Insights into the transcriptome profile of mature biofilm of Salmonella Typhimurium on stainless steels surface

• Transcriptome profile of S. Typhimurium biofilm was determined by RNA-seq.
• 618 and 897 genes were over-expressed and inhibited in biofilm, respectively.
• Two significant pathways were involved in biofilm formation.
• Four novel non-coding RNAs were observed in mature biofilm.

Salmonella is a worldwide food-borne pathogen, with many serotypes able to form biofilms under food processing environments; in particular the Typhimurium and Enteritidis serotypes. The cells in Salmonella biofilm are able to survive long-term even under food processing stresses, and subsequently may cause severe salmonellosis outbreaks. In this study, high-throughput sequencing (RNA-seq) was used to establish the whole transcriptome profile of mature biofilm and planktonic counterparts of Salmonella Typhimurium attached on stainless steels surface. The results showed that the gene expression patterns of S. Typhimurium biofilm cells were distinct from those of the planktonic counterparts, and 1515 genes were differentially expressed, with 618 genes over-expressed and 897 genes down-expressed in the biofilm cells. Among these differentially expressed transcripts, genes encoding membrane proteins, cytoplasmic proteins, curli productions, transcriptional regulators, cellulose biosynthesis and stress response proteins may play crucial roles in the maturation of Salmonella biofilm. Also, two significant pathways, carbon fixation and sulfur metabolism, were observed to be upregulated in mature biofilm. The gene expression levels obtained from RNA-seq were successfully validated using RT-qPCR assays with csgD, csrA, mgtC, fimA, marA and soxS genes. In addition, four novel non-coding small RNAs were found to be upregulated in mature biofilm. Our work may serve as a basis for further studies, examining the complex network systems that regulate Salmonella biofilm maturation and maintenance.