RT Journal Article
SR Electronic
T1 Achieving pan-microbiome biological insights via the dbBact knowledge base
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.02.27.482174
DO 10.1101/2022.02.27.482174
A1 Amnon Amir
A1 Eitan Ozel
A1 Yael Haberman
A1 Noam Shental
YR 2022
UL http://biorxiv.org/content/early/2022/07/28/2022.02.27.482174.abstract
AB 16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying the microbial world. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when analyzing their findings and interpret them in a broader context. To bridge this gap, we introduce dbBact, an open wiki-like bacterial knowledge base. dbBact combines information from hundreds of studies across diverse habitats, creating a collaborative central repository where 16S rRNA amplicon sequence variants (ASVs) are manually extracted from each study and assigned multiple ontology-based terms. Using the >900 studies of dbBact, covering more than 1,400,000 associations between 345,000 ASVs and 6,500 ontology terms, we show how the dbBact statistical and programmatic pipeline can augment standard microbiome analysis. We use multiple examples to demonstrate how dbBact leads to formulating novel hypotheses regarding inter-host similarities, intra-host sources of bacteria, and commonalities across different diseases, and helps detect environmental sources and identify contaminants.Competing Interest StatementThe authors have declared no competing interest.