Comparison of the Faecal Microbiota Composition Following a Dairy By-Product Supplemented Diet in Nero Siciliano and Large White × Landrace Pig Breeds

SIMPLE SUMMARY: The genetic background of the host, together with several other biotic and abiotic factors, including feeding, plays a crucial role in modulating the gut microbiota composition of many animal species. Furthermore, several authors have reported that the microbiota of native pig breeds, such as the Nero Siciliano, reflects distinctive traits that commercial crossbreds have lost. For this reason, the present study shows a comparison of the faecal microbiota composition, following a liquid whey-supplemented diet, in the Nero Siciliano and commercial (Large White × Landrace) pig breeds and the important role of the host genetics in the modulation in faecal microbial composition. ABSTRACT: The current study compared the faecal microbiota composition of two pig breeds (autochthonous vs. commercial) to understand what happens after the integration of liquid whey in the diet and what the role of the host genetic is. The trial was conducted for 60 days, and the faecal microbiota composition was investigated at three time points, T0, T1 (after 30 days) and T2 (after 60 days) in 30 female pigs (20 commercial crossbred and 10 Nero Siciliano pigs). The animals were divided into four groups (two control and two treatment groups). Generally, in both breeds, Firmicutes (51%) and Bacteroidota (36%) were the most abundant phylum whereas Prevotella, Treponema and Lactobacillus were the most abundant genera. The two breeds have a different reaction to a liquid whey diet. In fact, as shown by PERMANOVA analysis, the liquid whey significantly (p < 0.001) affects the microbiota composition of crossbreeds while not having an effect on the microbiota of the Nero Siciliano. Despite this, in both breeds Bifidobacterium and Ruminococcus have been positively influenced by liquid whey and they promote intestinal health, improve immunity, increase performance, and feed efficiency. In conclusion, the integration of liquid whey had a different effect on the Nero Siciliano and crossbred pig breeds, emphasizing the importance of the host genetic profile in determining the faecal bacterial composition.