Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis

A pilot integrative analysis of colonic gene expression, gut microbiota and immune infiltration in primary sclerosing cholangitis-inflammatory bowel disease: association of disease with bile acid pathways

(2020) Mohammed Nabil Quraishi et al.   Journal of Crohns & Colitis

Microbial butyrate synthesis indicates therapeutic efficacy of azathioprine in IBD patients

(2020) M Effenberger et al.   Journal of Crohns & Colitis

Metabolic and Innate Immune Cues Merge into a Specific Inflammatory Response via the UPR

(2019) Denis A. Mogilenko et al.   CELL

Immune effects of glycolysis or oxidative phosphorylation metabolic pathway in protecting against bacterial infection

(2019) Yan Li et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients with Inflammatory Bowel Diseases

(2019) Konrad Aden et al.   GASTROENTEROLOGY

Composition of the Intestinal Microbiota Determines the Outcome of Virus-Triggered Colitis in Mice

(2019) Silvia Bolsega et al.   Frontiers in Immunology

The still uncertain identity of the channel-forming unit(s) of the mitochondrial permeability transition pore

(2018) Christopher P. Baines et al.   CELL CALCIUM

Sex-based Differences in Incidence of Inflammatory Bowel Diseases—Pooled Analysis of Population-based Studies from Western Countries

(2018) Shailja C. Shah et al.   GASTROENTEROLOGY

Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection

(2018) Christoph A. Thaiss et al.   SCIENCE

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

(2018) Wei-Hung Pan et al.   Genome Medicine

Genome-wide DNA Methylation in Treatment-naïve Ulcerative Colitis

(2018) Hagar Taman et al.   Journal of Crohns & Colitis

ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING

(2018) Konrad Aden et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Toll-like Receptor 4–Induced Glycolytic Burst in Human Monocyte-Derived Dendritic Cells Results from p38-Dependent Stabilization of HIF-1α and Increased Hexokinase II Expression

(2018) Laure Perrin-Cocon et al.   JOURNAL OF IMMUNOLOGY

Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition

(2018) Marcus Fulde et al.   NATURE

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar

(2017) Felix Sommer et al.   GUT

Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease

(2017) Urko M Marigorta et al.   NATURE GENETICS

Mitochondrial permeability transition pore: sensitivity to opening and mechanistic dependence on substrate availability

(2017) Thomas Briston et al.   Scientific Reports

Cyclophilin D ablation is associated with increased end-ischemic mitochondrial hexokinase activity

(2017) Rianne Nederlof et al.   Scientific Reports

Cyclophilin D regulates the dynamic assembly of mitochondrial ATP synthase into synthasomes

(2017) Gisela Beutner et al.   Scientific Reports

Cyclophilin D regulates necrosis, but not apoptosis, of murine eosinophils

(2016) Xiang Zhu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology

(2016) Felix Sommer et al.   BIOESSAYS

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Hexokinase Is an Innate Immune Receptor for the Detection of Bacterial Peptidoglycan

(2016) Andrea J. Wolf et al.   CELL

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

(2016) Floris Imhann et al.   GUT

Molecular classification of Crohn's disease reveals two clinically relevant subtypes

(2016) Matthew Weiser et al.   GUT

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

(2016) Robert Häsler et al.   GUT

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

(2016) Kimberly A. Krautkramer et al.   MOLECULAR CELL

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux et al.   Nature Microbiology

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

(2015) A. A. Desouki et al.   BIOINFORMATICS

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

(2015) Laurence Macia et al.   Nature Communications

Site-specific programming of the host epithelial transcriptome by the gut microbiota

(2015) Felix Sommer et al.   GENOME BIOLOGY

Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits

(2014) Filipe De Vadder et al.   CELL

Activation of Gpr109a, Receptor for Niacin and the Commensal Metabolite Butyrate, Suppresses Colonic Inflammation and Carcinogenesis

(2014) Nagendra Singh et al.   IMMUNITY

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

TLR-driven early glycolytic reprogramming via the kinases TBK1-IKKɛ supports the anabolic demands of dendritic cell activation

(2014) Bart Everts et al.   NATURE IMMUNOLOGY

Altered Mucus Glycosylation in Core 1 O-Glycan-Deficient Mice Affects Microbiota Composition and Intestinal Architecture

(2014) Felix Sommer et al.   PLoS One

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

(2014) Pamela V. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mitochondrial Permeability Transition Pore and Cancer: Molecular Mechanisms Involved in Cell Death

(2014) Massimo Bonora et al.   Frontiers in Oncology

Microbial Modulation of Energy Availability in the Colon Regulates Intestinal Transit

(2013) Anita Wichmann et al.   Cell Host & Microbe

TNFα and IL-17 cooperatively stimulate glucose metabolism and growth factor production in human colorectal cancer cells

(2013) Daniel S Straus   Molecular Cancer

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

(2013) Yukihiro Furusawa et al.   NATURE

In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture

(2013) Hiroyuki Miyoshi et al.   Nature Protocols

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Inhibition of complex I regulates the mitochondrial permeability transition through a phosphate-sensitive inhibitory site masked by cyclophilin D

(2012) Bo Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Hexokinase II knockdown results in exaggerated cardiac hypertrophy via increased ROS production

(2012) Rongxue Wu et al.   EMBO Molecular Medicine

Disruption of Hexokinase II–Mitochondrial Binding Blocks Ischemic Preconditioning and Causes Rapid Cardiac Necrosis

(2011) Kirsten M.A. Smeele et al.   CIRCULATION RESEARCH

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

(2011) Erik Larsson et al.   GUT

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

G Protein-Coupled Receptor 43 Is Essential for Neutrophil Recruitment during Intestinal Inflammation

(2009) C. Sina et al.   JOURNAL OF IMMUNOLOGY

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

(2009) Kendle M. Maslowski et al.   NATURE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE