Abstract

Introduction Early-life microbial colonization is fundamental to porcine health and production efficiency. However, the distinction between age-related development and weaning-induced shifts in the gut microbiota remains insufficiently characterized. Methods This study investigated the longitudinal development of fecal microbiota in Duroc × Landrace × Yorkshire piglets from birth to day 28. Results and discussion Using 16S rRNA gene sequencing, we first mapped the microbial development of suckling piglets, identifying a non-linear progression characterized by three distinct stages: initial colonization (days 1–7), rapid transition (days 14–21), and a stabilization stage (days 24–28). We then compared suckling piglets with those weaned at day 21. While no differences were observed on the day of weaning, weaned piglets exhibited significantly higher microbial richness and diversity by days 24 and 28 compared to suckling counterparts. β-diversity analysis confirmed a significant structural difference post-weaning, suggesting that weaning disrupt the developmental progress. Based on the LEfSe analysis and Random Forest models, Lactobacillus and Collinsella were identified as discriminative taxa in suckling and weaned piglets. These findings provide a map of microbial assembly and offer theoretical targets for mitigating weaning stress through microbial modulation.