Intestinal microbiota composition in free-range pigs is associated with the presence of Salmonella

Extensive pig systems are gaining importance as quality production systems and as standard for sustainable rural development and animal welfare. However, the effect of natural food on Salmonella epidemiology remains unknown. Here we assessed the presence of Salmonella in the intestinal content, the risks factors associated, and the gut microbiota composition in pigs selected from Salmonella-free and high prevalence farms. The pathogen was found in 32.2% of animals and 83.3% of farms, observing large prevalence differences between farms. Most of isolates were serovars Typhimurium monophasic (79.3%) and Bovismorbificans (10.3%), exhibiting multi-drug resistance (58.6%). Risk factor analysis identified feed composition, type/variety of vegetation available, and silos’ cleaning/disinfection, as mainly (p = 0.008) associated with Salmonella prevalence. Fixing these factors, clear differences in the intestinal microbiota were found between Salmonella-positive and Salmonella-negative populations, showing the former increasing Proteobacteria and decreasing Bacteroides populations. Butyrate and propionate producers, including Clostridium, Turibacter, Bacteroidaceae_UC, and Lactobacillus were enriched in the Salmonella-negative group whereas acetate producers like Sporobacter, Escherichia or Enterobacter were more abundant in the Salmonella-positive group. Overall, our results suggest that the presence of Salmonella in free-range pigs’ gut is directly related to the natural vegetation accessible, determining the composition of the intestinal microbiota.