Maternal Microbial Reservoirs Are Associated with Early Bacterial and Archaeal Community Assembly in Neonatal Hu Lambs

Early-life microbial community assembly is important for gastrointestinal development, immune maturation, and feed utilization in young ruminants, but the maternal reservoirs associated with neonatal lamb gut microbial profiles remain insufficiently defined. This exploratory study characterized bacterial and archaeal communities in maternal vaginal secretions, amniotic fluid, and colostrum, together with rectal feces from Hu lambs at birth and at 5 days of age, using 16S rRNA gene amplicon sequencing in six matched ewe–lamb pairs. Alpha-diversity differences were evaluated using the Kruskal–Wallis test followed by pairwise Wilcoxon rank-sum tests where appropriate, beta-diversity was assessed by principal coordinate analysis based on Bray–Curtis distance, and discriminatory taxa were identified using LEfSe; statistical significance was defined as p < 0.05. Microbial community structure differed among sample types. Feces collected at birth showed low bacterial richness and a distinct community profile, whereas feces from 5-day-old lambs displayed higher bacterial richness and a more complex taxonomic composition. Shared-ASV and LEfSe analyses suggested that vaginal-associated taxa were more closely associated with the initial fecal microbiota at birth, while colostrum-associated taxa were more evident in day-5 feces. Archaeal communities showed weaker separation than bacterial communities, but methanogenic lineages became more distinguishable by day 5. These findings suggest that early gut microbial assembly in Hu lambs is associated with multiple maternal reservoirs and rapid postnatal ecological selection. However, due to the limited sample size, short observation period, lack of formal source-tracking analysis, and absence of low-biomass negative controls, the results should be interpreted cautiously as preliminary associations rather than definitive evidence of vertical transmission.