Achieving pan-microbiome biological insights via the dbBact knowledge base

Amnon Amir, Eitan Ozel, Yael Haberman, Noam Shental

Research output: Contribution to journalArticlepeer-review


16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when interpreting their own findings in a broader context. To bridge this gap, we introduce dbBact-a novel pan-microbiome resource. dbBact combines manually curated information from studies across diverse habitats, creating a collaborative central repository of 16S rRNA amplicon sequence variants (ASVs), which are assigned multiple ontology-based terms. To date dbBact contains information from more than 1000 studies, which include 1500000 associations between 360000 ASVs and 6500 ontology terms. Importantly, dbBact offers a set of computational tools allowing users to easily query their own datasets against the database. To demonstrate how dbBact augments standard microbiome analysis we selected 16 published papers, and reanalyzed their data via dbBact. We uncovered novel inter-host similarities, potential intra-host sources of bacteria, commonalities across different diseases and lower host-specificity in disease-Associated bacteria. We also demonstrate the ability to detect environmental sources, reagent-borne contaminants, and identify potential cross-sample contaminations. These analyses demonstrate how combining information across multiple studies and over diverse habitats leads to better understanding of underlying biological processes.

Original languageEnglish
Pages (from-to)6593-6608
Number of pages16
JournalNucleic Acids Research
Issue number13
StatePublished - 21 Jul 2023

Bibliographical note

Funding Information:
N.S. is funded by the Ministry of Science, Technology & Space, Israel [3-16033]. Funding for open access charge: Open university internal fund.

Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.


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