Faecal filtrate transplantation in neonatal pigs induces gut microbiota changes and reduces mortality and diarrhoea

Enteritis and gut microbiome dysbiosis cause morbidity and mortality in suckling and weanling pigs. We hypothesised that oral faecal filtrate transplantation (FFT) from healthy sow donors to neonatal piglets would modulate gut colonization, prevent diarrhoea, and improve survival and growth. Piglets were randomised to receive oral FFT (n =150) or placebo (CON, n =150) daily for six days. Colon microbiota composition was analysed by 16S rRNA gene amplicon and metagenomic sequencing on days 27 and 41, alongside resistome, blood lactate and immunoglobulin (Ig) G, and gut enzymatic activity analysis. Growth, diarrhoea, and survival were monitored throughout. Baseline characteristics, including birth weight, blood lactate, and IgG, were similar between groups. The FFT reduced post-weaning diarrhoea and mortality pre- and post-weaning ( p < 0.05). This reduction was associated with distinct changes in the faecal microbiota composition, including the enrichment of metagenome-assembled genomes assigned to beneficial bacterial families such as Oscillospiraceae and Lachnospiraceae . The FFT also influenced β-diversity and gut enzymatic activity, suggesting a broader intestinal health impact. Importantly, FFT did not increase antimicrobial resistance genes of public health concern. The FFT recipients exhibited higher body weights during suckling, though no significant weight differences post-weaning. Mucosal disaccharidase and aminopeptidase activities were lower in FFT piglets on day 41 ( p < 0.05), while plasma intestinal fatty-acid binding protein levels remained similar. In conclusion, FFT reduced post-weaning diarrhoea and mortality, influenced gut microbiota and enzymatic activity, and tended to promote suckling growth. If approved, FFT could support weaning and reduce antimicrobial use in pig production.