The Digestive Disease Data Science Commons: Microbiome Datasets

Microbiome studies performed by CSIBD investigators have generated integrated longitudinal molecular profiles of microbial activity during disease from methods including metagenomics, metatranscriptomics, and metabolomics. Datasets below provide a valuable resource to the community to enable future research and improve our ability to understand, diagnose, and treat IBD.

Large-scale integrative studies

  • The Integrative Human Microbiome Project

    The IHMP, also known as Human Microbiome Project 2 (HMP2), is a large-scale initiative designed to explore host–microbiome interplay, including immunity, metabolism, and dynamic molecular activity, to gain a more holistic view of host–microbe interactions over time.

    Disease-targeted projects within iHMP comprised pregnancy and preterm birth (PTB); inflammatory bowel diseases (IBD); and stressors that affect individuals with prediabetes. 

    IBD-focused research integrated longitudinal molecular profiles of microbial and host activity by analysing 1,785 stool samples, 651 intestinal biopsies, and 529 quarterly blood samples from 132 individuals and collected over the course of one year each. Key studies led by CSIBD investigators and colleagues can be found below.

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

    The Inflammatory Bowel Disease Multi'omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

    Gut microbiome structure and metabolic activity in inflammatory bowel disease

    Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort.

    Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

    Analysis of paired metagenomes and metatranscriptomes associated with patients with inflammatory bowel disease (IBD) and non-IBD controls over time provides some insights into microbial community variation and potential pathways influencing IBD symptoms.

    Strains, functions and dynamics in the expanded Human Microbiome Project

    Updates from the Human Microbiome Project analyse the largest known body-wide metagenomic profile of human microbiome personalization.

    Structure, function and diversity of the healthy human microbiome

    The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

  • Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study

    In 2008, the Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn's Disease (RISK) study began at 28 centres in the USA and Canada. This study has established the largest cohort of pediatric patients newly diagnosed with uncomplicated Crohn's disease, providing a critical and unique resource for research into the origins and progression of pediatric IBD. 

    As part of a multiinstitutional effort in the RISK Consortium, CSIBD investigators and colleagues derived a risk-stratification model for a complicated disease behaviour based on clinical, serological, gene expression, and microbial factors defined at diagnosis, and the effects of early anti-TNFα therapy. Their work suggests that a more rational and personalised approach to disease management in newly diagnosed children is possible.

Featured: Bacterial strains adapted to inflammatory bowel disease

  • Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

    Kumbhari A, Cheng TNH, Ananthakrishnan AN, Kochar B, Burke KE, Shannon K, Lau H, Xavier RJ, Smillie CS.

    A team led by Christopher Smillie, 2022 PFS awardee, analyzed fecal metagenomes and identified hundreds of ancient strains enriched in IBD patients. These strains have adapted over millions of years to survive in the difficult environment imposed by inflammation, outcompeting healthy strains during bouts of heightened inflammation. Moreover, health-associated strains were predictive of an inflammation biomarker, indicating their possible protective role and potential as a diagnostic tool.

    The study leveraged a vast resource of 6,138 metagenomes to infer 142,022 strain genotypes within 822 people with IBD and 1,257 non-IBD controls. The largest dataset analyzed was longitudinally collected by CSIBD investigators overseeing the Prospective Registry in IBD Study at MGH (PRISM) cohort.

CSIBD Studies