Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

Assessing the impact of protein extraction methods for human gut metaproteomics

(2018) Xu Zhang et al.   Journal of Proteomics

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

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

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria

(2017) Rosalind A. Gilbert et al.   Frontiers in Microbiology

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson 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

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

(2016) Benjamin Bolduc et al.   ISME Journal

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

(2016) Lindsey M Solden et al.   ISME Journal

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

(2016) Rebecca A. Daly et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Exploring the sheep rumen microbiome for carbohydrate-active enzymes

(2015) Lucas Dantas Lopes et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

The rumen microbial metagenome associated with high methane production in cattle

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

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

(2015) Konstantinos T. Konstantinidis et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803

(2014) Antje Kabisch et al.   ISME Journal

Simultaneous UPLC–MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats

(2014) Katheryn M. Goodrich et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

(2014) Johan Larsbrink et al.   NATURE

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation?

(2014) A. E. Naas et al.   mBio

Determining the culturability of the rumen bacterial microbiome

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

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

(2012) Henrik Aspeborg et al.   BMC EVOLUTIONARY BIOLOGY

Glycan recognition by the Bacteroidetes Sus-like systems

(2012) David N Bolam et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2011) M. Hess et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Revisions of Rump Fat and Body Scoring Indices for Deer, Elk, and Moose

(2010) Rachel C. Cook et al.   JOURNAL OF WILDLIFE MANAGEMENT

Structure of a SusD Homologue, BT1043, Involved in MucinO-Glycan Utilization in a Prominent Human Gut Symbiont†,‡

(2009) Nicole Koropatkin et al.   BIOCHEMISTRY

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

(2009) Kendle M. Maslowski et al.   NATURE

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

Advances in microbial ecosystem concepts and their consequences for ruminant agriculture

(2008) J. E. Edwards et al.   Animal

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe