Microbiota composition of an autochthonous Krškopolje pig breed reared in two different organic production systems

It has been shown that different production systems (conventional vs. pasture-raised pigs) and co-rearing of pigs with other livestock influence the gut microbiota composition in pigs. In this study, two independent trials were conducted to investigate the 16S fecal microbiota of the autochthonous Krškopolje pig. In each trial, three study groups were analyzed: ( i ) pasture-raised pigs cohabiting with small ruminants (group L1, farm 1), ( ii ) indoor-raised pigs without contact with other farm animals (group L2, farm 2) and fed the same commercial organic feed as the other two groups, and ( iii ) pasture-raised pigs cohabiting with cattle (group L3, farm 2). The pigs were sampled four times during the grower-finisher period, corresponding to the different seasons. A total of 18 and 22 pigs were included in trials 1 and 2, respectively. Alpha diversity was comparable between the study groups and the pigs of different age categories. The two predominant bacterial phyla in all three groups were Bacteroidota and Firmicutes. Significant differences in microbiota composition were found between pigs of different age categories in both trials (nonparametric MANOVA, p  < 0.008). The microbiota composition of pigs from group L1 was significantly different from that of pigs from groups L2 and L3, whereas groups L2 and L3 tended to be more similar in both trials. The present results indicate that the trial and the farm of origin have a significant influence on the pig gut microbiota, and that their influence is more pronounced than that of the housing system.