Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet

Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

(2018) Łukasz Krych et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity

(2018) Eric C. Keen et al.   TRENDS IN MICROBIOLOGY

A human gut phage catalog correlates the gut phageome with type 2 diabetes

(2018) Yingfei Ma et al.   Microbiome

Reproducible protocols for metagenomic analysis of human faecal phageomes

(2018) Andrey N. Shkoporov et al.   Microbiome

Comparing phenotypic variation between inbred and outbred mice

(2018) Alexander H. Tuttle et al.   NATURE METHODS

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome

(2017) Tao Zuo et al.   GUT

The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host

(2017) Qi Sam et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Vendor effects on murine gut microbiota influence experimental abdominal sepsis

(2017) Tobias Hilbert et al.   JOURNAL OF SURGICAL RESEARCH

The Human Gut Phage Community and Its Implications for Health and Disease

(2017) Pilar Manrique et al.   Viruses-Basel

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

(2017) Ilias Lagkouvardos et al.   PeerJ

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Impact of the gut microbiota on rodent models of human disease

(2017) Axel Kornerup Hansen et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime

(2017) Randi Lundberg et al.   Scientific Reports

MetaCoMET: a web platform for discovery and visualization of the core microbiome

(2016) Yi Wang et al.   BIOINFORMATICS

Potential benefits of physical activity during pregnancy for the reduction of gestational diabetes prevalence and oxidative stress

(2016) Marcela Cid et al.   EARLY HUMAN DEVELOPMENT

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Influence of high-fat diet on gut microbiota

(2015) E. Angela Murphy et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

The human gut microbiota and virome: Potential therapeutic implications

(2015) Emidio Scarpellini et al.   DIGESTIVE AND LIVER DISEASE

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

(2015) Adina Howe et al.   ISME Journal

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France)

(2015) Xu Zhong et al.   RESEARCH IN MICROBIOLOGY

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

(2015) Aaron C. Ericsson et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

(2014) Manon D. Schulz et al.   NATURE

Characterization of the gut microbiota in leptin deficient obese mice – Correlation to inflammatory and diabetic parameters

(2014) M. Ellekilde et al.   RESEARCH IN VETERINARY SCIENCE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Bacteriophages: an underestimated role in human and animal health?

(2014) Marianne De Paepe et al.   Frontiers in Cellular and Infection Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome

(2014) Rachel Marine et al.   Microbiome

Altered gut microbiota and activity in a murine model of autism spectrum disorders

(2013) Caroline G.M. de Theije et al.   BRAIN BEHAVIOR AND IMMUNITY

Gut Microbiota Affects Sensitivity to Acute DSS-induced Colitis Independently of Host Genotype

(2013) Brigitta M. Brinkman et al.   INFLAMMATORY BOWEL DISEASES

Gut Microbiota Composition Modifies Fecal Metabolic Profiles in Mice

(2013) Ying Zhao et al.   JOURNAL OF PROTEOME RESEARCH

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse

(2012) C. H. F. Hansen et al.   DIABETOLOGIA

Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity

(2012) Eileen F Murphy et al.   GUT

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Gut Microbiota Composition Is Correlated to Grid Floor Induced Stress and Behavior in the BALB/c Mouse

(2012) Katja Maria Bangsgaard Bendtsen et al.   PLoS One

A composite bacteriophage alters colonization by an intestinal commensal bacterium

(2012) B. A. Duerkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Intestinal Microbiota Affect Central Levels of Brain-Derived Neurotropic Factor and Behavior in Mice

(2011) Premysl Bercik et al.   GASTROENTEROLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice

(2011) M. A. Kriegel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulation of Mucosal Immune Response, Tolerance, and Proliferation in Mice Colonized by the Mucin-Degrader Akkermansia muciniphila

(2011) Muriel Derrien et al.   Frontiers in Microbiology

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity

(2009) Marie A. Hildebrandt et al.   GASTROENTEROLOGY

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology