Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis

Dysbiosis of gut microbiota in Polish patients with ulcerative colitis: a pilot study

(2021) Oliwia Zakerska-Banaszak et al.   Scientific Reports

Massive expansion of human gut bacteriophage diversity

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

Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

(2021) Moïra B Dion et al.   NUCLEIC ACIDS RESEARCH

Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut

(2021) Steven G. Sutcliffe et al.   Viruses-Basel

Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

(2021) Mihnea R. Mangalea et al.   Cell Host & Microbe

The dark side of the gut: Virome–host interactions in intestinal homeostasis and disease

(2021) Yuhao Li et al.   JOURNAL OF EXPERIMENTAL MEDICINE

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

(2021) Adam J. Hockenberry et al.   PeerJ

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner

(2020) Mohammadali Khan Mirzaei et al.   Cell Host & Microbe

Pathway paradigms revealed from the genetics of inflammatory bowel disease

(2020) Daniel B. Graham et al.   NATURE

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

(2020) Mohammad Tauqeer Alam et al.   Gut Pathogens

Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model

(2020) Torben Sølbeck Rasmussen et al.   GUT

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer

(2020) Farnaz Fouladi et al.   ISME Journal

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

(2020) Lucas P. P. Braga et al.   Microbiome

High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease

(2020) Jee-Yon Lee et al.   Cell Host & Microbe

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts

(2020) Kosuke Fujimoto et al.   Cell Host & Microbe

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

(2020) Tao Zuo et al.   Cell Host & Microbe

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

(2020) Lorraine A. Draper et al.   BMC BIOLOGY

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

(2019) Graham J. Britton et al.   IMMUNITY

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease

(2019) Hengameh Chloé Mirsepasi-Lauridsen et al.   CLINICAL MICROBIOLOGY REVIEWS

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

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

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

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

Administration of Akkermansia muciniphila Ameliorates Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice

(2019) Xiaoyuan Bian et al.   Frontiers in Microbiology

Defining the human gut host–phage network through single-cell viral tagging

(2019) Mária Džunková et al.   Nature Microbiology

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice

(2019) Derek M. Lin et al.   Frontiers in Cellular and Infection Microbiology

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

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

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

(2018) Jeffrey K. Cornuault et al.   Microbiome

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

(2018) Nicholas A. Bokulich et al.   Microbiome

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Murine colitis reveals a disease-associated bacteriophage community

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

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohnʼs Disease

(2018) Melissa A. Fernandes et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

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

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Analysis of Microbiome Data in the Presence of Excess Zeros

(2017) Abhishek Kaul et al.   Frontiers in Microbiology

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

(2017) Christopher Staley et al.   Microbiome

Human Microbiota-Associated Mice: A Model with Challenges

(2016) Marie-Claire Arrieta et al.   Cell Host & Microbe

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis

(2016) Yingting Zhou et al.   Biomed Research International

Piggyback-the-Winner in host-associated microbial communities

(2016) Cynthia B Silveira et al.   npj Biofilms and Microbiomes

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

(2015) Manuel Kleiner et al.   BMC GENOMICS

Faecalibacterium prausnitzii prevents physiological damages in a chronic low-grade inflammation murine model

(2015) Rebeca Martín et al.   BMC MICROBIOLOGY

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

(2015) Jason M. Norman et al.   CELL

Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model

(2015) Jane M. Natividad et al.   INFLAMMATORY BOWEL DISEASES

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Phenotypic Resistance and the Dynamics of Bacterial Escape from Phage Control

(2014) James J. Bull et al.   PLoS One

Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF−/−mice

(2014) Shai Bel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

(2013) Jonathan McCafferty et al.   ISME Journal

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Reduced Diversity and Imbalance of Fecal Microbiota in Patients with Ulcerative Colitis

(2012) Hideyuki Nemoto et al.   DIGESTIVE DISEASES AND SCIENCES

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

(2012) David Berry et al.   ISME Journal

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS