Database-driven approach to microbiome research

A screenshot of our microbiomeDB website.

High-throughput sequencing has revolutionized microbiology by allowing scientists to complement culture-based approaches with culture-independent profiling of complex microbial communities. Whether studying these communities in soil, on plants, or in animals, the collection of community composition data is often accompanied with rich metadata that describes the source from which the sample was derived, how samples were treated prior to collection, and how they were processed after collection. Increasingly, the goal of microbiome experiments is to understand how these various attributes represented by the metadata, influence the microbial community. MicrobiomeDB was developed as a discovery tool that empowers researchers to fully leverage their experimental metadata to construct queries that interrogate microbiome datasets.

Biologists and database developers working together

This project is only possible because of a close collaboration with the database development group responsible for VEuPathDB, an NIH Bioinformatics Resource Center (BRC). The same database development group, with funding from the Bill and Melinda Gates Foundation, has created ClinEpiDB, a resource for clinical and epidemological data. MicrobiomeDB was built by leveraging this substantial existing database infrastructure.

Making new discoveries with microbiomeDB

We recently used microbiomeDB to interrogate clinical and microbiome data to understand how natural parasite infections impact the human gut microbiome (see preprint here).

A focus on enteric diseases

Our goal is to create a comprehensive platform for comparative microbiome studies. We currently host the largest collection of human microbiome data from enteric diseases in lower- and middle-income countries (LMICs). Looking ahead, we plan to expand our data loading capacity to handle shotgun metagenomic data. We also hope to add private user workspaces that will allow anyone to analyze their own data using microbiomeDB filter tools and visualization apps.

Get your data on microbiomeDB!

If you’re interested in having us host your published microbiome dataset on microbiomeDB, please contact us here.


© 2020. Dan Beiting. All rights reserved.