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

<i>Bifidobacterium bifidum</i> 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 <i>B. bifidum</i> biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both <i>B. bifidum</i> 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 <i>vanY</i>, <i>pstS</i>, <i>degP</i>, <i>groS</i>, <i>infC</i>, <i>groL</i>, <i>yajC</i>, <i>tadB</i> and <i>sigA</i>) 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 <i>asd</i>, <i>atpB</i>, <i>degP</i>, <i>folC</i>, <i>ilvE</i>, <i>metC</i>, <i>pheA</i>, <i>pstS</i>, <i>pyrE</i>, <i>serB</i>, <i>ulaE</i>, <i>yajC</i> and <i>zwf</i>. 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 <i>B. bifidum</i> biofilm formation.