Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights

SIMPLE SUMMARY: The concept of modernization of pig production systems should not rely only on new technological inputs and opportunities, but should also address societal expectations regarding animal well-being while maintaining product quality. The Alentejano (AL) pig is a fatty breed from Portugal traditionally raised outdoors, surgically castrated, and slaughtered at heavy weights for its renowned high-quality meat and meat products. The gastrointestinal tract of pigs harbors a diverse ecosystem of microorganisms that play a major role in feed digestion, nutrient absorption, and in the synthesis and metabolism of skatole, one of the main sources of the unpleasant boar taint. Our study aimed to investigate gut microbiota changes in heavy AL pigs fed with a new high-fiber diet, aiming to reduce the skatole-producing microbiota, while also exploring the effects of surgical castration in that community. The pigs that were fed the new diet presented higher abundances of species responsible for breaking down complex carbohydrate substrates, while castrated pigs presented lower abundances of probiotic bacteria, normally associated with better gut health and lower body fat. Utilizing fiber-enriched diets remains a promising approach to address boar taint in intact animals, especially when sourced from locally produced legumes and agricultural by-products, which can also contribute to broader sustainability objectives. ABSTRACT: This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq(®) System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers’ acceptance of pork products from non-castrated male pigs.