Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain

Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria

(2022) Nicholas A. Pudlo et al.   mSystems

Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers

(2022) Melissa Dsouza et al.   Cell Host & Microbe

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation

(2021) Simone Becattini et al.   Cell Host & Microbe

The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial

(2021) Dina Kao et al.   Lancet Gastroenterology & Hepatology

Causative Microbes in Host-Microbiome Interactions

(2021) Graham J. Britton et al.   Annual Review of Microbiology

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

(2021) Shuo Han et al.   NATURE

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

(2021) Varun Aggarwala et al.   Nature Microbiology

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

TLR5 participates in the TLR4 receptor complex and promotes MyD88-dependent signaling in environmental lung injury

(2020) Salik Hussain et al.   eLife

A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant

(2020) Jonathan P. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defined microbiota transplant restores Th17/RORγt+regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

(2020) Graham J. Britton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

(2019) Graham J. Britton et al.   IMMUNITY

Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis

(2019) Samuel P. Costello et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Gut microbiota density influences host physiology and is shaped by host and microbial factors

(2019) Eduardo J Contijoch et al.   eLife

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis

(2019) Isabella Lengfelder et al.   Frontiers in Immunology

Microbiota maintain colonic homeostasis by activating TLR2/MyD88/PI3K signaling in IL-10–producing regulatory B cells

(2019) Yoshiyuki Mishima et al.   JOURNAL OF CLINICAL INVESTIGATION

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen

(2018) Karina K. Sanchez et al.   CELL

Applications of Immunomodulatory Immune Synergies to Adjuvant Discovery and Vaccine Development

(2018) Janine K. Tom et al.   TRENDS IN BIOTECHNOLOGY

Safe Recombinant Outer Membrane Vesicles that Display M2e Elicit Heterologous Influenza Protection

(2017) Hannah C. Watkins et al.   MOLECULAR THERAPY

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

(2017) Monica Viladomiu et al.   Science Translational Medicine

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection

(2016) Colleen R. Kelly et al.   ANNALS OF INTERNAL MEDICINE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

(2016) Nicholas Edward Ilott et al.   ISME Journal

Ustekinumab as Induction and Maintenance Therapy for Crohn’s Disease

(2016) Brian G. Feagan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe

(2016) Sena Bae et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Distinct Commensals Induce Interleukin-1β via NLRP3 Inflammasome in Inflammatory Monocytes to Promote Intestinal Inflammation in Response to Injury

(2015) Sang-Uk Seo et al.   IMMUNITY

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria

(2014) Peyman Alavi et al.   BMC GENOMICS

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

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

Fc receptor is not required for inducing antibodies but plays a critical role in conferring protection after influenza M2 vaccination

(2014) Yu-Na Lee et al.   IMMUNOLOGY

Microbiota-Dependent Crosstalk Between Macrophages and ILC3 Promotes Intestinal Homeostasis

(2014) A. Mortha et al.   SCIENCE

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

The dynamics of a family’s gut microbiota reveal variations on a theme

(2014) Patrick D Schloss et al.   Microbiome

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Fecal microbiome transplantation for recurrent Clostridium difficile infection: Report on a case series

(2012) Timothy A. Rubin et al.   ANAEROBE

Environmental conditioning in the control of macrophage thrombospondin-1 production

(2012) Jezrom B. Fordham et al.   Scientific Reports

Treating Clostridium difficile Infection With Fecal Microbiota Transplantation

(2011) Johan S. Bakken et al.   Clinical Gastroenterology and Hepatology

Chronic Intestinal Inflammation Induces Stress-Response Genes in Commensal Escherichia coli

(2011) Laura G. Patwa et al.   GASTROENTEROLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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

Regulation of Adaptive Immunity by the Innate Immune System

(2010) A. Iwasaki et al.   SCIENCE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Functional Modulation of Dendritic Cells and Macrophages by Japanese Encephalitis Virus through MyD88 Adaptor Molecule-Dependent and -Independent Pathways

(2009) A. G. Aleyas et al.   JOURNAL OF IMMUNOLOGY

Signaling Crosstalk during Sequential TLR4 and TLR9 Activation Amplifies the Inflammatory Response of Mouse Macrophages

(2009) D. De Nardo et al.   JOURNAL OF IMMUNOLOGY

Lipoteichoic Acid Induces Unique Inflammatory Responses when Compared to Other Toll-Like Receptor 2 Ligands

(2009) Elizabeth M. Long et al.   PLoS One

Toll-like Receptors Activate Innate and Adaptive Immunity by using Dendritic Cell-Intrinsic and -Extrinsic Mechanisms

(2008) Baidong Hou et al.   IMMUNITY

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE