Microbial experience through housing in a farmyard-type environment alters intestinal barrier properties in mouse colons

[1]  A. Dufour,et al.  IgGFc-binding protein and MUC2 mucin produced by colonic goblet-like cells spatially interact non-covalently and regulate wound healing , 2023, Frontiers in Immunology.

[2]  X. Piao,et al.  The interaction among gut microbes, the intestinal barrier and short chain fatty acids , 2021, Animal nutrition.

[3]  J. Douwes,et al.  Cancer incidence in agricultural workers: Findings from an international consortium of agricultural cohort studies (AGRICOH) , 2021, Environment international.

[4]  J. Badger,et al.  Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity , 2021, Nature Metabolism.

[5]  K. Ullrich,et al.  Extensive variation in the intelectin gene family in laboratory and wild mouse strains , 2021, Scientific Reports.

[6]  Xuedong Zhou,et al.  Up-regulation of gasdermin C in mouse small intestine is associated with lytic cell death in enterocytes in worm-induced type 2 immunity , 2021, Proceedings of the National Academy of Sciences.

[7]  C. A. de la Motte,et al.  Human intelectin-1 (ITLN1) genetic variation and intestinal expression , 2021, Scientific Reports.

[8]  M. Bäckström,et al.  The IgGFc-binding protein FCGBP is secreted with all GDPH sequences cleaved but maintained by interfragment disulfide bonds , 2021, The Journal of biological chemistry.

[9]  L. Arike,et al.  An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function , 2021, Science.

[10]  M. Jenab,et al.  The Role of Gut Barrier Dysfunction and Microbiome Dysbiosis in Colorectal Cancer Development , 2021, Frontiers in Oncology.

[11]  A. Graham Naturalizing mouse models for immunology , 2021, Nature Immunology.

[12]  P. Boysen,et al.  A Model System for Feralizing Laboratory Mice in Large Farmyard-Like Pens , 2021, Frontiers in Microbiology.

[13]  K. Tsuchiya Switching from Apoptosis to Pyroptosis: Gasdermin-Elicited Inflammation and Antitumor Immunity , 2021, International journal of molecular sciences.

[14]  P. Boysen,et al.  Naturalizing laboratory mice by housing in a farmyard-type habitat confers protection against colorectal carcinogenesis , 2021, Gut microbes.

[15]  J. Tainer,et al.  PD-L1-Mediated Gasdermin C Expression Switches Apoptosis to Pyroptosis in Cancer Cells and Facilitates Tumor Necrosis , 2020, Nature Cell Biology.

[16]  Å. Keita,et al.  The Intestinal Barrier and Current Techniques for the Assessment of Gut Permeability , 2020, Cells.

[17]  J. Linseisen,et al.  Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes. , 2020, Cell host & microbe.

[18]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[19]  L. Arike,et al.  Calcium-activated chloride channel regulator 1 (CLCA1) forms non-covalent oligomers in colonic mucus and has mucin 2–processing properties , 2019, The Journal of Biological Chemistry.

[20]  M. Johansson,et al.  The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function , 2019, The Journal of experimental medicine.

[21]  J. Badger,et al.  Laboratory mice born to wild mice have natural microbiota and model human immune responses , 2019, Science.

[22]  A. Khoruts,et al.  Microbial Exposure Enhances Immunity to Pathogens Recognized by TLR2 but Increases Susceptibility to Cytokine Storm through TLR4 Sensitization. , 2019, Cell reports.

[23]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[24]  Y. Li,et al.  The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells , 2019, Immunity.

[25]  F. Greten,et al.  Inflammation and Cancer: Triggers, Mechanisms, and Consequences. , 2019, Immunity.

[26]  J. Vilo,et al.  g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) , 2019, Nucleic Acids Res..

[27]  Dave Singh,et al.  Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs. , 2018, JCI insight.

[28]  J. Allaire,et al.  The Intestinal Epithelium: Central Coordinator of Mucosal Immunity. , 2018, Trends in immunology.

[29]  P. de Vos,et al.  Sex and strain dependent differences in mucosal immunology and microbiota composition in mice , 2018, Biology of Sex Differences.

