Gut Microbiome Engineering for Improved Feed Efficiency and Disease Resistance in Nigerian Indigenous Pig Breeds

This study investigates the feasibility and mechanisms of gut microbiome engineering for improving feed efficiency and disease resistance in Nigerian indigenous pig breeds, developing an original framework for microbiome-mediated production improvement in tropical pigs. Nigerian indigenous pigs are hardy and disease-resistant but grow slowly, limiting their commercial attractiveness relative to exotic breeds. Their gut microbiome, shaped by evolution under low-input management conditions, may harbour beneficial microbial communities adapted to fibrous Nigerian diets that could be exploited for production improvement through strategic manipulation. This study characterises the gut microbiome of 80 Nigerian indigenous pigs and 40 Landrace pigs across farms in Plateau and Anambra States using 16S rRNA amplicon sequencing and shotgun metagenomics. Residual feed intake measurements over 84-day testing periods phenotype feed efficiency. Viral challenge with Porcine Epidemic Diarrhoea Virus tests disease resistance. Microbiome engineering strategies tested include faecal microbiota transplantation from high-efficiency donors, prebiotic supplementation targeting identified beneficial taxa, and probiotic consortia derived from indigenous pig gut isolates. Transcriptomic analysis of intestinal epithelial tissue characterises host responses to microbiome engineering treatments. Findings reveal that indigenous pigs harbour distinct microbial communities enriched in Treponema and Prevotella cellulolysicus compared to Landrace pigs, consistent with superior fibrolytic capacity. FMT from high-efficiency indigenous pig donors improves residual feed intake in recipient Landrace pigs by 22 percent. PEDV challenge mortality is 34 percent lower in indigenous pigs, associated with higher IgA secretion linked to specific Lactobacillus taxa. The study recommends targeted probiotic consortia development based on the identified beneficial indigenous pig gut taxa.

Keywords: gut microbiome, feed efficiency, Nigerian indigenous pigs, faecal microbiota transplantation, disease resistance.