Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

(2017) Yusuke Nagara et al.   PLoS One

Host Selection of Microbiota via Differential Adhesion

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

Ordering structured populations in multiplayer cooperation games

(2016) Jorge Peña et al.   Journal of the Royal Society Interface

Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia

(2016) Ryu Okumura 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

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed Spectral Imaging of 120 Different Fluorescent Labels

(2016) Alex M. Valm et al.   PLoS One

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel

(2015) Neelendu Dey et al.   CELL

Quantitative Imaging of Gut Microbiota Spatial Organization

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

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda 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

The biogeography of polymicrobial infection

(2015) Apollo Stacy et al.   NATURE REVIEWS MICROBIOLOGY

Gut biogeography of the bacterial microbiota

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

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

(2015) Hyun Jung Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

(2014) Nilusha Malmuthuge et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural insights into bacterial recognition of intestinal mucins

(2014) Sabrina Etzold et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments

(2014) G. Lambert et al.   Interface Focus

Impact of spatial distribution on the development of mutualism in microbes

(2014) Ákos T. Kovács   Frontiers in Microbiology

Innate and Adaptive Immunity Interact to Quench Microbiome Flagellar Motility in the Gut

(2013) Tyler C. Cullender et al.   Cell Host & Microbe

Mining the “glycocode”—exploring the spatial distribution of glycans in gastrointestinal mucin using force spectroscopy

(2013) A. Patrick Gunning et al.   FASEB JOURNAL

Divergent Mechanisms of Interaction of Helicobacter pylori and Campylobacter jejuni with Mucus and Mucins

(2013) Julie Ann Naughton et al.   INFECTION AND IMMUNITY

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities

(2013) Sylvie Estrela et al.   PLoS Computational Biology

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

Gastrointestinal transit measurements in mice with 99mTc-DTPA-labeled activated charcoal using NanoSPECT-CT

(2013) Parasuraman Padmanabhan et al.   EJNMMI Research

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast Renewal of the Distal Colonic Mucus Layers by the Surface Goblet Cells as Measured by In Vivo Labeling of Mucin Glycoproteins

(2012) Malin E. V. Johansson   PLoS One

CLASI-FISH: Principles of combinatorial labeling and spectral imaging

(2012) Alex M. Valm et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

(2012) Jonas Schluter et al.   PLOS BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Social evolution in multispecies biofilms

(2011) S. Mitri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging

(2011) A. M. Valm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Antibacterial Lectin RegIII  Promotes the Spatial Segregation of Microbiota and Host in the Intestine

(2011) S. Vaishnava et al.   SCIENCE

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Bacterial biogeography of the human digestive tract

(2011) Jennifer C. Stearns et al.   Scientific Reports

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Oral multispecies biofilm development and the key role of cell–cell distance

(2010) Paul E. Kolenbrander et al.   NATURE REVIEWS MICROBIOLOGY

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

(2008) Alan W. Walker et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS 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