Fecal microbiome dynamics across reproductive stages in primiparous Świniarka sheep: a longitudinal study

Abstract

Reproductive transitions in ruminants are accompanied by substantial endocrine and metabolic changes that may be associated with alterations in gut microbial communities. However, temporal variation in the fecal microbiome across reproductive stages in primitive sheep breeds remains poorly characterized. This longitudinal study aimed to characterize temporal patterns in the fecal microbiome in primiparous Świniarka sheep across three reproductive stages: mating (T1), lambing (T2), and the end of lactation (T3), using 16 S rRNA gene amplicon sequencing. Alpha diversity did not differ significantly between stages, although several indices showed numerically higher values at T2 and T3; these differences did not reach statistical significance in repeated-measures analyses. Beta diversity analyses based on Bray–Curtis, weighted UniFrac, and unweighted UniFrac distances showed overlapping community profiles, with no significant stage-associated differences after accounting for repeated measurements within animals (PERMANOVA, P > 0.05). The fecal microbiome was dominated by Firmicutes and Bacteroidota across all reproductive stages. Core microbiome analysis identified 28 genera present at a relative abundance of at least 0.1% in at least 80% of samples, together accounting for an average of 83.45% of the microbial community. PICRUSt2 identified 329 predicted MetaCyc pathways, none of which differed significantly among reproductive stages after false-discovery-rate correction. DESeq2 identified stage-associated differences in selected genus-level taxonomic features, with 14 significant features between T2 and T1, 13 between T3 and T1, and four between T3 and T2. Within this exploratory longitudinal cohort, reproductive stage was not associated with statistically detectable differences in alpha diversity, overall microbial community structure, or predicted functional pathway profiles genus-level abundance after correction for multiple testing. However, differential-abundance analysis identified stage-associated changes in selected genus-level. Dominant taxonomic features, particularly in comparisons of T2 profiles and T3 with T1. A high-abundance shared microbial core was observed across all stages, indicating limited global restructuring of the fecal microbiome detectable temporal variation under the studied conditions. These findings do not establish ecological resilience or equivalence among reproductive stages.