Gut microbiota composition in Krškopolje pigs under conventional and organic production systems
The Krškopolje pig is the only indigenous Slovenian pig breed being still farmed. The breed is characterised by its rusticity and adaptation to the traditional farming system and has a black coat colour with a white belt across shoulders and forelegs. Despite the limited number of animals, the breed is on the way of becoming more sustainable due to the growing interest for local traditional breeds, in particular for organic farming. The objective of our study (made within project TREASURE) was to characterise the gut microbiota composition in 36 Krškopolje pigs raised by using three different diets: conventional feed, conventional feed supplemented with alfalfa pellets and organic feed supplemented with alfalfa hay. The gut microbiota composition of all pigs at two time points (155 and 228 days-ofage) was determined by resequencing the bacterial 16S gene in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime's open-reference OTU calling subsampled method following author's recommendations. NMDS and PERMANOVA analyses performed by the Vegan R package showed significant effects of dietary regime, showing that the organic feed produces a differentiation of the gut microbiota composition when compared with the other two diets and the two time points analysed. This pilot study illustrates the power of metagenomic analyses for the identification of effects of diets in the farming conditions of local European pig breeds. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).