Integration of Transcriptome and Metabolome Reveals the Genes and Metabolites Involved in Bifidobacterium bifidum Biofilm Formation

Abstract

Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both B. bifidum biofilm and planktonic cells was performed to identify key genes and metabolites involved in biofilm formation. Two hundred thirty-five nonredundant differentially expressed genes (DEGs) (including vanY, pstS, degP, groS, infC, groL, yajC, tadB and sigA) and 219 nonredundant differentially expressed metabolites (including L-threonine, L-cystine, L-tyrosine, ascorbic acid, niacinamide, butyric acid and sphinganine) were identified. Thirteen pathways were identified during the integration of both transcriptomics and metabolomics data, including ABC transporters; quorum sensing; two-component system; oxidative phosphorylation; cysteine and methionine metabolism; glutathione metabolism; glycine, serine and threonine metabolism; and valine, leucine and isoleucine biosynthesis. The DEGs that relate to the integration pathways included asd, atpB, degP, folC, ilvE, metC, pheA, pstS, pyrE, serB, ulaE, yajC and zwf. The differentially accumulated metabolites included L-cystine, L-serine, L-threonine, L-tyrosine, methylmalonate, monodehydroascorbate, nicotinamide, orthophosphate, spermine and tocopherol. These results indicate that quorum sensing, two-component system and amino acid metabolism are essential during B. bifidum biofilm formation.

Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

“…Integrative analysis of transcriptomic, proteomic, and metabolomic data has been widely used to study biofilms in recent years [ 40 – 42 ]. Preliminary experiments found that the biofilms treated with CRAMP at a concentration of 62.5 µg/mL for 1 h exhibited the best eradication effect, and the changes in the transcription levels of biofilm-related genes were evident under this experimental condition.…”

Comparative Transcriptome Analysis of Shewanella putrefaciens WS13 Biofilms Under Cold Stress

“…YidC function as integral membrane chaperone/insertase associated with the classical SecYEG translocon, which could contribute to inhibit biofilm formation ( Hofbauer et al., 2018 ). The upregulated expression of the secY and yidC genes involved in extracellular polymeric substances was also observed in the stage of biofilm maturation of Bifidobacterium Longun FGSZY16M3 ( Liu et al., 2021 ). In this study, the secF gene expression was also highly increased by 2.06 fold, which encodes a component of the Sec translocon.…”

Multiomics reveals the mechanism of B. longum in promoting the formation of mixed-species biofilms

“…79 The ABC transporter protein was reported by Liu et al to be crucial in the formation of B. longum when studying the gene level differences between bacterial cells in biofilms and suspensions. 80 Using the two-component system was the primary strategy for microorganisms to respond to environmental changes and control their gene expression. For example, QseC found in Haemophilus parasuis , which was related to the two-component system, was mainly involved in stress tolerance and biofilm formation.…”