Review: The application of omics to rumen microbiota function

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

(2017) Olov Svartström et al.   ISME Journal

Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge

(2017) S.U. Wetzels et al.   JOURNAL OF DAIRY SCIENCE

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

(2017) Chen Qian et al.   JOURNAL OF PROTEOME RESEARCH

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

(2017) Ilma Tapio et al.   PLoS One

Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats

(2017) Leticia Abecia et al.   PLoS One

Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate

(2017) Camila S. Cunha et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Effect of Dietary Forage to Concentrate Ratios on Dynamic Profile Changes and Interactions of Ruminal Microbiota and Metabolites in Holstein Heifers

(2017) Jun Zhang et al.   Frontiers in Microbiology

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

(2017) Simon Deusch 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

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

(2017) Kees C. H. van der Ark et al.   Microbiome

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

A parts list for fungal cellulosomes revealed by comparative genomics

(2017) Charles H. Haitjema et al.   Nature Microbiology

Enterotypes in the landscape of gut microbial community composition

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

Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture

(2017) Samantha J. Noel et al.   PLoS One

Rumen Fluid Metabolomics Analysis Associated with Feed Efficiency on Crossbred Steers

(2017) Virginia M. Artegoitia et al.   Scientific Reports

Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows

(2016) Dipti W. Pitta et al.   ANAEROBE

Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen

(2016) Takumi Shinkai et al.   ANIMAL SCIENCE JOURNAL

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns

(2016) Emma Timmins-Schiffman et al.   ISME Journal

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

(2016) Lindsey M Solden et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

(2016) Kevin V. Solomon et al.   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

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

(2016) Ilma Tapio et al.   PLoS One

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

(2016) Kim-Anh Lê Cao et al.   PLoS One

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function

(2015) Shengyong Mao et al.   Scientific Reports

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Rumen Microbiome from Steers Differing in Feed Efficiency

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

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

(2014) Xin Dai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2014) Weibing Shi et al.   GENOME RESEARCH

Metabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows

(2014) S. Zhao et al.   LETTERS IN APPLIED MICROBIOLOGY

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

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

(2014) Raphy Zarecki et al.   PLoS Computational Biology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

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

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

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

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

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

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

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

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

The Bovine Ruminal Fluid Metabolome

(2012) Fozia Saleem et al.   Metabolomics

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

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

A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

(2012) Sandra Kittelmann et al.   PLoS One

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

(2012) Phillip B. Pope et al.   PLoS One

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

(2012) Xin Dai et al.   PLoS One

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

(2012) Derrick E. Fouts et al.   PLoS One

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools

(2011) Robert W. Li et al.   ENVIRONMENTAL MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

(2011) Meng Qi et al.   PLoS One

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

(2011) M. Hess et al.   SCIENCE

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Functional Gene Analysis Suggests Different Acetogen Populations in the Bovine Rumen and Tammar Wallaby Forestomach

(2010) E. J. Gagen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novel primers for 16S rRNA-based archaeal community analyses in environmental samples

(2010) Stephan Gantner et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium

(2010) Nikki Kenters et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Isolation and Identification of Cellulose-Binding Proteins from Sheep Rumen Contents

(2009) A. Toyoda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

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

Structure of the Archaeal Community of the Rumen

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