Influence of genetic background and the effect of liquid whey supplementation on the faecal microbiota composition in Nero siciliano and commercial crossbreed pigs

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 reflects distinctive traits that commercial crossbreeds have lost. Nero Siciliano pig is an important autochthonous Sicilian pig breed that has a marked lipolytic capacity. The aim of this study is to assess the composition of the faecal microbiota of two different genetic types of pigs reared within a farm where liquid whey was integrated in the feeding as dairy by-product. The faecal bacterial composition has been investigated at three time points, T0, T1 (after 30 days) and T2 (after 60 days), in two pig groups (Control and Treatment). Microbial genomic DNA has been extracted from stool samples collected directly from the rectal ampoule of 20 crossbreed (Large White×Landrace) pigs (10 Control and 10 Treatment) and 10 autochthonous (Nero Siciliano) pigs (5 Control and 5 Treatment). The 16S rDNA gene has been sequenced using an Illumina MiSeq platform and the clean reads (Phred-score ≥20) have been classified at phylum, family, and genus level, with an identity threshold of 75%, 87% and 95%, respectively, by using QIIME2. In both groups and population sets, Firmicutes (51%) was the most abundant phylum followed by Bacteroidetes (36%) whereas the most abundant genera were Prevotella, Treponema and Lactobacillus. The two pig genetic types have showed a different attitude towards liquid whey diet. In fact, as shown by beta diversity analysis, measured by Bray-Curtis distances, the microbiota of crossbreed samples has been significantly affected by liquid whey diet (PERMANOVA p < 0.001). The global microbial composition of Nero Siciliano samples has not been significantly affected by liquid whey diet. Despite this, the beneficial effects of liquid whey diet were present in both pig genetic types. In fact, based on differential abundance analysis, Bifidobacterium and Ruminococcus were more prevalent at T2 in all treated samples; several species of these genera can promote intestinal health, and this could be a positive consequence of liquid whey administration. In conclusion, this metagenomic study is a first step in understanding how the breeding system affects the composition of intestinal bacterial communities in different genetic types of pigs.