Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

(2021) Natalya Yutin et al.   Nature Communications

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

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

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese

(2021) Yoshihiko Tomofuji et al.   ANNALS OF THE RHEUMATIC DISEASES

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome

(2020) Eugene V. Koonin et al.   TRENDS IN MICROBIOLOGY

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

(2020) Mina Hojat Ansari et al.   BMC MICROBIOLOGY

The Gut Microbiota: Emerging Evidence in Autoimmune Diseases

(2020) Xuan Zhang et al.   TRENDS IN MOLECULAR MEDICINE

Increasing Prevalence of Antinuclear Antibodies in the United States

(2020) Gregg E. Dinse et al.   Arthritis & Rheumatology

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

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

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

Shining Light on Human Gut Bacteriophages

(2020) Emma Guerin et al.   Frontiers in Cellular and Infection Microbiology

A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology

(2020) Toshihiro Kishikawa et al.   Frontiers in Cellular and Infection Microbiology

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

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

Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal

(2019) Doua Azzouz et al.   ANNALS OF THE RHEUMATIC DISEASES

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

(2019) Jason Lloyd-Price et al.   NATURE

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition

(2019) Jian Yin et al.   ANNALS OF THE RHEUMATIC DISEASES

Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population

(2019) Toshihiro Kishikawa et al.   ANNALS OF THE RHEUMATIC DISEASES

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

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

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

(2019) Patrick A. de Jonge et al.   Viruses-Basel

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

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

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

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity

(2018) Eric C. Keen et al.   TRENDS IN MICROBIOLOGY

A human gut phage catalog correlates the gut phageome with type 2 diabetes

(2018) Yingfei Ma et al.   Microbiome

Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases

(2018) Marialbert Acosta-Herrera et al.   ANNALS OF THE RHEUMATIC DISEASES

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

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

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

The Human Gut Virome in Hypertension

(2018) Maozhen Han et al.   Frontiers in Microbiology

Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation

(2018) L. A. Draper et al.   Microbiome

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

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

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

Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis

(2017) Rebecca Rogier et al.   Microbiome

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

(2016) Maria Gutierrez-Arcelus et al.   NATURE REVIEWS GENETICS

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Dysbiosis Contributes to Arthritis Development via Activation of Autoreactive T Cells in the Intestine

(2016) Yuichi Maeda et al.   Arthritis & Rheumatology

Piggyback-the-Winner in host-associated microbial communities

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Jason M. Norman et al.   CELL

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Derivation and validation of the Systemic Lupus International Collaborating Clinics classification criteria for systemic lupus erythematosus

(2012) Michelle Petri et al.   ARTHRITIS AND RHEUMATISM

Gut Microbiota Composition and Activity in Relation to Host Metabolic Phenotype and Disease Risk

(2012) Elaine Holmes et al.   Cell Metabolism

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Diagnostic criteria for multiple sclerosis: 2010 Revisions to the McDonald criteria

(2011) Chris H. Polman et al.   ANNALS OF NEUROLOGY

CRISPR/Cas System and Its Role in Phage-Bacteria Interactions

(2010) Hélène Deveau et al.   Annual Review of Microbiology

2010 Rheumatoid arthritis classification criteria: An American College of Rheumatology/European League Against Rheumatism collaborative initiative

(2010) Daniel Aletaha et al.   ARTHRITIS AND RHEUMATISM