Understanding immune–microbiota interactions in the intestine

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

(2019) Edoardo Pasolli et al.   CELL

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

Healthy infants harbor intestinal bacteria that protect against food allergy

(2019) Taylor Feehley et al.   NATURE MEDICINE

Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis

(2019) Mark S. Ladinsky et al.   SCIENCE

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

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

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

(2019) Takeshi Tanoue et al.   NATURE

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

(2019) Julie Schulthess et al.   IMMUNITY

A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult

(2019) Ziad Al Nabhani et al.   IMMUNITY

Commensal Candida albicans Positively Calibrates Systemic Th17 Immunological Responses

(2019) Tzu-Yu Shao et al.   Cell Host & Microbe

Communication Between the Microbiota and Mammalian Immunity

(2018) Kyla S. Ost et al.   Annual Review of Microbiology

Commensal Koch's postulates: establishing causation in human microbiota research

(2018) B Anne Neville et al.   CURRENT OPINION IN MICROBIOLOGY

Defining the Impact of Host Genotypes on Microbiota Composition Requires Meticulous Control of Experimental Variables

(2018) Andy Wullaert et al.   IMMUNITY

Culturing the human microbiota and culturomics

(2018) Jean-Christophe Lagier et al.   NATURE REVIEWS MICROBIOLOGY

c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

(2018) Mo Xu et al.   NATURE

Modeling Human Digestive Diseases With CRISPR-Cas9–Modified Organoids

(2018) Masayuki Fujii et al.   GASTROENTEROLOGY

l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans

(2018) Robert A. Koeth et al.   JOURNAL OF CLINICAL INVESTIGATION

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition

(2017) Michail Mamantopoulos et al.   IMMUNITY

Moving beyond microbiome-wide associations to causal microbe identification

(2017) Neeraj K. Surana et al.   NATURE

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

(2017) Egle Cekanaviciute et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice

(2017) Kerstin Berer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural polyreactive IgA antibodies coat the intestinal microbiota

(2017) Jeffrey J. Bunker et al.   SCIENCE

Lactobacillus reuteriinduces gut intraepithelial CD4+CD8αα+T cells

(2017) Luisa Cervantes-Barragan et al.   SCIENCE

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

(2017) Monica Viladomiu et al.   Science Translational Medicine

The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition

(2017) Paul Lemire et al.   Cell Reports

The gut mycobiome of the Human Microbiome Project healthy cohort

(2017) Andrea K. Nash et al.   Microbiome

Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome

(2016) Aleksey Chudnovskiy et al.   CELL

Gut Microbial Metabolites Fuel Host Antibody Responses

(2016) Myunghoo Kim et al.   Cell Host & Microbe

Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response

(2016) Tiffany A. Reese et al.   Cell Host & Microbe

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study ParticipantsNovelty and Significance

(2016) Tanika N. Kelly et al.   CIRCULATION RESEARCH

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

(2016) Hilary P. Browne et al.   NATURE

The microbiota in adaptive immune homeostasis and disease

(2016) Kenya Honda et al.   NATURE

Normalizing the environment recapitulates adult human immune traits in laboratory mice

(2016) Lalit K. Beura et al.   NATURE

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice

(2016) Tze Guan Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

(2016) L. V. Blanton et al.   SCIENCE

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition

(2016) V. E. Wagner et al.   Science Translational Medicine

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways

(2016) Jian Tan et al.   Cell Reports

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community

(2015) Meghan Wymore Brand et al.   ILAR JOURNAL

Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A

(2015) Jeffrey J. Bunker et al.   IMMUNITY

Growth and host interaction of mouse segmented filamentous bacteria in vitro

(2015) Pamela Schnupf et al.   NATURE

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Individual intestinal symbionts induce a distinct population of ROR + regulatory T cells

(2015) E. Sefik et al.   SCIENCE

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy

(2015) Andrew L. Kau et al.   Science Translational Medicine

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Sphingolipids from a Symbiotic Microbe Regulate Homeostasis of Host Intestinal Natural Killer T Cells

(2014) Dingding An et al.   CELL

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

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

Foxp3+ T Cells Regulate Immunoglobulin A Selection and Facilitate Diversification of Bacterial Species Responsible for Immune Homeostasis

(2014) Shimpei Kawamoto et al.   IMMUNITY

Mining the Human Gut Microbiota for Effector Strains that Shape the Immune System

(2014) Philip P. Ahern et al.   IMMUNITY

An enteric virus can replace the beneficial function of commensal bacteria

(2014) Elisabeth Kernbauer et al.   NATURE

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

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

Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

(2013) Julia Cahenzli et al.   Cell Host & Microbe

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

(2013) M. I. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Host Specificity of Bacterial Pathogens

(2013) A. Baumler et al.   Cold Spring Harbor Perspectives in Medicine

The effects of intestinal microbial community structure on disease manifestation in IL-10-/- mice infected with Helicobacter hepaticus

(2013) Nabeetha A Nagalingam et al.   Microbiome

The Microbiome in Infectious Disease and Inflammation

(2012) Kenya Honda et al.   Annual Review of Immunology

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

(2012) Hachung Chung et al.   CELL

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

(2012) J. C. Arthur et al.   SCIENCE

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Commensal Bacteroides Species Induce Colitis in Host-Genotype-Specific Fashion in a Mouse Model of Inflammatory Bowel Disease

(2011) Seth M. Bloom et al.   Cell Host & Microbe

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Lactobacillus reuteri promotes Helicobacter hepaticus-associated typhlocolitis in gnotobiotic B6.129P2-IL-10tm1Cgn (IL-10−/−) mice

(2011) Mark T. Whary et al.   IMMUNOLOGY

TLR5-Deficient Mice Lack Basal Inflammatory and Metabolic Defects but Exhibit Impaired CD4 T Cell Responses to a Flagellated Pathogen

(2011) S. E. Letran et al.   JOURNAL OF IMMUNOLOGY

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

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

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells

(2010) Hsin-Jung Wu et al.   IMMUNITY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis

(2010) Y. K. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME BIOLOGY

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

(2009) Valérie Gaboriau-Routhiau et al.   IMMUNITY

Induction of Persistent Colitis by a Human Commensal, Enterotoxigenic Bacteroides fragilis, in Wild-Type C57BL/6 Mice

(2009) K.-J. Rhee et al.   INFECTION AND IMMUNITY

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

(2009) Shaoguang Wu et al.   NATURE MEDICINE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

(2008) Ivaylo I. Ivanov et al.   Cell Host & Microbe

ATP drives lamina propria TH17 cell differentiation

(2008) Koji Atarashi et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY