BugSigDB uncovers reproducible patterns of differential microbial abundance

Researchers from the CUNY Institute for Implementation Science in Population Health (ISPH) and their collaborators have unveiled BugSigDB, a community-editable database containing meticulously curated microbial signatures extracted from various published studies.

Their paper, titled “BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures,” has been published in Nature Biotechnology, and the public wiki is accessible at https://bugsigdb.org.

BugSigDB compiles crucial methods and findings, facilitating the systematic analysis of similarities among microbial signatures from independent studies. It also enables the examination of co-occurrence and co-exclusion of individual microbes and the identification of consensus signatures shared across multiple studies with similar health outcomes and exposures. This database aids in assessing variations in microbiome abundance within and across different experimental conditions, environments, or body sites.

Ludwig Geistlinger, the first author of the study, initiated this project during his postdoctoral tenure at CUNY SPH and currently serves as the associate director of computational biology at the Center for Computational Biomedicine at Harvard Medical School.

Dr. Geistlinger remarks, “BugSigDB represents the first comprehensive compilation of published microbial signatures, offering a means to compare host-associated microbial abundance variations across independent studies. It has revealed reproducible patterns of differential microbial abundance across diverse health outcomes that would have remained unnoticed through traditional literature review.”

Chloe Mirzayi, a recent CUNY SPH doctoral graduate and the second author of the study, expresses her satisfaction with mentoring BugSigDB interns, many of whom were CUNY SPH students. She notes their growth in critical literature analysis, result interpretation, and secondary data analysis.

Professor Levi Waldron, the senior author of the study, emphasizes the project’s significance, representing four years of collaboration involving nearly 60 student curators who incorporated close to 3,000 microbial signatures from 750 studies. Supported by software developers, CUNY students, and collaborators, the project has led to novel methods for harnessing this unique database.

BugSigDB operates on the same technology platform as Wikipedia, and Professor Waldron’s next objective is to engage more editors, fostering BugSigDB’s development as a dynamic database maintained by the broader microbiome research community.

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