Comparative Analysis of Mare Milk and Foal Faecal Microbiota in Kyrgyz Mare–Foal Pairs During the First 21 Days Postpartum

This pilot study characterised bacterial DNA profiles in 40 milk and 39 faecal samples from eight Kyrgyz mare–foal pairs collected at birth, 24 h, and days 7, 14, and 21 postpartum using V3–V4 16S rRNA gene sequencing. Permutation Friedman tests detected temporal differences in foal faecal Shannon diversity and observed feature counts (Holm-adjusted p = 0.020 for both), but not in milk. Faecal diversity was descriptively lower at 24 h and day 7 than at birth and increased at days 14–21. Animal-blocked weighted UniFrac PERMANOVA detected a temporal effect in faecal DNA profiles (Holm-adjusted p = 0.0028), but not in milk (p = 0.0956). Pair-blocked milk–faecal comparisons were significant at each time point (Holm-adjusted p = 0.0391), although differences in dispersion limit interpretation. Without sequenced negative controls, background contamination cannot be distinguished from genuine milk-associated bacterial DNA; therefore, milk profiles cannot be confidently attributed to resident milk microbiota. Observed taxonomic similarities do not demonstrate microbial transmission or milk-derived foal gut colonisation. Significance in faeces but not milk does not establish a difference between their temporal responses, which was not directly tested. These findings are exploratory and require controlled validation.