A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic pathogens

The microbiome of wild animals is believed to be co-evolved with the host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practice in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from 9 farms in Canada and 39 wild pigs sampled from three different locations on two continents (America and Europe) using 16S rRNA amplicon sequencing.