Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation

Propionic Acid Promotes the Virulent Phenotype of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli

(2020) Michael J. Ormsby et al.   Cell Reports

Short Chain Fatty Acids Modulate the Growth and Virulence of Pathosymbiont Escherichia coli and Host Response

(2020) Shiying Zhang et al.   Antibiotics-Basel

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

(2019) Julie Schulthess et al.   IMMUNITY

Yersiniabactin producing AIEC promote inflammation-associated fibrosis in gnotobiotic Il10-/- mice

(2019) Melissa Ellermann et al.   INFECTION AND IMMUNITY

Metabolite-Sensing Receptor Ffar2 Regulates Colonic Group 3 Innate Lymphoid Cells and Gut Immunity

(2019) Eunyoung Chun et al.   IMMUNITY

Dietary l-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut

(2019) Sho Kitamoto et al.   Nature Microbiology

Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B12-Dependent and Glycyl Radical Enzymes

(2018) Benjamin J. Levin et al.   BIOCHEMISTRY

Critical Role for the Microbiota in CX 3 CR1 + Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses

(2018) Myunghoo Kim et al.   IMMUNITY

The Pore-Forming Protein Gasdermin D Regulates Interleukin-1 Secretion from Living Macrophages

(2018) Charles L. Evavold et al.   IMMUNITY

IL-1β activation in response to Staphylococcus aureus lung infection requires inflammasome-dependent and independent mechanisms

(2018) Sílvia Pires et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Microbial metabolite sensor GPR43 controls severity of experimental GVHD

(2018) Hideaki Fujiwara et al.   Nature Communications

Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase

(2017) Ricardo Axayacatl Gonzalez-Garcia et al.   Microbial Cell Factories

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

IgA-coatedE. colienriched in Crohn’s disease spondyloarthritis promote TH17-dependent inflammation

(2017) Monica Viladomiu et al.   Science Translational Medicine

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis

(2017) Franziska Faber et al.   PLoS Pathogens

Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring

(2016) Shelly A. Buffington et al.   CELL

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

(2016) Claire L O'Brien et al.   GUT

Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism

(2016) Thomas C. Fung et al.   IMMUNITY

Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome

(2015) Laurence Macia et al.   Nature Communications

IL-10-producing CD4+ T cells negatively regulate fucosylation of epithelial cells in the gut

(2015) Yoshiyuki Goto et al.   Scientific Reports

Intestinal Monocyte-Derived Macrophages Control Commensal-Specific Th17 Responses

(2015) Casandra Panea et al.   Cell Reports

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Induction of Bacterial Antigen-Specific Colitis by a Simplified Human Microbiota Consortium in Gnotobiotic Interleukin-10-/- Mice

(2014) C. S. Eun et al.   INFECTION AND IMMUNITY

Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation

(2014) Belgin Dogan et al.   INFLAMMATORY BOWEL DISEASES

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Inhibition of Fucosylation Reshapes Inflammatory Macrophages and Suppresses Type II Collagen-Induced Arthritis

(2014) Jun Li et al.   Arthritis & Rheumatology

Intestinal lamina propria dendritic cells maintain T cell homeostasis but do not affect commensalism

(2013) Nathan E. Welty et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX3CR1hi cells

(2013) Gretchen E. Diehl et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

(2013) S. E. Winter et al.   SCIENCE

Interleukin 23 Production by Intestinal CD103+CD11b+ Dendritic Cells in Response to Bacterial Flagellin Enhances Mucosal Innate Immune Defense

(2012) Melissa A. Kinnebrew et al.   IMMUNITY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crohn disease–associated adherent-invasive E. coli bacteria target mouse and human Peyer’s patches via long polar fimbriae

(2011) Benoit Chassaing et al.   JOURNAL OF CLINICAL INVESTIGATION

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease

(2010) Dermot P.B. McGovern et al.   HUMAN MOLECULAR GENETICS

AP-1 Activated by Toll-like Receptors Regulates Expression of IL-23 p19

(2009) Weicheng Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cutting Edge: IL-23 Receptor GFP Reporter Mice Reveal Distinct Populations of IL-17-Producing Cells

(2009) Amit Awasthi et al.   JOURNAL OF IMMUNOLOGY

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

(2009) Kendle M. Maslowski et al.   NATURE

T cell transfer model of chronic colitis: concepts, considerations, and tricks of the trade

(2008) Dmitry V. Ostanin et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY