Characterizing the effect of in-feed antibiotics and zinc oxide removal in the taxonomic and functional microbiota traits of post-weaning pigs in commercial farms.

Post weaning diarrhoea (PWD) is a disease that causes economic problems and piglet mortality at weaning. Current restrictions limit the use of in-feed antibiotics (Ab) and therapeutic in-feed zinc oxide (ZnO) use was forbidden recently. Microbiome changes occurring at weaning comprise both a risk factor for and a consequence of PWD. In this study, shotgun metagenome sequencing was used to characterize microbiome changes at the first two weeks post weaning within three scenarios Ab ZnO and no medications on commercial farms using regularly antimicrobials in the post weaning period. The results from this study map the microbiome of piglets at weaning and will be useful to guide alternatives to antimicrobial compounds to keep or restore the microbial equilibrium at weaning.