Lignocellulose degradation capabilities and distribution of antibiotic resistance genes and virulence factors in Clostridium from the gut of giant pandas

Clostridium is a vital gut anaerobe in giant pandas (GPs), aiding bamboo digestion and gut homeostasis. The present study optimizes anaerobic culturing to isolate Clostridium species from GPs, evaluating their ecological roles in bamboo digestion while assessing associated pathogenic and antibiotic resistance threats. The results show that the enriching samples in liquid media facilitated the isolation of Clostridium species. A total of 14 species are obtained, with C. perfringens, C. sardiniense, and C. baratii being most prevalent. 86.30% of strains exhibit lignocellulose-degrading activity, with all C. butyricum strains displaying activity for β-glucosidase, xylanase, and manganese peroxidase. Genomic analysis identifies carbohydrate-active enzymes and metabolic pathways involved in lignocellulose degradation, short-chain fatty acid production, and essential amino acid biosynthesis. C. butyricum possesses the most hemicellulose- and cellulose-degrading genes. We also identify 19 antibiotic resistance genes (ARGs), predominantly glycopeptide-resistant van genes, and 23 virulence factors (VFs) encoded by 408 virulence genes (VGs). Notably, C. perfringens harbors the most ARGs and VFs, some of which are flanked by mobile genetic elements, suggesting risks of horizontal gene transfer. Overall, this study describes the dual role of Clostridium in GPs, contributing to dietary adaptation while also posing potential hazards due to pathogenic traits and antimicrobial resistance.