[30]  A. Gruber,et al.  Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity , 2018, EBioMedicine.

[31]  N. Ajami,et al.  Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance , 2017, Cell.

[32]  T. Kanneganti,et al.  ZBP1: Innate Sensor Regulating Cell Death and Inflammation. , 2017, Trends in immunology.

[33]  L. Hooper,et al.  Resistin-like molecule β is a bactericidal protein that promotes spatial segregation of the microbiota and the colonic epithelium , 2017, Proceedings of the National Academy of Sciences.

[34]  K. Foster,et al.  The evolution of the host microbiome as an ecosystem on a leash , 2017, Nature.

[35]  F. Bäckhed,et al.  Evolution, human-microbe interactions, and life history plasticity , 2017, The Lancet.

[36]  J. Chun,et al.  Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies , 2017, International journal of systematic and evolutionary microbiology.

[37]  A. Tanca,et al.  Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse , 2017, Front. Microbiol..

[38]  Sandra Fischer,et al.  Distributed under Creative Commons Cc-by 4.0 Rhea: a Transparent and Modular R Pipeline for Microbial Profiling Based on 16s Rrna Gene Amplicons , 2022 .

[39]  Gergely Katona,et al.  Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16 , 2016, Proceedings of the National Academy of Sciences.

[40]  M. Horn,et al.  IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies , 2016, Scientific Reports.

[41]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[42]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[43]  W. Haining,et al.  Recapitulating adult human immune traits in laboratory mice by normalizing environment , 2016, Nature.

[44]  F. Bäckhed,et al.  Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization. , 2015, Cell host & microbe.

[45]  M. Camilleri,et al.  Yamada's textbook of gastroenterology / , 2015 .

[46]  Erin Stevens,et al.  Differential Roles for Interleukin-23 and Interleukin-17 in Intestinal Immunoregulation. , 2015, Immunity.

[47]  D. Haller,et al.  Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men. , 2015, Molecular nutrition & food research.

[48]  F. Bäckhed,et al.  The composition of the gut microbiota shapes the colon mucus barrier , 2014, EMBO reports.

[49]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[50]  M. Johansson,et al.  Studies of mucus in mouse stomach, small intestine, and colon. II. Gastrointestinal mucus proteome reveals Muc2 and Muc5ac accompanied by a set of core proteins. , 2013, American journal of physiology. Gastrointestinal and liver physiology.

[51]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[52]  Jun Wang,et al.  The role of biogeography in shaping diversity of the intestinal microbiota in house mice , 2013, Molecular ecology.

[53]  M. Johansson,et al.  The gastrointestinal mucus system in health and disease , 2013, Nature Reviews Gastroenterology &Hepatology.

[54]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[55]  Hongzhe Li,et al.  Associating microbiome composition with environmental covariates using generalized UniFrac distances , 2012, Bioinform..

[56]  Elmar Pruesse,et al.  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..

[57]  M. Johansson,et al.  An ex vivo method for studying mucus formation, properties, and thickness in human colonic biopsies and mouse small and large intestinal explants , 2012 .

[58]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[59]  L. Meza-Zepeda,et al.  Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression , 2011, PloS one.

[60]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[61]  Dan R. Littman,et al.  Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria , 2009, Cell.

[62]  F. Haesebrouck,et al.  Helicobacter equorum: prevalence and significance for horses and humans. , 2009, FEMS immunology and medical microbiology.

[63]  M. Johansson,et al.  Proteomic analyses of the two mucus layers of the colon barrier reveal that their main component, the Muc2 mucin, is strongly bound to the Fcgbp protein. , 2009, Journal of proteome research.

[64]  A. Moorman,et al.  Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data , 2009, Nucleic acids research.

[65]  A. Velcich,et al.  The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria , 2008, Proceedings of the National Academy of Sciences.

[66]  T. Lumley,et al.  gplots: Various R Programming Tools for Plotting Data , 2015 .

[67]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[68]  M. Johansson,et al.  Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH. , 2012, Methods in molecular biology.

[69]  Cedric E. Ginestet ggplot2: Elegant Graphics for Data Analysis , 2011 .

[70]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010 .