Interspecies commensal interactions have nonlinear impacts on host immunity

Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes

(2021) Evgeny Kiner et al.   NATURE IMMUNOLOGY

Quantifying the effect of experimental perturbations at single-cell resolution

(2021) Daniel B. Burkhardt et al.   NATURE BIOTECHNOLOGY

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila

(2021) Bradford Becken et al.   mBio

Akkermansia muciniphila Exerts Strain-Specific Effects on DSS-Induced Ulcerative Colitis in Mice

(2021) Qing Liu et al.   Frontiers in Cellular and Infection Microbiology

Macroecological dynamics of gut microbiota

(2020) Brian W. Ji et al.   Nature Microbiology

Alterations of Akkermansia muciniphila in the inflammatory bowel disease patients with washed microbiota transplantation

(2020) Ting Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

(2020) Connie W.Y. Ha et al.   CELL

Gut microorganisms act together to exacerbate inflammation in spinal cords

(2020) Eiji Miyauchi et al.   NATURE

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis

(2019) Tomas Castro-Dopico et al.   IMMUNITY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis

(2019) Eduard Ansaldo et al.   SCIENCE

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

Serum Amyloid A Proteins Induce Pathogenic Th17 Cells and Promote Inflammatory Disease

(2019) June-Yong Lee et al.   CELL

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis

(2018) Joel R. Wilmore et al.   Cell Host & Microbe

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Gut microbiota utilize immunoglobulin A for mucosal colonization

(2018) G. P. Donaldson et al.   SCIENCE

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

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

(2018) Mo Xu et al.   NATURE

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity

(2018) Daniel F. Zegarra-Ruiz et al.   Cell Host & Microbe

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homeostatic Immunity and the Microbiota

(2017) Yasmine Belkaid et al.   IMMUNITY

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

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

(2017) Monica Viladomiu et al.   Science Translational Medicine

Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis

(2017) Lukas Bajer et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Mucus organisation is shaped by colonic content; a new view

(2017) J. B. J. Kamphuis et al.   Scientific Reports

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens

(2016) Melody Y. Zeng et al.   IMMUNITY

A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice

(2016) Hubert Plovier et al.   NATURE MEDICINE

Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry

(2016) Kathrin Moor et al.   Nature Protocols

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health

(2015) Jason L. Kubinak et al.   Cell Host & Microbe

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

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model

(2015) Eric M. Brown et al.   Nature Communications

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

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

(2014) Shimpei Kawamoto et al.   IMMUNITY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

(2013) A. Everard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

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

(2011) Daniel McDonald et al.   ISME Journal

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

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake

(2010) Julia Arnds et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

(2008) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA