Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

(2020) Sidhartha R. Sinha et al.   Cell Host & Microbe

Changing Global Epidemiology of Inflammatory Bowel Diseases—Sustaining Healthcare Delivery into the 21st Century

(2020) Ashwin N. Ananthakrishnan et al.   Clinical Gastroenterology and Hepatology

Pathway paradigms revealed from the genetics of inflammatory bowel disease

(2020) Daniel B. Graham et al.   NATURE

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level

(2020) Douglas J. Kenny et al.   Cell Host & Microbe

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

(2020) Masanori Funabashi et al.   NATURE

Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease

(2020) Lingjia Kong et al.   GASTROENTEROLOGY

ACG Clinical Guideline

(2019) David T. Rubin et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

TRAIL suppresses gut inflammation and inhibits colitogeic T-cell activation in experimental colitis via an apoptosis-independent pathway

(2019) I. T. Chyuan et al.   Mucosal Immunology

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

(2019) Jason Lloyd-Price et al.   NATURE

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients with Inflammatory Bowel Diseases

(2019) Konrad Aden et al.   GASTROENTEROLOGY

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships

(2019) Damian R. Plichta et al.   CELL

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review

(2019) Maria Manuela Estevinho et al.   Clinical Gastroenterology and Hepatology

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

(2018) Florian Plaza Oñate et al.   BIOINFORMATICS

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells

(2018) A. Butera et al.   Scientific Reports

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

Succinate receptor mediates intestinal inflammation and fibrosis

(2018) Dulce C. Macias-Ceja et al.   Mucosal Immunology

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

The Role of Succinate in the Regulation of Intestinal Inflammation

(2018) Jessica Connors et al.   Nutrients

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Defining Disease Severity in Inflammatory Bowel Diseases: Current and Future Directions

(2016) Laurent Peyrin-Biroulet et al.   Clinical Gastroenterology and Hepatology

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Biologic agents for IBD: practical insights

(2015) Silvio Danese et al.   Nature Reviews Gastroenterology & Hepatology

Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis: Analysis of a North American Cohort

(2014) Ashwin N Ananthakrishnan et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability

(2014) Erika Assarsson et al.   PLoS One

Reliability and Initial Validation of the Ulcerative Colitis Endoscopic Index of Severity

(2013) Simon P.L. Travis et al.   GASTROENTEROLOGY

Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

(2011) Yohei Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Loss of intestinal core 1–derived O-glycans causes spontaneous colitis in mice

(2011) Jianxin Fu et al.   JOURNAL OF CLINICAL INVESTIGATION

Caspase-8 regulates TNF-α-induced epithelial necroptosis and terminal ileitis

(2011) Claudia Günther et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS