Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses

Metatranscriptome of the Oral Microbiome in Health and Disease

(2018) J. Solbiati et al.   JOURNAL OF DENTAL RESEARCH

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut

(2018) Floor Hugenholtz et al.   PLoS One

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

(2018) Matthew L. Jenior et al.   mSphere

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism

(2018) Sarah Just et al.   Microbiome

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

(2017) Matthew C. Hibberd et al.   Science Translational Medicine

Community characteristics of the gut microbiomes of competitive cyclists

(2017) Lauren M. Petersen et al.   Microbiome

Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine

(2017) Xuejian Xiong et al.   Microbiome

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer

(2017) Scott G. Daniel et al.   mSystems

Genetic deletion of the bacterial sensor NOD2 improves murine Crohn’s disease-like ileitis independent of functional dysbiosis

(2016) D Corridoni et al.   Mucosal Immunology

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males

(2016) Shih-Wei Lee et al.   PLoS One

Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression

(2015) Ana E. Duran-Pinedo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

(2015) Dennis Versluis et al.   Scientific Reports

Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis

(2015) Susan Yost et al.   Genome Medicine

Microbiota diversity and gene expression dynamics in human oral biofilms

(2014) Alfonso Benítez-Páez et al.   BMC GENOMICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

Gene expression of lactobacilli in murine forestomach biofilms

(2014) Clarissa Schwab et al.   Microbial Biotechnology

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active Players

(2013) Luke K. Ursell et al.   Cell Metabolism

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

(2012) David Berry et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

(2012) Xuejian Xiong et al.   PLoS One

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

(2010) C. C. G. M. Booijink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge

(2010) Shaomei He et al.   ENVIRONMENTAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

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

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS