Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria

TL;DR

This study explores how nine gut bacteria form a multi-species biofilm by analyzing gene activity and metabolites, revealing key genes and substances involved in the process.

Contribution

The study identifies specific genes and metabolites that enhance multi-species biofilm formation compared to single-species biofilms.

Findings

740 common differentially expressed genes (DEGs) regulate pathways related to bacterial motility and communication.

L-arginine, l-serine, guanosine, and hypoxanthine are key metabolites linked to biofilm formation.

Combined transcriptome and metabolome analysis reveals 26 DEGs correlated with amino acid and purine metabolism pathways.

Abstract

Biofilms are one of the ways microorganisms exist in natural environments. In recent years, research has gradually shifted its focus to exploring the complexity and interactions of multi-species biofilms. A study showed that nine gut bacteria can form a multi-species biofilm on wheat fibers (M9 biofilm). However, the previous study did not clarify the reasons why M9 exhibited a better biofilm formation ability than the mono-species biofilms. In this study, the gene expression levels and metabolic accumulation of the M9 multi-species biofilm and biofilms of each individual bacterium were analyzed using transcriptomes and metabolomes. The differentially expressed genes (DEGs) showed that there were 740 common DEGs that existed in all of the nine groups, and they could regulate five pathways related to bacterial motility, cellular communication, and signal transduction. The metabolome results revealed that many peptides/amino acids and derivatives were produced in the M9 biofilm. Furthermore, purine metabolism was significantly enhanced in the M9 biofilm. L-arginine, l-serine, guanosine, and hypoxanthine were the common differentially accumulated metabolites (DAMs). The combined analysis of the transcriptomes and metabolomes showed that there were 26 common DEGs highly correlated with the four common DAMs, and they were involved in five metabolic pathways related to amino acids and purines. These results indicate that M9 can regulate multi-species biofilm formation by modulating genes related to bacterial motility, cellular communication, signal transduction, and the metabolism of amino acids and purines. This study provides insights into the interactions of microbial biofilms.

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