High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

[1]  Paul J. McMurdie,et al.  Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer , 2017, Gut.

[2]  A. Rosenfeld,et al.  Urinary Microbiome and Cytokine Levels in Women With Interstitial Cystitis. , 2017, Obstetrics and gynecology.

[3]  J. White,et al.  Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth , 2016, Front. Microbiol..

[4]  R. Colwell,et al.  Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak , 2016, BMC Microbiology.

[5]  J. Keenan,et al.  Screening for enterotoxigenic Bacteroides fragilis in stool samples. , 2016, Anaerobe.

[6]  D. Pardoll,et al.  The Myeloid Immune Signature of Enterotoxigenic Bacteroides Fragilis-Induced Murine Colon Tumorigenesis , 2016, Mucosal Immunology.

[7]  Kaitlin J. Flynn,et al.  Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer , 2016, mSphere.

[8]  M. Hattori,et al.  Two FOXP3+CD4+ T cell subpopulations distinctly control the prognosis of colorectal cancers , 2016, Nature Medicine.

[9]  P. Schloss,et al.  Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions , 2016, Genome Medicine.

[10]  Y. Nie,et al.  Association of Fusobacterium nucleatum infection with colorectal cancer in Chinese patients. , 2016, World journal of gastroenterology.

[11]  F. Ryan,et al.  Tumour-associated and non-tumour-associated microbiota in colorectal cancer , 2016, Gut.

[12]  Jun Yu,et al.  Gut mucosal microbiome across stages of colorectal carcinogenesis , 2015, Nature Communications.

[13]  Caroline H. Johnson,et al.  Metabolism links bacterial biofilms and colon carcinogenesis. , 2015, Cell metabolism.

[14]  P. Goldberg,et al.  Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer , 2015, PloS one.

[15]  S. Jonjić,et al.  Binding of the Fap2 protein of Fusobacterium nucleatum to human inhibitory receptor TIGIT protects tumors from immune cell attack. , 2015, Immunity.

[16]  H. Qin,et al.  Microbiota disbiosis is associated with colorectal cancer , 2015, Front. Microbiol..

[17]  Yiping W Han,et al.  Fusobacterium nucleatum: a commensal-turned pathogen. , 2015, Current opinion in microbiology.

[18]  A. Mira,et al.  Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers , 2015, Journal of Gastroenterology.

[19]  E. Platz,et al.  The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[20]  A. Sol,et al.  Fap2 of Fusobacterium nucleatum Is a Galactose-Inhibitable Adhesin Involved in Coaggregation, Cell Adhesion, and Preterm Birth , 2015, Infection and Immunity.

[21]  K. Kinzler,et al.  Microbiota organization is a distinct feature of proximal colorectal cancers , 2014, Proceedings of the National Academy of Sciences.

[22]  C. Sears,et al.  Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis. , 2014, The Journal of clinical investigation.

[23]  D. Knights,et al.  Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment , 2014, Genome Medicine.

[24]  P. Schloss,et al.  The Human Gut Microbiome as a Screening Tool for Colorectal Cancer , 2014, Cancer Prevention Research.

[25]  X. Liang,et al.  Co-occurrence of driver and passenger bacteria in human colorectal cancer , 2014, Gut Pathogens.

[26]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[27]  P. Gajer,et al.  An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform , 2014, Microbiome.

[28]  Z. Ma,et al.  Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota , 2013, The ISME Journal.

[29]  Thomas Bjarnsholt,et al.  The in vivo biofilm. , 2013, Trends in microbiology.

[30]  Jesse R. Zaneveld,et al.  Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences , 2013, Nature Biotechnology.

[31]  M. Meyerson,et al.  Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. , 2013, Cell host & microbe.

[32]  M. R. Rubinstein,et al.  Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/β-catenin signaling via its FadA adhesin. , 2013, Cell host & microbe.

[33]  Amy M. Sheflin,et al.  Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults , 2013, PloS one.

[34]  Richard A. Moore,et al.  Co-occurrence of anaerobic bacteria in colorectal carcinomas , 2013, Microbiome.

