Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities

• DOI: 10.1093/bioinformatics/btad236
• Publication Date: 2023-06-30T08:16:09Z
• Authors: Qi Wang; Michael Nute; Todd J Treangen
• Keywords: Bacteria; Crohn Disease; Microbiota; Humans; Metagenome; Bioinformatics of Microbes and Microbiomes; 3. Good health; Gastrointestinal Microbiome

Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge bacteria driving interactions microbiomes remains unknown, limiting our ability fully decipher and control communities.We present a novel approach for identifying species microbiomes. Bakdrive infers ecological networks given metagenomic sequencing samples identifies minimum sets driver (MDS) using theory. has three key innovations this space: (i) it leverages inherent information from identify species, (ii) explicitly takes host-specific variation into consideration, (iii) does not require known network. extensive simulated data, we demonstrate identified healthy donor introducing them the disease samples, can restore gut microbiome recurrent Clostridioides difficile (rCDI) infection patients state. We also applied two real datasets, rCDI Crohn's patients, uncovering consistent with previous work. represents capturing interactions.Bakdrive is open-source available at: https://gitlab.com/treangenlab/bakdrive.