Comparing the effect of faecal microbiota and faecal filtrate transplantations on intestinal health in weaned piglets

Abstract Background Faecal microbiota transplantation (FMT) and faecal filtrate transplantation (FFT) have emerged as promising methods to prevent intestinal dysbiosis and diarrhoea in piglets after weaning. The aim of this study was to compare the effects of FMT and FFT on intestinal health and microbiota dynamics in weaned piglets. Thirty-six 28-day old piglets were allocated into three treatment groups (FMT, FFT, and control, n = 12 each) at an experimental farm. Intact and filtered faeces from healthy sows were lyophilised, encapsulated, and administered upon arrival (day 0) and after 4 days (day 4). Clinical status, faecal consistency, and body weight were monitored over three weeks. Faecal samples were collected on days 4, 7, 11, 16, and 21 for microbiome analysis. On day 21, piglets were euthanized, and intestinal tissues were collected for morphometric analysis and ileal IgA measurement. Results Both FMT and FFT altered gut microbial composition, with an increased abundance of short-chain fatty acid (SCFA) producing genera and species. FMT induced the most significant changes on days 4 and 7 post-transplantation, whereas FFT led to sustained changes over time. FMT significantly improved intestinal morphology, increasing villus-to-crypt ratios in the jejunum, ileum, and duodenum, while the effect of FFT was limited to the duodenum. In addition, FMT increased secretory IgA (sIgA) concentrations in ileal content indicating microbiota-induced immune modulation. No differences in clinical signs, faecal scores, weight gain or abundance of antimicrobial resistance genes were observed among groups. Conclusions These results demonstrate that freeze-drying encapsulated FMT and FFT are safe and effective approaches to modulate the gut microbiota in weaned piglets, with FMT offering additional benefits for intestinal development and immunity.