[35]  Zhigang Zhang,et al.  Diversified pattern of the human colorectal cancer microbiome , 2013, Gut Pathogens.

[36]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[37]  Lauren M. Bragg,et al.  Fast, accurate error-correction of amplicon pyrosequences using Acacia , 2012, Nature Methods.

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

[39]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[40]  B. Birren,et al.  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. , 2012, Genome research.

[41]  Richard A. Moore,et al.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. , 2012, Genome research.

[42]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[43]  Rob Knight,et al.  Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities , 2011, Current protocols in bioinformatics.

[44]  Tanja Magoc,et al.  FLASH: fast length adjustment of short reads to improve genome assemblies , 2011, Bioinform..

[45]  P. Woster,et al.  Polyamine catabolism contributes to enterotoxigenic Bacteroides fragilis-induced colon tumorigenesis , 2011, Proceedings of the National Academy of Sciences.

[46]  Liping Zhao,et al.  Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers , 2011, The ISME Journal.

[47]  Andrea K. Bartram,et al.  Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads , 2011, Applied and Environmental Microbiology.

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

[49]  N. Hall,et al.  Towards the Human Colorectal Cancer Microbiome , 2011, PloS one.

[50]  Andrea K. Bartram,et al.  Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads , 2011, Applied and Environmental Microbiology.

[51]  J. Tap,et al.  Microbial Dysbiosis in Colorectal Cancer (CRC) Patients , 2011, PloS one.

[52]  Wen-Han Yu,et al.  The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information , 2010, Database J. Biol. Databases Curation.

[53]  W. D. de Vos,et al.  Mucin-bacterial interactions in the human oral cavity and digestive tract , 2010, Gut microbes.

[54]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[55]  Cynthia L Sears,et al.  A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses , 2009, Nature Medicine.

[56]  C. Sears Enterotoxigenic Bacteroides fragilis: a Rogue among Symbiotes , 2009, Clinical Microbiology Reviews.

[57]  P. Harris,et al.  Research electronic data capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support , 2009, J. Biomed. Informatics.

[58]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[59]  B. Gulluoglu,et al.  A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. , 2006, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[60]  Yun Zhou,et al.  Identification and Characterization of a Novel Adhesin Unique to Oral Fusobacteria , 2005, Journal of bacteriology.

[61]  H. Lochs,et al.  Spatial Organization and Composition of the Mucosal Flora in Patients with Inflammatory Bowel Disease , 2005, Journal of Clinical Microbiology.

[62]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[63]  Sara E. Miller,et al.  Microbial Biofilms in the Gut: Visualization by Electron Microscopy and by Acridine Orange Staining , 2004, Ultrastructural pathology.

[64]  H. Harmsen,et al.  Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. , 2002, International journal of systematic and evolutionary microbiology.

[65]  Richard C Boucher,et al.  Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. , 2002, The Journal of clinical investigation.

[66]  Cynthia L Sears,et al.  Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation. , 2001, Gastroenterology.

[67]  P. Boyle,et al.  ABC of colorectal cancer: Epidemiology , 2000, BMJ.

[68]  R. Genco,et al.  Interactions between Periodontal Bacteria and Human Oral Epithelial Cells: Fusobacterium nucleatum Adheres to and Invades Epithelial Cells , 2000, Infection and Immunity.

[69]  J. Costerton,et al.  Bacterial biofilms: a common cause of persistent infections. , 1999, Science.

[70]  C. Sears,et al.  Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  P. Kolenbrander,et al.  Adhere today, here tomorrow: oral bacterial adherence , 1993, Journal of bacteriology.

[72]  L. Moore,et al.  Coaggregation of Fusobacterium nucleatum, Selenomonas flueggei, Selenomonas infelix, Selenomonas noxia, and Selenomonas sputigena with strains from 11 genera of oral bacteria , 1989, Infection and immunity.

[73]  Jens Roat Kultima,et al.  Molecular Systems Biology Peer Review Process File Potential of Fecal Microbiota for Early Stage Detection of Colorectal Cancer Transaction Report , 2022 .