Impacts of farming practices on pig gut microbiota and their interactions with soil microbial communities in tropical agroecosystems.

Livestock farming systems are associated with differences microbial communities in both animals and soils, yet the ecological mechanisms linking these compartments remain poorly understood. This study investigated the effects of contrasting farming systems (intensive vs. agroecological) on the gut microbiota of Creole pigs and associated soil microbial communities in farms located in Guadeloupe (French West Indies). Fecal and soil samples were analyzed using 16S and 18S Ribosomal Ribonucleic Acid (rRNA) genes metabarcoding to characterize bacterial, archaeal and fungal diversity. Pig gut microbiota was dominated by Bacillota (63.44% and 67.55% for intensive and agroecological raised pigs respectively) and Bacteroidota (24.70% and 18.56% for intensive and agroecological raised pigs respectively), whereas soils were mainly dominated by Acidobacteriota (14.61% and 17.48% for plowed and unplowed soil respectively), Actinomycetota (7.61% and 9.05% for plowed and unplowed soil respectively), and Bacillota (6.62% and 9.87% for plowed and unplowed soil respectively), indicating limited taxonomic overlap. Agroecological management was associated with higher relative abundances of Bacillota and Euryarchaeota in pigs and greater fungal diversity in soils. A total of 234 operational taxonomic units (OTUs) were common to all four groups (pig gut-agroecological, pig gut-intensive, plowed soil and unplowed soil), representing the microbial taxa shared between gut and soil environments; however, these taxa were generally abundant in the gut and rare in soils. These results suggest an ecological link between pigs and soil microbial communities that may be mediated by environmental processes. This underscores the interconnectedness of animal and environmental health within a One Health framework.