Cause or effect? The spatial organization of pathogens and the gut microbiota in disease

Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms

(2020) David VanInsberghe et al.   Nature Microbiology

Short-range interactions govern the dynamics and functions of microbial communities

(2020) Alma Dal Co et al.   Nature Ecology & Evolution

The Network of Colonic Host Defense Peptides as an Innate Immune Defense Against Enteropathogenic Bacteria

(2020) Graham A. D. Blyth et al.   Frontiers in Immunology

The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis

(2020) Sho Kitamoto et al.   CELL

The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages

(2020) Marta Lourenço et al.   Cell Host & Microbe

The Evolution of Mass Cell Suicide in Bacterial Warfare

(2020) Elisa T. Granato et al.   CURRENT BIOLOGY

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

(2020) Alexander Zaborin et al.   mSystems

Enterohaemorrhagic Escherichia coli activates nitrate respiration to benefit from the inflammatory response for initiation of microcolony-formation

(2020) Risa Nada et al.   BMC MICROBIOLOGY

Host–microbiota maladaptation in colorectal cancer

(2020) Alina Janney et al.   NATURE

Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts

(2020) Leonor García-Bayona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

(2020) Fabian Imdahl et al.   Nature Microbiology

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

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

(2019) Jason Lloyd-Price et al.   NATURE

The Evolution and Ecology of Bacterial Warfare

(2019) Elisa T. Granato et al.   CURRENT BIOLOGY

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis

(2019) Eduard Ansaldo et al.   SCIENCE

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients

(2019) Azadeh Saffarian et al.   mBio

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

Growing, evolving and sticking in a flowing environment: understanding IgA interactions with bacteria in the gut

(2019) Daniel Hoces et al.   IMMUNOLOGY

Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

(2019) Iradj Sobhani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota

(2018) Carolina Tropini et al.   CELL

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut

(2018) Joana G. Lopes et al.   ISME Journal

Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them

(2018) Matthew T. Sorbara et al.   Mucosal Immunology

TheVibrio choleraetype VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts

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

Microbes vs. chemistry in the origin of the anaerobic gut lumen

(2018) Elliot S. Friedman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota utilize immunoglobulin A for mucosal colonization

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

Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model

(2018) Andrew J. Hryckowian et al.   Nature Microbiology

Bacterial Cohesion Predicts Spatial Distribution in the Larval Zebrafish Intestine

(2018) Brandon H. Schlomann et al.   BIOPHYSICAL JOURNAL

A Surface-Induced Asymmetric Program Promotes Tissue Colonization by Pseudomonas aeruginosa

(2018) Benoît-Joseph Laventie et al.   Cell Host & Microbe

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

(2018) et al.   NATURE

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

(2018) Tommi Vatanen et al.   NATURE

Fight them or feed them: how the intestinal mucus layer manages the gut microbiota

(2018) Bjoern O Schroeder   Gastroenterology Report

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Siderophore-mediated iron acquisition and modulation of host-bacterial interactions

(2017) Melissa Ellermann et al.   FREE RADICAL BIOLOGY AND MEDICINE

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

(2017) Christian Milani et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Assembly, structure, function and regulation of type III secretion systems

(2017) Wanyin Deng et al.   NATURE REVIEWS MICROBIOLOGY

Effect of water flow and chemical environment on microbiota growth and composition in the human colon

(2017) Jonas Cremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials

(2017) Brad A. Krajina et al.   ACS Central Science

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Host Selection of Microbiota via Differential Adhesion

(2016) Kirstie McLoughlin et al.   Cell Host & Microbe

Interactions between the microbiota and pathogenic bacteria in the gut

(2016) Andreas J. Bäumler et al.   NATURE

Microcins mediate competition among Enterobacteriaceae in the inflamed gut

(2016) Martina Sassone-Corsi et al.   NATURE

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel

(2016) Jonas Cremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SalmonellaTyphimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut

(2016) Thibault G. Sana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion

(2016) G. M. H. Birchenough et al.   SCIENCE

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

(2016) Frank Schreiber et al.   Nature Microbiology

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria

(2015) Naama Geva-Zatorsky et al.   NATURE MEDICINE

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

(2015) Jeremy J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial biofilms and the human intestinal microbiome

(2015) Willem M de Vos   npj Biofilms and Microbiomes

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

The Enteric Two-Step: nutritional strategies of bacterial pathogens within the gut

(2014) Jessica A. Ferreyra et al.   CELLULAR MICROBIOLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations

(2014) Y. Yawata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Motility and Chemotaxis Mediate the Preferential Colonization of Gastric Injury Sites by Helicobacter pylori

(2014) Eitaro Aihara et al.   PLoS Pathogens

Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

(2013) Laura Wrzosek et al.   BMC BIOLOGY

Complex Interactions Among Diet, Gastrointestinal Transit, and Gut Microbiota in Humanized Mice

(2013) Purna C. Kashyap et al.   GASTROENTEROLOGY

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota

(2012) N. Kamada et al.   SCIENCE

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine

(2008) A. J. Fabich et al.   INFECTION AND IMMUNITY

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