Bioprospecting of the goat’s GIT microbiota and pretreatment strategies for enhanced sugarcane bagasse degradation and biomethane production

Abstract

The gastrointestinal tract of goats (Capra hircus) harbors a diverse array of carbohydrate-active enzyme (CAZyme)-producing microorganisms that play a crucial role in fiber degradation and nutrient cycling. However, the dynamics and functional potential of these microbial communities remain underexplored, limiting their application in sustainable bioenergy production. This study applied functional metagenomics and microbiological profiling to investigate CAZyme-producing microorganisms in South African goats. The ruminal gastrointestinal tract samples were collected to evaluate microbial communities capable of producing cellulases and other carbohydrate-degrading enzymes. Microbial diversity varied across gastrointestinal compartments, with the abomasum exhibiting reduced alpha diversity, likely due to its acidic environment. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla, with Proteobacteria being particularly abundant in the abomasum. Functional profiling revealed that most genes were involved in metabolism, including xenobiotic biodegradation, while carbohydrate-active enzyme (CAZyme) analysis showed hlycoside hydrolases as the predominant class. Higher CAZyme abundance in the reticulum and omasum suggested compartmentalized microbial activity and adaptation to dietary substrates. Genera such as Proteus and Bacillus were isolated, identified, and screened for enzyme activity, growth rates, and substrate utilization after further processing of the GIT samples. This revealed Proteus mirabilis KC94 (KC94) as the most promising strain. KC94 exhibited strong, stable enzyme activity across a broad pH and temperature range, with peak production at 84 hours. Genetic analysis confirmed the presence of key glycoside hydrolase genes (GH39, GH45, GH48). Short-term pretreatment with KC94 significantly improved cellulose hydrolysis, as shown by higher glucose release, and altered the elemental composition of sugarcane bagasse (SCB) by balancing nutrients and reducing sulfur content. Biomethane potential (BMP) assays demonstrated that KC94-pretreated SCB achieved the highest methane yield, with up to 25% improvement over controls and faster, sustained production. The goat rumen microbiota displayed dynamic adaptations to varying dietary inputs, highlighting their potential for bioprospecting in sustainable bioenergy systems. Collectively, the findings demonstrate the applicability of goat-derived microbial communities for cellulase production and lignocellulosic biomass conversion, offering an eco-friendly alternative to chemical pretreatment methods