Cohort Study Tracks Post-Weaning Faecal Microbiota Changes in Healthy Piglets

In an observational cohort study examining bacterial faecal microbiota development in piglets, researchers found that weaning induced gut microbiota imbalances and altered faecal consistency across all evaluated groups, even in piglets that displayed no clinical signs of post-weaning diarrhoea. The findings demonstrated that no single microbiota composition could predict a weaning process free from gut disturbances. Furthermore, clear differences in faecal microbiota composition were observed between piglets before and after weaning, with bacterial profiles varying across the study period, between herds with different health statuses, and between repeated sampling series on the same farm.

The study investigated faecal microbiota development during the first three weeks post-weaning in apparently healthy piglets across three commercial farms. Commercial weaning involves a sudden separation of piglets from the sow alongside an abrupt transition to a grain-based diet, an adaptation phase during which disease-associated bacteria such as enterotoxin-producing Escherichia coli can proliferate and cause post-weaning diarrhoea. To evaluate bacterial shifts during this window, rectal swab samples were collected before weaning and on days 3, 7, 10, 14, and 21 after weaning, yielding four distinct sampling series across the herds.

The three participating farms featured differing health backgrounds and management approaches. Farm 1, which had no clinical signs of post-weaning diarrhoea, was sampled in two separate series. Farm 2 experienced intermittent problems with post-weaning diarrhoea, and Farm 3 administered high-dose zinc oxide following weaning. Bacterial faecal microbiota from the swabs was analyzed using 16S rRNA gene sequencing targeting the V3-V4 variable regions. Among the identified amplicon sequence variants, 99 percent were classified at the phylum level and 84 percent were classified at the family level.

Taxonomic classification showed that Firmicutes and Bacteroidota were the two dominant phyla across all study groups. Significant differences in bacterial abundance emerged between the herds. In Farm 2, which had intermittent diarrhoea issues, the relative abundance of Proteobacteria was significantly higher compared to the other study groups (P < 0.05). In addition, piglets in the second sampling series from Farm 1 showed a significantly higher relative abundance of bacteria from the family Prevotellaceae. Measurements of alpha diversity increased post-weaning in all study groups except for Farm 3, while beta diversity analysis indicated an increasing similarity between piglet microbiota over time and across farms.

The researchers concluded that the significantly higher relative abundance of Proteobacteria in Farm 2 could be a contributing factor to the recurring post-weaning diarrhoea problems seen in that herd. Meanwhile, the use of high-dose zinc oxide in Farm 3 appeared to delay the maturation of the gut microbiota, though the authors stated that further studies are needed to confirm this observation. Overall, the findings show that gut microbiota shifts and faecal changes occur routinely following weaning regardless of clinical disease, reflecting variable bacterial development across different farm conditions.

Subject of Research: Bacterial faecal microbiota development post-weaning in healthy piglets across different herd health environments

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

Article References: Klahr Fritz, M., Rosendal, T., Leijon, M., Sannö, A., Wallgren, P., & Sjölund, M. (2026). A cohort study of the bacterial faecal microbiota development post-weaning in healthy piglets in pig herds with different intestinal health status. BMC Microbiology, 26(1), Article 974. https://doi.org/10.1186/s12866-026-05888-7

Image Credits: AI Generated

DOI: 10.1186/s12866-026-05888-7

Keywords: piglets, gut microbiota, weaning, faecal microbiota, Proteobacteria, zinc oxide, 16S rRNA sequencing, post-weaning diarrhoea, cohort, bacterial, faecal, microbiota