Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome

[1]  R. Eri,et al.  Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths , 2020, Microorganisms.

[2]  B. McSharry,et al.  Manipulation of the Innate Immune Response by Varicella Zoster Virus , 2020, Frontiers in Immunology.

[3]  M. De Paepe,et al.  New insights into intestinal phages , 2020, Mucosal Immunology.

[4]  T. Sutton,et al.  Gut Bacteriophage: Current Understanding and Challenges , 2019, Front. Endocrinol..

[5]  A. Kurilshikov,et al.  Studying the gut virome in the metagenomic era: challenges and perspectives , 2019, BMC Biology.

[6]  L. Moretta,et al.  Human NK Cells and Herpesviruses: Mechanisms of Recognition, Response and Adaptation , 2019, Front. Microbiol..

[7]  Sang-Uk Seo,et al.  Virome-host interactions in intestinal health and disease. , 2019, Current opinion in virology.

[8]  E. Hollister,et al.  Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut , 2019, Viruses.

[9]  M. Surette,et al.  Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review. , 2019, Gastroenterology.

[10]  D. Tscharke,et al.  Functional paralysis of human natural killer cells by alphaherpesviruses , 2019, PLoS pathogens.

[11]  E. V. Usachev,et al.  Broad Bactericidal Activity of the Myoviridae Bacteriophage Lysins LysAm24, LysECD7, and LysSi3 against Gram-Negative ESKAPE Pathogens , 2019, Viruses.

[12]  J. Walter,et al.  Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri. , 2019, Cell host & microbe.

[13]  A. Hart,et al.  The gut virome: the ‘missing link’ between gut bacteria and host immunity? , 2019, Therapeutic advances in gastroenterology.

[14]  V. Rimoldi,et al.  Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease , 2018, Gut microbes.

[15]  Morris A. Swertz,et al.  Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome , 2018, Science Translational Medicine.

[16]  R. Krajmalnik-Brown,et al.  Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study , 2018, BMC Microbiology.

[17]  Jun Yu,et al.  Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer , 2018, Gut.

[18]  R. Pellicano,et al.  Irritable bowel syndrome: the clinical approach. , 2018, Panminerva medica.

[19]  Jun Yu,et al.  Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes. , 2018, Gastroenterology.

[20]  S. Ng,et al.  Urbanization and the gut microbiota in health and inflammatory bowel disease , 2018, Nature Reviews Gastroenterology & Hepatology.

[21]  D. Lamarre,et al.  Viruses Seen by Our Cells: The Role of Viral RNA Sensors , 2018, Journal of immunology research.

[22]  Katharina Eisenächer,et al.  Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity , 2018, Viruses.

[23]  E. Wine,et al.  The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It , 2018, Cancers.

[24]  B. B. Finlay,et al.  Good Bug, Bad Bug: Breaking through Microbial Stereotypes. , 2018, Cell host & microbe.

[25]  O. Cinek,et al.  Virome Sequencing of Stool Samples. , 2018, Methods in molecular biology.

[26]  R. Schmitz,et al.  Archaea Are Interactive Components of Complex Microbiomes. , 2018, Trends in microbiology.

[27]  W. D. de Vos,et al.  The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota , 2017, Microbiology and Molecular Biology Reviews.

[28]  S. Oka,et al.  PCR detection of human herpesviruses in colonic mucosa of individuals with inflammatory bowel disease: Comparison with individuals with immunocompetency and HIV infection , 2017, PloS one.

[29]  S. Carding,et al.  Review article: the human intestinal virome in health and disease , 2017, Alimentary pharmacology & therapeutics.

[30]  P. Tomazic,et al.  The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study , 2017, Scientific Reports.

[31]  T. Vatanen,et al.  Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children , 2017, Proceedings of the National Academy of Sciences.

[32]  Y. Ringel,et al.  The Gut Microbiome in Irritable Bowel Syndrome and Other Functional Bowel Disorders. , 2017, Gastroenterology clinics of North America.

[33]  D. Kelsell,et al.  Corrigendum: ADAM17/EGFR axis promotes transglutaminase-dependent skin barrier formation through phospholipase C γ1 and protein kinase C pathways , 2017, Scientific Reports.

[34]  Andrew J. Davison,et al.  Consensus statement: Virus taxonomy in the age of metagenomics , 2017, Nature Reviews Microbiology.

[35]  Minhu Chen,et al.  Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta‐analysis , 2017, Journal of gastroenterology and hepatology.

[36]  Rémi Brazeilles,et al.  Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome. , 2017, Gastroenterology.

[37]  E. Koonin,et al.  Virus taxonomy in the age of metagenomics , 2017 .

[38]  G. Pazour,et al.  Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness , 2017, Scientific Reports.

[39]  N. Troy,et al.  Respiratory viral infections and host responses; insights from genomics , 2016, Respiratory Research.

[40]  D. Drossman,et al.  Rome IV-Functional GI Disorders: Disorders of Gut-Brain Interaction. , 2016, Gastroenterology.

[41]  A. Benson,et al.  Molecular characterization of the intestinal microbiota in patients with and without abdominal bloating. , 2016, American journal of physiology. Gastrointestinal and liver physiology.

[42]  Ron Milo,et al.  Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans , 2016, Cell.

[43]  R. Spiller,et al.  Irritable bowel syndrome , 2015, Nature Reviews Disease Primers.

[44]  Y. Ringel,et al.  The Intestinal Microbiota and Irritable Bowel Syndrome. , 2015, Journal of clinical gastroenterology.

[45]  Yanjiao Zhou,et al.  Early life dynamics of the human gut virome and bacterial microbiome in infants , 2015, Nature Medicine.

[46]  Tanja Woyke,et al.  Viral dark matter and virus–host interactions resolved from publicly available microbial genomes , 2015, eLife.

[47]  A. Gasbarrini,et al.  The human gut microbiota and virome: Potential therapeutic implications , 2015, Digestive and Liver Disease.

[48]  Yong Zhang,et al.  Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria , 2015, Inflammatory bowel diseases.

[49]  A. Focà,et al.  Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? , 2015, Mediators of inflammation.

[50]  D. Raoult,et al.  Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans? , 2015, Viruses.

[51]  Jenny Sauk,et al.  Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease , 2015, Cell.

[52]  J. Sanderson,et al.  Characterization of virus-like particles associated with the human faecal and caecal microbiota. , 2014, Research in microbiology.

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

[54]  S. Collins.  A role for the gut microbiota in IBS , 2014, Nature Reviews Gastroenterology &Hepatology.

[55]  R. Edwards,et al.  A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes , 2014, Nature Communications.

[56]  Colin Hill,et al.  Exploiting gut bacteriophages for human health. , 2014, Trends in microbiology.

[57]  B. La Scola,et al.  Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries , 2014, Virology Journal.

[58]  H. Dupont,et al.  Review article: evidence for the role of gut microbiota in irritable bowel syndrome and its potential influence on therapeutic targets , 2014, Alimentary pharmacology & therapeutics.

[59]  Herbert W Virgin,et al.  The Virome in Mammalian Physiology and Disease , 2014, Cell.

[60]  H. Virgin,et al.  Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities , 2014, Gastroenterology.

[61]  Michael I. Love,et al.  Differential analysis of count data – the DESeq2 package , 2013 .

[62]  M. Pop,et al.  Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.

[63]  Jonathan L. Schmid-Burgk,et al.  Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP , 2013, Nature.

[64]  L. Hooper,et al.  Resident viruses and their interactions with the immune system , 2013, Nature Immunology.

[65]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[66]  E. Delwart.  A Roadmap to the Human Virome , 2013, PLoS pathogens.

[67]  D. Sinderen,et al.  Gut microbiota composition correlates with diet and health in the elderly , 2012, Nature.

[68]  E. Zoetendal,et al.  Intestinal microbiota in functional bowel disorders: a Rome foundation report , 2012, Gut.

[69]  Y. Ringel,et al.  Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea‐predominant irritable bowel syndrome , 2012, Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.

[70]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[71]  Marcus J Claesson,et al.  An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota , 2011, Gut.

[72]  A. Iwasaki,et al.  Genome–virome interactions: examining the role of common viral infections in complex disease , 2011, Nature Reviews Microbiology.

[73]  M. Roossinck.  The good viruses: viral mutualistic symbioses , 2011, Nature Reviews Microbiology.

[74]  T. Ley,et al.  Latent herpesvirus infection arms NK cells. , 2010, Blood.

[75]  Florent E. Angly,et al.  Viral diversity and dynamics in an infant gut. , 2008, Research in microbiology.

[76]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.