Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

(2019) Fuyong Li et al.   Microbiome

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens

(2019) Chaoliang Wen et al.   ISME Journal

Assessment of rumen bacteria in dairy cows with varied milk protein yield

(2019) M.Y. Xue et al.   JOURNAL OF DAIRY SCIENCE

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

Symposium review: Host–rumen microbe interactions may be leveraged to improve the productivity of dairy cows

(2018) D.M. Bickhart et al.   JOURNAL OF DAIRY SCIENCE

Serum metabolome profiling revealed potential biomarkers for milk protein yield in dairy cows

(2018) Xuehui Wu et al.   Journal of Proteomics

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Rumen-protected B vitamin complex supplementation during the transition period and early lactation alters endometrium mRNA expression on day 14 of gestation in lactating dairy cows

(2018) Manveen Kaur et al.   JOURNAL OF DAIRY SCIENCE

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

(2018) Gareth Frank Difford et al.   PLoS Genetics

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

(2017) Amelia Camarinha-Silva et al.   GENETICS

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

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

(2017) Amelia Camarinha-Silva et al.   GENETICS

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

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

Riboflavin transport and metabolism in humans

(2016) Maria Barile et al.   JOURNAL OF INHERITED METABOLIC DISEASE

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

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

The rumen microbial metagenome associated with high methane production in cattle

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

Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model

(2015) Sheng-Yong Mao et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolomics of Four Biofluids from Dairy Cows: Potential Biomarkers for Milk Production and Quality

(2015) Hui-Zeng Sun et al.   JOURNAL OF PROTEOME RESEARCH

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Bacterial Flagella: Twist and Stick, or Dodge across the Kingdoms

(2015) Yannick Rossez et al.   PLoS Pathogens

Rumen Microbiome from Steers Differing in Feed Efficiency

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

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

(2014) Weibing Shi et al.   GENOME RESEARCH

Short communication: Genetic relationships between claw disorders, protein yield, and somatic cell score by days in milk

(2014) E. Gernand et al.   JOURNAL OF DAIRY SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Effects of management practices on yield and quality of milk from smallholder dairy units in urban and peri-urban Morogoro, Tanzania

(2014) Kejeri A. Gillah et al.   TROPICAL ANIMAL HEALTH AND PRODUCTION

Associations between herd-level feeding management practices, feed sorting, and milk production in freestall dairy farms

(2013) A.D. Sova et al.   JOURNAL OF DAIRY SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Effect of biotin on milk performance of dairy cattle: A meta-analysis1

(2011) B. Chen et al.   JOURNAL OF DAIRY SCIENCE

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

MetPA: a web-based metabolomics tool for pathway analysis and visualization

(2010) J. Xia et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

(2010) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Food consumption trends and drivers

(2010) J. Kearney   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

Biotin

(2009) Janos Zempleni et al.   BIOFACTORS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Plant Cell Wall Breakdown by Anaerobic Microorganisms from the Mammalian Digestive Tract

(2008) Harry J. Flint et al.   Annals of the New York Academy of Sciences

Advances in separation science applied to metabonomics

(2008) Li Xiayan et al.   ELECTROPHORESIS