Previous studies have revealed that both the production environment (conventional versus pasture-based) and the co-housing of pigs with other farm species can alter gut microbial communities. The present research involved two separate experiments aimed at profiling the 16S fecal microbiota of the native Krškopolje pig breed. Each experiment included three treatment categories: (i) pigs raised on pasture together with small ruminants (group L1, farm 1), (ii) pigs kept indoors without any contact with other livestock (group L2, farm 2), receiving the same organic diet as the remaining groups, and (iii) pigs raised outdoors in shared pastures with cattle (group L3, farm 2). Sampling occurred four times throughout the grower–finisher stage, aligning with seasonal variation. In total, 18 animals were assessed in the first trial and 22 in the second. Alpha-diversity values did not differ notably across groups or age categories. Across all groups, Firmicutes and Bacteroidota dominated the microbial composition. Clear microbial shifts were associated with age (nonparametric MANOVA, p < 0.008) in both trials. Microbial patterns in L1 differed significantly from L2 and L3, while the latter two were more closely aligned. Findings suggest that the specific trial setup and farm location exert a stronger impact on gut microbial profiles than housing type alone.
