Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease

[1]  J. Wells,et al.  Microbial Regulation of Host Physiology by Short-chain Fatty Acids. , 2021, Trends in microbiology.

[2]  M. Hall,et al.  Broad spectrum antibiotics and risk of graft-versus-host disease in pediatric patients transplanted for acute leukemia: association of carbapenem use with risk of acute GVHD. , 2021, Transplantation and cellular therapy.

[3]  S. Mazmanian,et al.  Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice , 2020, Nature Microbiology.

[4]  Daigo Hashimoto,et al.  Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation. , 2020, The New England journal of medicine.

[5]  Francesco Asnicar,et al.  Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 , 2019, Nature Biotechnology.

[6]  Tae Woo Kim,et al.  Alteration of the intestinal microbiota by broad-spectrum antibiotic use correlates with the occurrence of intestinal graft-versus-host disease. , 2019, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[7]  W. D. de Vos,et al.  Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment during Hematopoietic Stem Cell Transplantation. , 2019, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[8]  Ryan R. Wick,et al.  Performance of neural network basecalling tools for Oxford Nanopore sequencing , 2019, Genome Biology.

[9]  C. Flowers,et al.  Antimicrobial Prophylaxis for Adult Patients With Cancer-Related Immunosuppression: ASCO and IDSA Clinical Practice Guideline Update. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[10]  D. Hashimoto,et al.  The association between the incidence of intestinal graft‐vs‐host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation , 2018, Clinical transplantation.

[11]  A. Goodman,et al.  The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. , 2018, Cell host & microbe.

[12]  Yu Lin,et al.  Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.

[13]  Tetsuya Hayashi,et al.  R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versus-host disease , 2017, The Journal of experimental medicine.

[14]  Vincent Lombard,et al.  PULDB: the expanded database of Polysaccharide Utilization Loci , 2017, Nucleic Acids Res..

[15]  Xiaowei Zhan,et al.  Antibiotic-Induced Depletion of Anti-inflammatory Clostridia Is Associated with the Development of Graft-versus-Host Disease in Pediatric Stem Cell Transplantation Patients. , 2017, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[16]  C. Quince,et al.  VSEARCH: a versatile open source tool for metagenomics , 2016, PeerJ.

[17]  Robert C. Edgar,et al.  UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing , 2016, bioRxiv.

[18]  Eric P. Nawrocki,et al.  NCBI prokaryotic genome annotation pipeline , 2016, Nucleic acids research.

[19]  Y. Taur,et al.  Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice , 2016, Science Translational Medicine.

[20]  G. Wong,et al.  Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics , 2016, Front. Microbiol..

[21]  K. Takeda,et al.  Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia , 2016, Nature.

[22]  Corinne Rossi,et al.  Gut microbiome derived metabolites modulate intestinal epithelial cell damage and mitigate Graft-versus-Host Disease , 2016, Nature Immunology.

[23]  S. McColl,et al.  Donor colonic CD103+ dendritic cells determine the severity of acute graft-versus-host disease , 2015, The Journal of experimental medicine.

[24]  Z. Hua,et al.  Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Mouse Feces , 2015, Applied and Environmental Microbiology.

[25]  P. Allen,et al.  Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles. , 2015, Cell host & microbe.

[26]  L. Tailford,et al.  Mucin glycan foraging in the human gut microbiome , 2015, Front. Genet..

[27]  D. Huson,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[28]  A. Viale,et al.  The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. , 2014, Blood.

[29]  A. Mócsai,et al.  Neutrophil granulocytes recruited upon translocation of intestinal bacteria enhance graft-versus-host disease via tissue damage , 2014, Nature Medicine.

[30]  Daniel Wolff,et al.  Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease. , 2014, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[31]  Michaela A. Teravest,et al.  Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats , 2014, Biotechnology and bioengineering.

[32]  A. Rudensky,et al.  Metabolites produced by commensal bacteria promote peripheral regulatory T cell generation , 2013, Nature.

[33]  L. Xia,et al.  Mucin-type O-glycans and their roles in intestinal homeostasis. , 2013, Glycobiology.

[34]  W. Garrett,et al.  The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis , 2013, Science.

[35]  E. Martens,et al.  Dynamic responses of Bacteroides thetaiotaomicron during growth on glycan mixtures , 2013, Molecular microbiology.

[36]  C. Philippe,et al.  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, BMC Biology.

[37]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[38]  A. Macpherson,et al.  Interactions Between the Microbiota and the Immune System , 2012, Science.

[39]  R. Khanin,et al.  Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation , 2012, The Journal of experimental medicine.

[40]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[41]  L. Joshi,et al.  Periodic acid-Schiff's reagent assay for carbohydrates in a microtiter plate format. , 2011, Analytical biochemistry.

[42]  P. Allen,et al.  Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. , 2011, Cell host & microbe.

[43]  Eric C. Martens,et al.  Sulfatases and a Radical S-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont, Bacteroides thetaiotaomicron* , 2011, The Journal of Biological Chemistry.

[44]  G. Nava,et al.  Diversity of the autochthonous colonic microbiota , 2011, Gut microbes.

[45]  K. Sepkowitz,et al.  Clinical practice guideline for the use of antimicrobial agents in neutropenic patients with cancer: 2010 update by the infectious diseases society of america. , 2011, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[46]  R. Knight,et al.  UniFrac: an effective distance metric for microbial community comparison , 2011, The ISME Journal.

[47]  K. Honda,et al.  Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species , 2011, Science.

[48]  R. Mackie,et al.  Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes , 2011, Molecular microbiology.

[49]  Donovan H. Parks,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[50]  J. Gordon,et al.  Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. , 2008, Cell host & microbe.

[51]  R. Knight,et al.  Worlds within worlds: evolution of the vertebrate gut microbiota , 2008, Nature Reviews Microbiology.

[52]  J. Gordon,et al.  Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. , 2008, Structure.

[53]  J. Gordon,et al.  Functional Genomic and Metabolic Studies of the Adaptations of a Prominent Adult Human Gut Symbiont, Bacteroides thetaiotaomicron, to the Suckling Period* , 2006, Journal of Biological Chemistry.

[54]  Benjamin P. Westover,et al.  Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont , 2005, Science.

[55]  S. Nakaji,et al.  The fermentation of different dietary fibers is associated with fecal clostridia levels in men. , 2004, The Journal of nutrition.

[56]  G. Pier,et al.  Transgenic Cystic Fibrosis Mice Exhibit Reduced Early Clearance of Pseudomonas aeruginosa from the Respiratory Tract1 , 2001, The Journal of Immunology.

[57]  P Stothard,et al.  The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. , 2000, BioTechniques.

[58]  G. Hill,et al.  The primacy of the gastrointestinal tract as a target organ of acute graft-versus-host disease: rationale for the use of cytokine shields in allogeneic bone marrow transplantation. , 2000, Blood.

[59]  J. Crawford,et al.  An experimental model of idiopathic pneumonia syndrome after bone marrow transplantation: I. The roles of minor H antigens and endotoxin. , 1996, Blood.

[60]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[61]  Atsushi Sasaki,et al.  Genome analysis , 2008 .

[62]  Claude-Alain H. Roten,et al.  Theoretical and practical advances in genome halving , 2004 .