Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Three‐dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut

(2020) Wei Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Highly multiplexed spatial mapping of microbial communities

(2020) Hao Shi et al.   NATURE

High-resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach

(2019) Connie Fung et al.   PLOS BIOLOGY

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

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Gut microbiota utilize immunoglobulin A for mucosal colonization

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

Spatial interference scale as a determinant of microbial range expansion

(2018) Venhar Celik Ozgen et al.   Science Advances

A beginner’s guide to tissue clearing

(2017) Pablo Ariel   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

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

(2017) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces

(2017) Robin Tecon et al.   Scientific Reports

Host Selection of Microbiota via Differential Adhesion

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

Spatial structure, cooperation and competition in biofilms

(2016) Carey D. Nadell et al.   NATURE REVIEWS MICROBIOLOGY

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

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling

(2016) William H. DePas et al.   mBio

Tools for the Microbiome: Nano and Beyond

(2015) Julie S. Biteen et al.   ACS Nano

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

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

(2015) Jennifer B Treweek et al.   Nature Protocols

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Heterogeneity across the murine small and large intestine

(2014) Rowann Bowcutt   WORLD JOURNAL OF GASTROENTEROLOGY

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis

(2013) Malin E V Johansson et al.   GUT

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

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

(2013) Sylvie Estrela et al.   PLoS Computational Biology

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

The human commensal Bacteroides fragilis binds intestinal mucin

(2011) Julie Y. Huang et al.   ANAEROBE

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

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

The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

(2011) J. L. Round et al.   SCIENCE

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

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

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