Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation

Abstract

Bacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Although adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here, we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We determined that bile-dependent biofilm formation involves the production of the DNase BT3563 or its homologs, degrading extracellular DNA (eDNA) in several B. thetaiotaomicron strains. Our study therefore shows that, although biofilm matrix eDNA provides a biofilm-promoting scaffold in many studied Firmicutes and Proteobacteria, BT3563-mediated eDNA degradation is required to form B. thetaiotaomicron biofilm in the presence of bile.

An integrated transcriptomics–functional genomics approach reveals a small RNA that modulatesBacteroides thetaiotaomicronsensitivity to tetracyclines

“…2c; Supplementary Fig. S5e, g) that are both known to contribute to Bacteroides fitness under bile stress (Bechon et al, 2022; Liu et al, 2021). In case of the BT_2792 – BT_2795 operon that encodes a bile salt tolerance-conveying efflux pump (Liu et al, 2021), we observed a TSS and alternative start codon 60 nt downstream of the annotated one (red and black ‘ATG’ in Fig.…”

“…f, Gentamicin vs. TYG control. g, Venn diagrams display the overlap of bile salts-specific gene expression (significantly upregulated) between our dataset and that obtained in (Bechon et al, 2022). The associated heat map depicts highly upregulated operons including components of two efflux systems ( BT_2793-BT_2795 , BT_2685-BT_2689 ) as well as an outer membrane protein and a calcineurin superfamily phosphohydrolase ( BT_0691-BT_0692 ).…”

“…2c; Supplementary Fig. S5e, g) that are both known to contribute to Bacteroides fitness under bile stress (Bechon et al, 2022;Liu et al, 2021).…”

“…S4: Transcript levels of all annotated B. thetaiotaomicron PUL systems, BT4338 regulon members, capsular polysaccharides, and conjugative transposons. For each condition and each replicate, the read counts per million (CPM) mapped to individual PUL genes (as inferred from PULDB (Terrapon et al, 2018)), to individual members of the BT4338 regulon as inferred from (Supplementary Table S3B in (Townsend et al, 2020) display the overlap of bile salts-specific gene expression (significantly upregulated) between our dataset and that obtained in (Bechon et al, 2022). The associated heat map depicts highly upregulated operons including components of two efflux systems (BT_2793-BT_2795, BT_2685-BT_2689) as well as an outer membrane protein and a calcineurin superfamily phosphohydrolase (BT_0691-BT_0692).…”

Peanut supplementation affects compositions and functions of gut microbiome in Ugandan children

“…This alignment reinforces our contention that peanut supplementation can effectively act as a dietary adjunct, fostering the development of gut microbes that participate in the metabolism of food substrate. Furthermore, the escalation of Bacteroides thetaiotaomicron , a contributor to bile-dependent gut biofilm formation, 50 following 90 days of supplementation is noteworthy. This suggests a direct potential benefit to the host in terms of bolstering gut maturation.…”