Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet

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

(2016) Takumi Shinkai et al.   ANIMAL SCIENCE JOURNAL

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

(2016) Fuyong Li et al.   Frontiers in Microbiology

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

(2016) Yue Jiang et al.   Microbiome

Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

(2015) M. B. Couger et al.   Biotechnology for Biofuels

Effect of camelina oil or live yeasts (Saccharomyces cerevisiae) on ruminal methane production, rumen fermentation, and milk fatty acid composition in lactating cows fed grass silage diets

(2015) A.R. Bayat et al.   JOURNAL OF DAIRY SCIENCE

The Role of Ciliate Protozoa in the Rumen

(2015) Charles J. Newbold et al.   Frontiers in Microbiology

Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85

(2015) Meagan C. Burnet et al.   PLoS One

Biomass Utilization by Gut Microbiomes

(2014) Bryan A. White et al.   Annual Review of Microbiology

Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. Strain JDR-2

(2014) Neha Sawhney et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Using structure to inform carbohydrate binding module function

(2014) D Wade Abbott et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Saccharide breakdown and fermentation by the honey bee gut microbiome

(2014) Fredrick J. Lee et al.   ENVIRONMENTAL MICROBIOLOGY

Improved culturability of cellulolytic rumen bacteria and phylogenetic diversity of culturable cellulolytic and xylanolytic bacteria newly isolated from the bovine rumen

(2014) Thet Nyonyo et al.   FEMS MICROBIOLOGY ECOLOGY

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

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation?

(2014) A. E. Naas et al.   mBio

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

Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides

(2013) Cherie J. Ziemer   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

(2013) Noha H. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

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

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows

(2013) Lingling Wang et al.   PLoS One

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

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

Abundance and Genetic Diversity of Microbial Polygalacturonase and Pectate Lyase in the Sheep Rumen Ecosystem

(2012) Peng Yuan 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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

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

Cellulosilyticum ruminicola, a Newly Described Rumen Bacterium That Possesses Redundant Fibrolytic-Protein-Encoding Genes and Degrades Lignocellulose with Multiple Carbohydrate- Borne Fibrolytic Enzymes

(2010) S. Cai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptomic Analyses of Xylan Degradation byPrevotella bryantiiand Insights into Energy Acquisition by Xylanolytic Bacteroidetes

(2010) Dylan Dodd et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

(2010) Dylan Dodd et al.   MOLECULAR MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proteomic identification of CBM37-containing cellulases produced by the rumen cellulolytic bacterium Ruminococcus albus 20 and their putative involvement in bacterial adhesion to cellulose

(2009) Harivony Rakotoarivonina et al.   ARCHIVES OF MICROBIOLOGY

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Development of a RT-qPCR method for the quantification of Fibrobacter succinogenes S85 glycoside hydrolase transcripts in the rumen content of gnotobiotic and conventional sheep

(2009) Christel Béra-Maillet et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

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

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion — Review

(2008) Y. Kobayashi et al.   FOLIA MICROBIOLOGICA

Cell Surface Enzyme Attachment Is Mediated by Family 37 Carbohydrate-Binding Modules, Unique to Ruminococcus albus

(2008) A. Ezer et al.   JOURNAL OF BACTERIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH