Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows

Hot topic: Selecting cattle for low residual feed intake did not affect daily methane production but increased methane yield

(2019) H.E. Flay et al.   JOURNAL OF DAIRY SCIENCE

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle

(2019) Beatriz Delgado et al.   Scientific Reports

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

(2019) Fuyong Li et al.   Microbiome

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

(2019) R. John Wallace et al.   Science Advances

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets

(2018) Marc D. Auffret et al.   Frontiers in Microbiology

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

(2018) Florian Plaza Oñate et al.   BIOINFORMATICS

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

(2018) Sharon A. Huws et al.   Frontiers in Microbiology

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

(2018) Gareth Frank Difford et al.   PLoS Genetics

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

(2017) Rebecca Danielsson et al.   Frontiers in Microbiology

The ruminal microbiome associated with methane emissions from ruminant livestock

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

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

(2016) T. Wongnate et al.   SCIENCE

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

(2016) Janine Kamke et al.   Microbiome

Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

(2015) Kelsea A. Jewell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The rumen microbial metagenome associated with high methane production in cattle

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

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

(2015) Paul J. Weimer   Frontiers in Microbiology

Rumen Microbiome from Steers Differing in Feed Efficiency

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

Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

(2015) Matthew Sean McCabe et al.   PLoS One

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

Genome-Wide Regression and Prediction with the BGLR Statistical Package

(2014) P. Perez et al.   GENETICS

Potential Role of the Bovine Rumen Microbiome in Modulating Milk Composition and Feed Efficiency

(2014) Elie Jami et al.   PLoS One

Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep

(2014) Sandra Kittelmann et al.   PLoS One

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries

(2014) Patricio Jeraldo et al.   PLoS One

RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

(2014) Henning Seedorf et al.   PeerJ

Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies

(2013) S. C. Leahy et al.   Animal

Technical options for the mitigation of direct methane and nitrous oxide emissions from livestock: a review

(2013) P. J. Gerber et al.   Animal

Methane emissions from beef and dairy cattle: Quantifying the effect of physiological stage and diet characteristics1

(2013) P. Ricci et al.   JOURNAL OF ANIMAL SCIENCE

Methyl-Coenzyme M Reductase from Methanogenic Archaea: Isotope Effects on the Formation and Anaerobic Oxidation of Methane

(2013) Silvan Scheller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle

(2013) Elizabeth M. Ross et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Methane mitigation in ruminants: from microbe to the farm scale

(2009) C. Martin et al.   Animal

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

integrOmics: an R package to unravel relationships between two omics datasets

(2009) Kim-Anh Lê Cao et al.   BIOINFORMATICS