The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation

(2020) Chao Yang et al.   Cell Host & Microbe

Nitrate from diet might fuel gut microbiota metabolism: Minding the gap between redox signaling and inter-kingdom communication

(2020) Bárbara S. Rocha et al.   FREE RADICAL BIOLOGY AND MEDICINE

The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria

(2020) Chang Liu et al.   Nature Communications

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

(2020) Till R. Lesker et al.   Cell Reports

Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities

(2020) Claudia Eberl et al.   Frontiers in Microbiology

Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer

(2020) Thergiory Irrazabal et al.   Nature Communications

Muribaculum gordoncarteri sp. nov., an anaerobic bacterium from the faeces of C57BL/6J mice

(2020) Sou Miyake et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

(2019) Ilias Lagkouvardos et al.   Microbiome

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota

(2019) Tingting Ju et al.   ISME Journal

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Parasutterella , in association with irritable bowel syndrome and intestinal chronic inflammation

(2018) Yan-Jie Chen et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbiota and reproducibility of rodent models

(2017) Craig L Franklin et al.   LAB ANIMAL

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome

(2017) Mikayla A. Borton et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions

(2017) Jocelyn M. Choo et al.   mSphere

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome

(2016) Jiangwei Yao et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Increased Enterococcus faecalis infection is associated with clinically active Crohn disease

(2016) Youlian Zhou et al.   MEDICINE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mechanisms of inflammation-driven bacterial dysbiosis in the gut

(2016) M Y Zeng et al.   Mucosal Immunology

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

(2016) Jennifer T. Lau et al.   Genome Medicine

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

(2016) Kate L. Ormerod et al.   Microbiome

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

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

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

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

A Multihit Model

(2015) Lydia M. Keubler et al.   INFLAMMATORY BOWEL DISEASES

Towards biome-specific analysis of meta-omics data

(2015) Youssef Darzi et al.   ISME Journal

A comprehensive repertoire of prokaryotic species identified in human beings

(2015) Perrine Hugon et al.   LANCET INFECTIOUS DISEASES

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Insights into the Role of Erysipelotrichaceae in the Human Host

(2015) Nadeem O. Kaakoush   Frontiers in Cellular and Infection Microbiology

Correction: Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions

(2015) Mauro Tiso et al.   PLoS One

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Gut Microbial Metabolism Drives Transformation of Msh2-Deficient Colon Epithelial Cells

(2014) Antoaneta Belcheva et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria

(2014) Conor J. Meehan et al.   Genome Biology and Evolution

Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age

(2014) Jan P. Meier-Kolthoff et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection

(2014) Duy M. Dinh et al.   JOURNAL OF INFECTIOUS DISEASES

Analysis of the Intestinal Lumen Microbiota in an Animal Model of Colorectal Cancer

(2014) Qingchao Zhu et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The role of oxidative stress during inflammatory processes

(2013) Jérôme Lugrin et al.   BIOLOGICAL CHEMISTRY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Nitrate and periplasmic nitrate reductases

(2013) Courtney Sparacino-Watkins et al.   CHEMICAL SOCIETY REVIEWS

High-fat diet alters gut microbiota physiology in mice

(2013) Hannelore Daniel et al.   ISME Journal

Gut Microbiota Composition Modifies Fecal Metabolic Profiles in Mice

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

(2013) Lukasz Krych et al.   PLoS One

Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer

(2013) B. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

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

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

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

(2012) Weiguang Chen et al.   PLoS One

Inflammation Drives Dysbiosis and Bacterial Invasion in Murine Models of Ileal Crohn’s Disease

(2012) Melanie Craven et al.   PLoS One

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

(2012) J. C. Arthur et al.   SCIENCE

Metabolism of Oligosaccharides and Starch in Lactobacilli: A Review

(2012) Michael G. Gänzle et al.   Frontiers in Microbiology

Intestinal antimicrobial peptides during homeostasis, infection, and disease

(2012) Luciana R. Muniz et al.   Frontiers in Immunology

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

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

Klebsiella pneumoniaeincreases the risk of inflammation and colitis in a murine model of intestinal bowel disease

(2011) In-Ah Lee et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Iron Homeostasis and the Inflammatory Response

(2010) Marianne Wessling-Resnick   Annual Review of Nutrition

McKay agar enables routine quantification of the 'Streptococcus milleri' group in cystic fibrosis patients

(2010) C. D. Sibley et al.   JOURNAL OF MEDICAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences