A cohort study of the bacterial faecal microbiota development post-weaning in healthy piglets in pig herds with different intestinal health status

Abstract Background Weaning of piglets in commercial production involves a sudden separation from the sow and an abrupt switch to a grain-based feed. During this phase of gut microbiota adaptation, disease-associated bacteria, such as enterotoxin-producing Escherichia coli , can proliferate, causing post-weaning diarrhoea (PWD). An observational cohort study of the faecal microbiota development during the first three weeks post-weaning in apparently healthy piglets from three farms was conducted. Four sample series were made, where Farm 1, which had no clinical signs of PWD, was sampled twice. Farm 2 had intermittent PWD problems, and Farm 3 used high-dose zinc oxide (ZnO) after weaning. Rectal swab samples were collected before weaning and on days 3, 7, 10, 14 and 21 after weaning. The bacterial faecal microbiota was assessed using 16S rRNA V3-V4 variable region sequencing. Results Of the identified amplicon sequence variants, 99% and 84% could be classified at the phylum and family level, respectively. Firmicutes and Bacteroidota were the two dominant phyla in all study groups. In Farm 2, with intermittent PWD problems, the relative abundance of Proteobacteria was significantly higher compared to the other study groups ( P < 0.05). There was a significantly higher relative abundance of bacteria from the family Prevotellaceae in the second study group from Farm 1. The alpha diversity increased post-weaning in all study groups except for Farm 3, which used ZnO. Beta diversity showed an increased similarity between the piglets’ microbiota over time and across farms. Conclusions A difference between the gut microbiota of piglets before and after weaning was found in all study groups. Weaning led to an imbalance in gut microbiota and changes to the faecal consistency, even in piglets without clinical PWD. The faecal microbiota composition differed between study groups and across the study period, also between repeated samplings of the same farm. The higher relative abundance of Proteobacteria in the herd with intermittent PWD problems could be a contributing factor to the recurring issues with PWD in this herd. The use of ZnO seemed to have delayed the maturation of the microbiota, although further studies are needed to confirm this. Overall, the results show that no single microbiota composition can predict weaning without gut disturbances.