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

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau

(2016) Ya-Qin Wei et al.   ANAEROBE

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

(2016) Matthew H. Foley et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

(2016) Lizi Bensoussan et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

(2016) Connor T Skennerton et al.   ISME Journal

Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract

(2016) Cedric C. Laczny et al.   Frontiers in Microbiology

The rumen microbial metagenome associated with high methane production in cattle

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

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

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

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii

(2015) Xiaolei Ze et al.   mBio

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

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

A Polysaccharide Utilization Locus from an Uncultured Bacteroidetes Phylotype Suggests Ecological Adaptation and Substrate Versatility

(2014) A. K. Mackenzie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of hemicellulolytic enzyme mixtures for plant biomass deconstruction on target biotechnological applications

(2014) Rosana Goldbeck et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet

(2014) Dishita D. Patel et al.   GENE

High-Throughput DNA Sequencing of the Ruminal Bacteria from Moose (Alces alces) in Vermont, Alaska, and Norway

(2014) Suzanne L. Ishaq et al.   MICROBIAL ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains

(2014) Bareket Dassa et al.   PLoS One

Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs

(2014) Emma Ransom-Jones et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

How do gut microbes break down dietary fiber?

(2014) Nicolas Terrapon et al.   TRENDS IN BIOCHEMICAL SCIENCES

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation?

(2014) A. E. Naas et al.   mBio

Monitoring the rumen pectinolytic bacteriaTreponema saccharophilumusing real-time PCR

(2013) Jing Liu et al.   FEMS MICROBIOLOGY ECOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

(2013) D. P. R. Herlemann et al.   mBio

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Molecular Diversity of Methanogens in Fecal Samples From Captive Sumatran Orangutans (Pongo abelii)

(2012) HANNAH V. FACEY et al.   AMERICAN JOURNAL OF PRIMATOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

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

(2012) Henrik Aspeborg et al.   BMC EVOLUTIONARY BIOLOGY

Insight into the bacterial gut microbiome of the North American moose (Alces alces)

(2012) Suzanne L Ishaq et al.   BMC MICROBIOLOGY

A biomolecular isolation framework for eco-systems biology

(2012) Hugo Roume et al.   ISME Journal

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

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

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

(2011) G. Suen et al.   JOURNAL OF BACTERIOLOGY

The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist

(2011) Garret Suen et al.   PLoS One

Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

(2011) J. L. A. Bras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

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

(2011) M. Hess et al.   SCIENCE

Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions, as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis

(2010) M. Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional Annotation of Fibrobacter succinogenes S85 Carbohydrate Active Enzymes

(2010) Phillip Brumm et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Mining metagenomes for novel cellulase genes

(2010) Cheng-Jie Duan et al.   BIOTECHNOLOGY LETTERS

Variability of treponemes in the rumen of ruminants

(2010) L. Sikorová et al.   FOLIA MICROBIOLOGICA

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

(2010) Sinead C. Leahy et al.   PLoS One

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

(2010) P. B. Pope et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for a novel mechanism of microbial cellulose degradation

(2009) David B. Wilson   CELLULOSE

Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

(2009) Margret E. Berg Miller et al.   PLoS One

Noncellulosomal cohesin- and dockerin-like modules in the three domains of life

(2008) Ayelet Peer et al.   FEMS MICROBIOLOGY LETTERS

Degradation of forage chicory by ruminal fibrolytic bacteria

(2008) X.Z. Sun et al.   JOURNAL OF APPLIED MICROBIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE