Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice

(2021) Umang Jain et al.   SCIENCE

Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity

(2021) Amanda Carroll-Portillo et al.   Viruses-Basel

Bacteriophage uptake by mammalian cell layers represents a potential sink that may impact phage therapy

(2021) Marion C. Bichet et al.   iScience

Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome

(2021) Simone Dallari et al.   Cell Host & Microbe

The human virome: assembly, composition and host interactions

(2021) Guanxiang Liang et al.   NATURE REVIEWS MICROBIOLOGY

Genetic and phenotypic spectrum associated with IFIH1 gain‐of‐function

(2020) Gillian I. Rice et al.   HUMAN MUTATION

Pathway paradigms revealed from the genetics of inflammatory bowel disease

(2020) Daniel B. Graham et al.   NATURE

Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19

(2020) Annsea Park et al.   Cell Host & Microbe

The dynamics of the stool virome in very early onset inflammatory bowel disease

(2020) Guanxiang Liang et al.   Journal of Crohns & Colitis

The stepwise assembly of the neonatal virome is modulated by breastfeeding

(2020) Guanxiang Liang et al.   NATURE

Label or Concept – What Is a Pathobiont?

(2020) Lara Jochum et al.   TRENDS IN MICROBIOLOGY

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

(2020) Sonja Lang et al.   GASTROENTEROLOGY

Illuminating the human virome in health and disease

(2020) Fatemeh Adiliaghdam et al.   Genome Medicine

Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases

(2020) Iliyan D. Iliev et al.   GASTROENTEROLOGY

Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection

(2019) Johanna M. Sweere et al.   SCIENCE

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

(2019) Lasha Gogokhia et al.   Cell Host & Microbe

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

IFN-I and IL-22 mediate protective effects of intestinal viral infection

(2019) Jessica A Neil et al.   Nature Microbiology

Virus structures constrain transmission modes

(2019) Frederic D. Bushman et al.   Nature Microbiology

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

The future of faecal transplants

(2019) Edward M. Giles et al.   NATURE REVIEWS MICROBIOLOGY

Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling

(2019) Lei Liu et al.   NATURE IMMUNOLOGY

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Regulation of cGAS- and RLR-mediated immunity to nucleic acids

(2019) Andrea Ablasser et al.   NATURE IMMUNOLOGY

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Critical Role for the Microbiota in CX 3 CR1 + Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses

(2018) Myunghoo Kim et al.   IMMUNITY

CX3CR1+mononuclear phagocytes control immunity to intestinal fungi

(2018) Irina Leonardi et al.   SCIENCE

Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study

(2018) Christopher DeBoever et al.   Nature Communications

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Murine colitis reveals a disease-associated bacteriophage community

(2018) Breck A. Duerkop et al.   Nature Microbiology

Detection of Microbial Infections Through Innate Immune Sensing of Nucleic Acids

(2018) Xiaojun Tan et al.   Annual Review of Microbiology

A Map of Toll-like Receptor Expression in the Intestinal Epithelium Reveals Distinct Spatial, Cell Type-Specific, and Temporal Patterns

(2018) April E. Price et al.   IMMUNITY

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease

(2017) Jérôme Legoff et al.   NATURE MEDICINE

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers

(2017) Sophie Nguyen et al.   mBio

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells

(2017) Timo A. Lehti et al.   Nature Communications

Reciprocal Inflammatory Signaling Between Intestinal Epithelial Cells and Adipocytes in the Absence of Immune Cells

(2017) Yu Takahashi et al.   EBioMedicine

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

Enteric Viruses Ameliorate Gut Inflammation via Toll-like Receptor 3 and Toll-like Receptor 7-Mediated Interferon-β Production

(2016) Jin-Young Yang et al.   IMMUNITY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Utility of Lymphoblastoid Cell Lines for Induced Pluripotent Stem Cell Generation

(2016) Satish Kumar et al.   Stem Cells International

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

Intestinal Commitment and Maturation of Human Pluripotent Stem Cells Is Independent of Exogenous FGF4 and R-spondin1

(2015) Kaisa Tamminen et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The Virome in Mammalian Physiology and Disease

(2014) Herbert W. Virgin   CELL

Macrophage Activation and Polarization: Nomenclature and Experimental Guidelines

(2014) Peter J. Murray et al.   IMMUNITY

An enteric virus can replace the beneficial function of commensal bacteria

(2014) Elisabeth Kernbauer et al.   NATURE

Commensal microbes and interferon-  determine persistence of enteric murine norovirus infection

(2014) M. T. Baldridge et al.   SCIENCE

Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences

(2013) F. O. Martinez et al.   BLOOD

Cytosolic Sensing of Viruses

(2013) Delphine Goubau et al.   IMMUNITY

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intestinal macrophages: well educated exceptions from the rule

(2013) Ehud Zigmond et al.   TRENDS IN IMMUNOLOGY

Human Enterovirus Species B in Ileocecal Crohn’s Disease

(2013) Niklas Nyström et al.   Clinical and Translational Gastroenterology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Interleukin 23 Production by Intestinal CD103+CD11b+ Dendritic Cells in Response to Bacterial Flagellin Enhances Mucosal Innate Immune Defense

(2012) Melissa A. Kinnebrew et al.   IMMUNITY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

IFN-  determines the intestinal epithelial antiviral host defense

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

Mitochondrial antiviral signaling protein (MAVS) monitors commensal bacteria and induces an immune response that prevents experimental colitis

(2011) X.-D. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Pathogenesis of type 1 diabetes mellitus: interplay between enterovirus and host

(2010) Didier Hober et al.   Nature Reviews Endocrinology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Identification of Loss of Function Mutations in Human Genes Encoding RIG-I and MDA5

(2009) Taeko Shigemoto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of a Novel Astrovirus (Astrovirus VA1) Associated with an Outbreak of Acute Gastroenteritis

(2009) S. R. Finkbeiner et al.   JOURNAL OF VIROLOGY

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One