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

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

(2017) Amelia Camarinha-Silva et al.   GENETICS

Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows

(2017) M. Schären et al.   JOURNAL OF DAIRY SCIENCE

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

(2017) Amelia Camarinha-Silva et al.   GENETICS

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

Medicinal herbs as a potential strategy to decrease methane production by rumen microbiota: a systematic evaluation with a focus on Perilla frutescens seed extract

(2016) Jiakun Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Interchangeability between methane measurements in dairy cows assessed by comparing precision and agreement of two non-invasive infrared methods

(2016) G.F. Difford et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits

(2016) Yuliaxis Ramayo-Caldas et al.   ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

(2016) Lindsey M Solden et al.   ISME Journal

Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle12

(2016) K. A. Donoghue et al.   JOURNAL OF ANIMAL SCIENCE

Heritability estimates for enteric methane emissions from Holstein cattle measured using noninvasive methods

(2016) Jan Lassen et al.   JOURNAL OF DAIRY SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Measuring Methane Production from Ruminants

(2016) Julian Hill et al.   TRENDS IN BIOTECHNOLOGY

Genetic and genomic relationship between methane production measured in breath and fatty acid content in milk samples from Danish Holsteins

(2016) J. Lassen et al.   Animal Production 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

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

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

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

Genetic and environmental control of host-gut microbiota interactions

(2015) Elin Org et al.   GENOME RESEARCH

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows

(2014) Fabio S. Lima et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

(2014) Guillaume Borrel et al.   BMC GENOMICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Rethinking “Enterotypes”

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

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

(2014) Weibing Shi et al.   GENOME RESEARCH

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

(2014) Alejandro Caro-Quintero et al.   ISME Journal

Invited review: Enteric methane in dairy cattle production: Quantifying the opportunities and impact of reducing emissions

(2014) J.R. Knapp et al.   JOURNAL OF DAIRY SCIENCE

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

(2014) Sandra Kittelmann et al.   PLoS One

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

Low-methane yield sheep have smaller rumens and shorter rumen retention time

(2013) John P. Goopy et al.   BRITISH JOURNAL OF NUTRITION

SPECIAL TOPICS — Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options1

(2013) A. N. Hristov et al.   JOURNAL OF ANIMAL SCIENCE

Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata

(2013) Takao Iino et al.   MICROBES AND ENVIRONMENTS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

(2012) Elizabeth M Ross et al.   BMC GENETICS

Factors associated with ruminal pH at herd level

(2012) T. Geishauser et al.   JOURNAL OF DAIRY SCIENCE

Accuracy of noninvasive breath methane measurements using Fourier transform infrared methods on individual cows

(2012) J. Lassen 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

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The Chimeric Genome of Sphaerochaeta: Nonspiral Spirochetes That Break with the Prevalent Dogma in Spirochete Biology

(2012) A. Caro-Quintero et al.   mBio

Chimpanzees and humans harbour compositionally similar gut enterotypes

(2012) Andrew H. Moeller et al.   Nature Communications

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages

(2010) Yunhong Kong et al.   FEMS MICROBIOLOGY ECOLOGY

Mitigation of enteric methane emissions through improving efficiency of energy utilization and productivity in lactating dairy cows

(2010) T. Yan et al.   JOURNAL OF DAIRY SCIENCE

Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents1

(2010) P.J. Weimer et al.   JOURNAL OF DAIRY SCIENCE

Methane and carbon dioxide ratio in excreted air for quantification of the methane production from ruminants

(2010) J. Madsen et al.   Livestock Science

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Structure of the Archaeal Community of the Rumen

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

Redirecting rumen fermentation to reduce methanogenesis

(2008) T. A. McAllister et al.   Australian journal of experimental agriculture