A cell atlas of microbe-responsive processes in the zebrafish intestine

Human gastrointestinal epithelia of the esophagus, stomach, and duodenum resolved at single-cell resolution

(2021) Georg A. Busslinger et al.   Cell Reports

EpCAM (CD326) Regulates Intestinal Epithelial Integrity and Stem Cells via Rho-Associated Kinase

(2021) Takeshi Ouchi et al.   Cells

Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine

(2021) Jia Wen et al.   Science Advances

Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health

(2020) Adrià López Nadal et al.   Frontiers in Immunology

Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes

(2020) Arnaud Lavergne et al.   BMC BIOLOGY

Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium

(2020) Jennifer K. Heppert et al.   Nature Reviews Gastroenterology & Hepatology

Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

(2019) Caitlin C. Murdoch et al.   PLoS Pathogens

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Development and organization of the zebrafish intestinal epithelial stem cell niche

(2019) Jianlong Li et al.   DEVELOPMENTAL DYNAMICS

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Effects of Cholecystokinin (CCK) on Gut Motility in the Stomachless Fish Ballan Wrasse (Labrus bergylta)

(2019) Hoang T. M. D. Le et al.   Frontiers in Neuroscience

Valid Post-clustering Differential Analysis for Single-Cell RNA-Seq

(2019) Jesse M. Zhang et al.   Cell Systems

Somatostatin stimulates colonic MUC2 expression through SSTR5-Notch-Hes1 signaling pathway

(2019) Shuailing Song et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut

(2019) Jieun Park et al.   DEVELOPMENTAL CELL

The zebrafish as a model for gastrointestinal tract–microbe interactions

(2019) Erika M. Flores et al.   CELLULAR MICROBIOLOGY

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling

(2018) Joshua V. Troll et al.   DEVELOPMENT

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Microbial regulation of the L cell transcriptome

(2018) Tulika Arora et al.   Scientific Reports

Intestinal microbiome adjusts the innate immune setpoint during colonization through negative regulation of MyD88

(2018) Bjørn E. V. Koch et al.   Nature Communications

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

(2017) James M. Davison et al.   GENOME RESEARCH

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

(2017) Colin R. Lickwar et al.   PLOS BIOLOGY

Cholecystokinin—From Local Gut Hormone to Ubiquitous Messenger

(2017) Jens F. Rehfeld   Frontiers in Endocrinology

The intestinal tuft cell nanostructure in 3D

(2017) Ben Hoover et al.   Scientific Reports

Enteroendocrine Cells: Chemosensors in the Intestinal Epithelium

(2016) Fiona M. Gribble et al.   Annual Review of Physiology

Identification of Ly2 members as antimicrobial peptides from zebrafish Danio rerio

(2016) Xuemin Liu et al.   BIOSCIENCE REPORTS

The zebrafish as a model to study intestinal inflammation

(2016) Sylvia Brugman   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Patterning mechanisms of the sub-intestinal venous plexus in zebrafish

(2016) Michela Goi et al.   DEVELOPMENTAL BIOLOGY

Identification and expression of a new Ly6 gene cluster in zebrafish Danio rerio, with implications of being involved in embryonic immunity

(2016) Man Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Notch regulates BMP responsiveness and lateral branching in vessel networks via SMAD6

(2016) Kevin P. Mouillesseaux et al.   Nature Communications

Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota

(2016) Travis J Wiles et al.   PLOS BIOLOGY

Regulation of Stem Cell Proliferation and Cell Fate Specification by Wingless/Wnt Signaling Gradients Enriched at Adult Intestinal Compartment Boundaries

(2016) Ai Tian et al.   PLoS Genetics

Interleukin-22: Immunobiology and Pathology

(2015) Jarrod A. Dudakov et al.   Annual Review of Immunology

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

The composition of the zebrafish intestinal microbial community varies across development

(2015) W Zac Stephens et al.   ISME Journal

The water channel aquaporin-1a1 facilitates movement of CO2 and ammonia in zebrafish (Danio rerio) larvae

(2015) K. Talbot et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Lymphatic vessels arise from specialized angioblasts within a venous niche

(2015) J. Nicenboim et al.   NATURE

Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets

(2015) Michelle L Robinette et al.   NATURE IMMUNOLOGY

Cancer and the gut microbiota: An unexpected link

(2015) Laurence Zitvogel et al.   Science Translational Medicine

Endothelial Cell Self-fusion during Vascular Pruning

(2015) Anna Lenard et al.   PLOS BIOLOGY

Aquaporin 1 Is Involved in Acid Secretion by Ionocytes of Zebrafish Embryos through Facilitating CO2 Transport

(2015) Jiun-Lin Horng et al.   PLoS One

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling

(2014) A. L. Alvers et al.   DEVELOPMENT

Epidermal cells help coordinate leukocyte migration during inflammation through fatty acid-fuelled matrix metalloproteinase production

(2014) Christopher J. Hall et al.   Nature Communications

Zebrafish as a model to study live mucus physiology

(2014) Irena Jevtov et al.   Scientific Reports

The bHLH transcription factor Ascl1a is essential for the specification of the intestinal secretory cells and mediates Notch signaling in the zebrafish intestine

(2013) Lydie C. Flasse et al.   DEVELOPMENTAL BIOLOGY

Loss of ascl1a prevents secretory cell differentiation within the zebrafish intestinal epithelium resulting in a loss of distal intestinal motility

(2013) Gillian Roach et al.   DEVELOPMENTAL BIOLOGY

Inducible progenitor-derived Wingless regulates adult midgut regeneration inDrosophila

(2012) Julia B Cordero et al.   EMBO JOURNAL

Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling

(2012) Christoph Reinhardt et al.   NATURE

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Smooth muscle caldesmon modulates peristalsis in the wild type and non-innervated zebrafish intestine

(2012) J. Abrams et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development

(2012) J. Galindo-Villegas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda

(2011) Joost J van Soest et al.   BMC IMMUNOLOGY

The inhibitory effect of environmental ammonia on Danio rerio LPS induced acute phase response

(2011) A.F. Gonçalves et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Regulatory mechanisms of thymus and T cell development

(2011) Dongyuan Ma et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Microbial Colonization Induces Dynamic Temporal and Spatial Patterns of NF-κB Activation in the Zebrafish Digestive Tract

(2011) Michelle Kanther et al.   GASTROENTEROLOGY

Expression patterns of lgr4 and lgr6 during zebrafish development

(2011) Kentaro Hirose et al.   GENE EXPRESSION PATTERNS

Evidence for a core gut microbiota in the zebrafish

(2011) Guus Roeselers et al.   ISME Journal

Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression

(2011) Dag Henrik Reikvam et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Nucleotide oligomerization domain-containing proteins instruct T cell helper type 2 immunity through stromal activation

(2011) J. G. Magalhaes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual oxidase in the intestinal epithelium of zebrafish larvae has anti-bacterial properties

(2010) Maria Vega Flores et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine

(2010) Zhengyuan Wang et al.   BMC GENOMICS

Moesin1 and Ve-cadherin are required in endothelial cells during in vivo tubulogenesis

(2010) Y. Wang et al.   DEVELOPMENT

The role of meis1 in primitive and definitive hematopoiesis during zebrafish development

(2010) A. Cvejic et al.   HAEMATOLOGICA

Deletion of Tis7 Protects Mice from High-Fat Diet-Induced Weight Gain and Blunts the Intestinal Adaptive Response Postresection

(2010) Cong Yu et al.   JOURNAL OF NUTRITION

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88

(2010) S. E. Cheesman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wnt Signaling, Lgr5, and Stem Cells in the Intestine and Skin

(2009) Andrea Haegebarth et al.   AMERICAN JOURNAL OF PATHOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Adenomatous polyposis coli regulates Drosophila intestinal stem cell proliferation

(2009) W.-C. Lee et al.   DEVELOPMENT

Invasive and indigenous microbiota impact intestinal stem cell activity through multiple pathways in Drosophila

(2009) N. Buchon et al.   GENES & DEVELOPMENT

hnRNP I Inhibits Notch Signaling and Regulates Intestinal Epithelial Homeostasis in the Zebrafish

(2009) Jing Yang et al.   PLoS Genetics

Intestinal Differentiation in Zebrafish Requires Cdx1b, a Functional Equivalent of Mammalian Cdx2

(2008) Maria Vega C. Flores et al.   GASTROENTEROLOGY

Paracrine Wingless signalling controls self-renewal of Drosophila intestinal stem cells

(2008) Guonan Lin et al.   NATURE

Methods for generating and colonizing gnotobiotic zebrafish

(2008) Linh N Pham et al.   Nature Protocols

Intestinal alkaline phosphatase is a gut mucosal defense factor maintained by enteral nutrition

(2008) R. F. Goldberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA