| Summary: | We investigated the effects of early intervention with maternal fecal microbiota and antibiotics on gut microbiota and the metabolites. Five litters of healthy neonatal piglets (Duroc × Landrace × Yorkshire, nine piglets in each litter) were used. Piglets in each litter were orally treated with saline (CO), amoxicillin treatment (AM), or maternal fecal microbiota transplantation (MFMT) on days 1⁻6, with three piglets in each treatment. Results were compared to the CO group. MFMT decreased the relative abundances of <i>Clostridium sensu stricto</i> and <i>Parabacteroides</i> in the colon on day 7, whereas the abundance of <i>Blautia</i> increased, and the abundance of <i>Corynebacterium</i> in the stomach reduced on day 21. AM reduced the abundance of <i>Arcanobacterium</i> in the stomach on day 7 and reduced the abundances of <i>Streptococcus</i> and <i>Lachnoclostridium</i> in the ileum and colon on day 21, respectively. The metabolite profile indicated that MFMT markedly influenced carbohydrate metabolism and amino acid (AA) metabolism on day 7. On day 21, carbohydrate metabolism and AA metabolism were affected by AM. The results suggest that MFMT and AM discriminatively modulate gastrointestinal microflora and alter the colonic metabolic profiles of piglets and show different effects in the long-term. MFMT showed a location-specific influence on the gastrointestinal microbiota.
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