Diversity and functions of the sheep faecal microbiota: a multi-omic characterization

High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity

(2016) Emmanuel Denou et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

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

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

(2015) Sandra Kittelmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing

(2015) Shuai Peng et al.   JOURNAL OF APPLIED GENETICS

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

(2015) S. J. Yaung et al.   Molecular Systems Biology

Emergence of azole-resistant Candida albicans in small ruminants

(2015) R. S. N. Brilhante et al.   MYCOPATHOLOGIA

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

(2015) Alessandro Tanca et al.   PROTEOMICS

Flagellar motility of the pathogenic spirochetes

(2015) Charles W. Wolgemuth   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis

(2015) Yan Zeng et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

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

(2015) Shengyong Mao et al.   Scientific Reports

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

(2015) Brett Wagner Mackenzie et al.   Frontiers in Microbiology

Rumen microbial communities influence metabolic phenotypes in lambs

(2015) Diego P. Morgavi et al.   Frontiers in Microbiology

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

(2015) Marcia L. Hart et al.   PLoS One

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

(2014) Weibing Shi et al.   GENOME RESEARCH

In VitroReassembly of the Ribose ATP-binding Cassette Transporter Reveals a Distinct Set of Transport Complexes

(2014) Matthew C. Clifton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae

(2014) T. Castro-Carrera et al.   JOURNAL OF DAIRY SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

(2014) Gabriel de la Fuente et al.   PLoS One

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

(2013) F. Kohrs et al.   ANAEROBE

New aspects and strategies for methane mitigation from ruminants

(2013) Sanjay Kumar et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The ability of rumen ciliates, Eudiplodinium maggii, Diploplastron affine, and Entodinium caudatum, to use the murein saccharides

(2013) G. Belzecki et al.   FOLIA MICROBIOLOGICA

Investigation of bacterial diversity in the feces of cattle fed different diets1

(2013) M. Kim et al.   JOURNAL OF ANIMAL SCIENCE

Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans

(2013) Elsa Petit et al.   PLoS One

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

(2013) Tomáš Větrovský et al.   PLoS One

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of theEscherichia coliproteome

(2013) Alessandro Tanca et al.   PROTEOMICS

Methanogens and Methanogenesis in the Rumens and Ceca of Lambs Fed Two Different High-Grain-Content Diets

(2012) M. Popova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations

(2011) Orin C. Shanks et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

As yet uncultured bacteria phylogenetically classified asPrevotella,Lachnospiraceaeincertae sedis and unclassifiedBacteroidales,ClostridialesandRuminococcaceaemay play a predominant role in ruminal biohydrogenation

(2011) Sharon A. Huws et al.   ENVIRONMENTAL MICROBIOLOGY

Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State

(2011) M. L. Oldham et al.   SCIENCE

Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle

(2010) L. M. Durso et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A Multitask ATPase Serving Different ABC-Type Sugar Importers in Bacillus subtilis

(2010) M. J. Ferreira et al.   JOURNAL OF BACTERIOLOGY

Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach

(2010) Lisa M. Durso et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME BIOLOGY

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

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

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Butyrate modulates oxidative stress in the colonic mucosa of healthy humans

(2008) Henrike M. Hamer et al.   CLINICAL NUTRITION

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH