Integrated Microbiota and Metabolomics Analysis of Candida utilis CU-3 Solid-State Fermentation Effects on Cottonseed Hull-Based Feed

Solid-state microbial fermentation (SSMF) has been established as an effective bioprocessing strategy to augment the nutritional value of plant-derived feed substrates while reducing anti-nutritional factors (ANFs). However, there have been limited studies on the effects of microbial solid-state fermentation on the nutritional value and potential functional components in cottonseed hulls. This study investigated the nutritional enhancement of cottonseed hulls through anaerobic solid-state fermentation mediated by <i>Candida utilis</i> CU-3, while exploring the functional potential of the fermented feed by analyzing fungal community dynamics and metabolite profiling. The laboratory-preserved free gossypol-degrading strain <i>Candida utilis</i> CU-3 was inoculated into unsterilized, crushed, and screened cottonseed hulls for solid-state fermentation at room temperature for 10 days. The results demonstrated that, compared to the control group, the experimental group achieved a 61.90% increase in free gossypol degradation rate, a 27.78% improvement in crude protein content, and a 5.07% reduction in crude fiber, while crude fat showed no significant difference. During the fermentation process, microbial diversity decreased, and <i>Candida utilis</i> CU-3 became the dominant species. Untargeted metabolomics data revealed that cottonseed hulls inoculated with <i>Candida utilis</i> CU-3 produced functional bioactive compounds during fermentation, including chrysin, myricetin (anti-inflammatory, antibacterial, and antioxidant activities), and ginsenoside Rh2 (anticancer, antibacterial, and neuroprotective properties). This study demonstrates that inoculating <i>Candida utilis</i> CU-3 into cottonseed hulls enhances their health-promoting potential through the biosynthesis of diverse functional metabolites, providing a theoretical foundation for improving the nutritional profile of cottonseed hull-fermented feed.