A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments

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

(2017) Rebecca Danielsson et al.   Frontiers in Microbiology

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification

(2017) Di Jin et al.   Frontiers in Microbiology

Effects of corn silage and grass silage in ruminant rations on diurnal changes of microbial populations in the rumen of dairy cows

(2016) Melanie B. Lengowski et al.   ANAEROBE

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

(2016) Thilo Muth et al.   Expert Review of Proteomics

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

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

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

(2016) Fuyong Li et al.   Frontiers in Microbiology

The impact of sequence database choice on metaproteomic results in gut microbiota studies

(2016) Alessandro Tanca et al.   Microbiome

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

Exploring the Goat Rumen Microbiome from Seven Days to Two Years

(2016) Lizhi Wang et al.   PLoS One

Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota

(2015) Ondrej Polansky 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

Enteric methane production, rumen volatile fatty acid concentrations, and milk fatty acid composition in lactating Holstein-Friesian cows fed grass silage- or corn silage-based diets

(2015) S. van Gastelen et al.   JOURNAL OF DAIRY SCIENCE

Catching the tip of the iceberg - Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota

(2015) Simon Deusch et al.   PROTEOMICS

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

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions

(2015) Katharina Burbach et al.   MicrobiologyOpen

News in livestock research — use of Omics -technologies to study the microbiota in the gastrointestinal tract of farm animals

(2015) Simon Deusch et al.   Computational and Structural Biotechnology Journal

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

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

(2014) Henning Seedorf et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge

(2014) Renee M. Petri et al.   PLoS One

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

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

Determining the culturability of the rumen bacterial microbiome

(2014) Christopher J. Creevey et al.   Microbial Biotechnology

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative Analysis of Microbial Profiles in Cow Rumen Fed with Different Dietary Fiber by Tagged 16S rRNA Gene Pyrosequencing

(2013) Honglada Thoetkiattikul et al.   CURRENT MICROBIOLOGY

Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing

(2013) Amélia Camarinha-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

Effect of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines in dairy cows

(2013) Ruiyang Zhang et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Metaproteome analysis of the microbial communities in agricultural biogas plants

(2013) R. Heyer et al.   New Biotechnology

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

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

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

(2013) Jana Seifert et al.   PROTEOMICS

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

Diversity of gut methanogens in herbivorous animals

(2012) B. St-Pierre et al.   Animal

Comparative Survey of Rumen Microbial Communities and Metabolites across One Caprine and Three Bovine Groups, Using Bar-Coded Pyrosequencing and1H Nuclear Magnetic Resonance Spectroscopy

(2012) Hyo Jung Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

(2012) Ciara A. Carberry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

‘Omics’ of the mammalian gut – new insights into function

(2012) Regina Lamendella et al.   CURRENT OPINION IN BIOTECHNOLOGY

Effect of diet and absence of protozoa on the rumen microbial community and on the representativeness of bacterial fractions used in the determination of microbial protein synthesis1

(2012) A. Belanche et al.   JOURNAL OF ANIMAL SCIENCE

A metabolomics approach to uncover the effects of grain diets on rumen health in dairy cows

(2012) F. Saleem et al.   JOURNAL OF DAIRY SCIENCE

Effects of feeding Mediterranean buffalo sorghum silage versus maize silage on the rumen microbiota and milk fatty acid content

(2012) Sharon Ann Huws et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

The Bovine Ruminal Fluid Metabolome

(2012) Fozia Saleem et al.   Metabolomics

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

(2012) Elie Jami et al.   PLoS One

Functional Metagenomics Unveils a Multifunctional Glycosyl Hydrolase from the Family 43 Catalysing the Breakdown of Plant Polymers in the Calf Rumen

(2012) Manuel Ferrer et al.   PLoS One

Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

(2011) Yohei Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Microbiome analysis of dairy cows fed pasture or total mixed ration diets

(2011) Alexandre B. de Menezes et al.   FEMS MICROBIOLOGY ECOLOGY

Status of the phylogenetic diversity census of ruminal microbiomes

(2011) Minseok Kim et al.   FEMS MICROBIOLOGY ECOLOGY

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

RUMINANT NUTRITION SYMPOSIUM: Productivity, digestion, and health responses to hindgut acidosis in ruminants1

(2011) T. F. Gressley et al.   JOURNAL OF ANIMAL SCIENCE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet

(2010) S. C. Fernando et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively

(2010) E. Salvetti et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Cadaverine Covalently Linked to Peptidoglycan Is Required for Interaction between the Peptidoglycan and the Periplasm-Exposed S-Layer-Homologous Domain of Major Outer Membrane Protein Mep45 in Selenomonas ruminantium

(2010) S. Kojima et al.   JOURNAL OF BACTERIOLOGY

Invited review: Ruminant ecology and evolution: Perspectives useful to ruminant livestock research and production

(2010) T.J. Hackmann et al.   JOURNAL OF DAIRY SCIENCE

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

(2010) Karuna Chourey et al.   JOURNAL OF PROTEOME RESEARCH

Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows

(2010) Burim N. Ametaj et al.   Metabolomics

Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

Rumen Bacterial Diversity Dynamics Associated with Changing from Bermudagrass Hay to Grazed Winter Wheat Diets

(2009) Dipti W. Pitta et al.   MICROBIAL ECOLOGY

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea

(2008) Yuchen Liu et al.   Annals of the New York Academy of Sciences

Structure of the Archaeal Community of the Rumen

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

Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses

(2008) H. Morita et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)

(2008) Nico Jehmlich et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Quantitative metabolomics using NMR

(2008) David S. Wishart   TRAC-TRENDS IN ANALYTICAL CHEMISTRY