Biovalorization of lignocellulosic biomass through fermentation for pathogen suppression: decoding critical carbohydrate-active enzyme genes and associated transcription factors

Carbohydrate-active enzyme (CAZyme) genes and their transcription factors (TFs) are crucial for the fermentation of lignocellulosic biomass to inhibit pathogen. However, the diversity of CAZyme genes and the complexity of TFs identification limit the efficient biovalorization of bio-resources. This study aimed to inhibit the pathogen Ralstonia solanacearum by fermenting two substrates (chrysanthemum and peanut stems) with Bacillus amyloliquefaciens, while employing multi-omics and machine learning to analyze key CAZyme genes as well as their TFs. The results showed that the water-soluble extracts (WSEs) from fermented chrysanthemum stem (days 6-7) exhibited strong antimicrobial activity. Glycosyl transferase (GT) and polysaccharide lyase (PL) gene sets were enriched significantly during chrysanthemum stem fermentation. Genes, encoding a UDP-glycosyltransferase (GT1) and encoding a pectin lyase (PL1), were identified as key and correlated with the inhibition rate significantly. Through computational prediction, we further revealed the sigma factor RpoE as an indirect positive regulator of PL1 gene expression. Our study provides valuable insights into the identification of key CAZyme genes and the rapid discovery of their TFs, offering a foundation and promising direction for future optimization of fermentation technology.