Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet

SIMPLE SUMMARY: Liquid feeding is an alternative practice employed in swine production that allows the recovery of low-cost liquid by-products to reduce environmental impact. This type of feeding can positively affect animal’s gut health, well-being, and performance. Liquid whey is a palatable feed and it can represent a resource to administer ingredients without additional costly processes. Nowadays, the study of the gut microbiome is considered a relevant tool due to the impact of this research field on host health, well-being, and growth. Therefore, this study investigated the fecal microbiota of the autochthonous pig breed Nero Siciliano fed a liquid whey co-feed-supplemented diet using a metagenomics approach. ABSTRACT: The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3–V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.