Comparative genomics of Clostridium tyrobutyricum reveals signatures of environment-specific adaptation and metabolic potentials

Abstract

Clostridium tyrobutyricum is a promising microbial host for the anaerobic production of bio-based chemicals, especially butyric acid. However, the limited genetic traits of C. tyrobutyricum resulted in its constrained applicability in the food industry due to the absence of publicly available data. We performed a comparative genomic analysis of 13 C. tyrobutyricum strains isolated from different habitats to investigate the adaptation mechanisms and metabolic potentials of the C. tyrobutyricum strains isolated from fermentation environments (FE). The results showed that the genetic diversity of FE- associated C. tyrobutyricum strains was higher than that of strains isolated from non-fermentation environments (NFE). Based on evaluating safety-related genes, FE-associated strains were likely non-pathogenic to humans or animals. Many environmental adaptation-related genes involved in energy production and conversion, phosphotransferase system (PTS), etc., were significantly enriched in FE-associated strains, which was conducive to their survival in the corresponding habitats. The analysis of carbohydrate-active enzymes revealed that the CAZyme categories of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) were found to be significantly enriched in FE-associated strains, which was beneficial for carbohydrate utilization (including starch, cellulose, etc.). Fermentation experiments revealed that strains isolated from the Chinese liquor fermentation environment were capable of decomposing carbohydrates and producing organic acids. Collectively, this study provided insights into the genomic features of C. tyrobutyricum and the theoretical basis for further use, research, and development of these strains.