fed TMR: effect of dosing technique and faecal collection time

(2014) P. Bani et al.   Animal Production Science

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Variation among individual dairy cows in methane measurements made on farm during milking

(2012) P.C. Garnsworthy et al.   JOURNAL OF DAIRY SCIENCE

On-farm methane measurements during milking correlate with total methane production by individual dairy cows

(2012) P.C. Garnsworthy et al.   JOURNAL OF DAIRY SCIENCE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis

(2011) D. V. ZAYKIN   JOURNAL OF EVOLUTIONARY BIOLOGY

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs

(2010) David R. Yáñez-Ruiz et al.   FEMS MICROBIOLOGY ECOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-Term Monensin Supplementation Does Not Significantly Affect the Quantity or Diversity of Methanogens in the Rumen of the Lactating Dairy Cow

(2008) S. E. Hook et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structure of the Archaeal Community of the Rumen

(2008) P. H. Janssen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii

(2008) Carlett Ramirez-Farias et al.   BRITISH JOURNAL OF NUTRITION