Abstract
BACKGROUND: The gut microbiome is regarded as an important source of information to better understand and improve health and growth in animals. However, there is a knowledge gap concerning the effects of management and health in commercial farms on the porcine faecal microbiome. This study aimed to identify the main factors associated with differences in microbiota alpha and beta diversity, resistome and functional profiles between and within farms and to study the associations between microbiome and farm characteristics. The faecal microbiomes at four production stages were examined in 18 farms, using shotgun sequencing. RESULTS: Microbiota richness increased with age while evenness and Simpson diversity decreased. Production stage was associated with microbiota composition, resistome and functional profiles, and most differences in the microbiome were observed between weaned pigs and older animals. Microbiota richness, diversity and evenness were higher in farms that purchased feed and in those with lower salmonella prevalence. Microbiota composition was associated with use of zinc oxide and medicated feed in young pigs and with health, biosecurity and feed form in older pigs. Feed form was associated with resistome, functional profiles and especially with core microbiota, as dry fed pigs showed higher abundances of Streptococcus alactolyticus. CONCLUSIONS: Consistent patterns of alpha and beta diversity were observed across farms with contrasting characteristics, suggesting that the faecal microbiota in commercial pig farms is primarily driven by diet and age, rather than health. Associations between microbiome, salmonella prevalence and diet suggested that diet induced changes in the microbiome may be a determining factor in gut colonization and infection by pathogens. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40813-025-00480-3.