Inter-breed diversity and temporal dynamics of the fecal microbiota in two local chicken breeds from karst regions in China.

The aim of this study was to investigate the temporal dynamics and inter-breed differences of fecal microbiota in two indigenous chicken breeds from Guizhou during the early post-hatch period. Six hundred chicks, including 300 Guizhou yellow chickens (GY) and 300 Changshun green-shell egg chickens (CG), were reared under identical conditions, and fecal samples were collected at post-hatch days 1, 3, 7, 14, 30, and 45. Microbial communities were analyzed using 16S rRNA gene sequencing. Alpha diversity analysis revealed a progressive increase in microbial richness and diversity with age in both breeds, with CG peaking at day 45 and GY at day 30. Beta diversity analysis indicated breed-specific clustering, reflecting distinct temporal succession patterns. Taxonomic profiling showed Bacillota as the dominant phylum across all time points, while Enterococcus and Ligilactobacillus were the core genera, with early samples enriched in Escherichia-Shigella and Clostridium. LEfSe analysis identified age- and breed-specific microbial biomarkers, demonstrating a general trend of early dominance by Clostridia and Escherichia-Shigella, mid-stage enrichment of diverse genera including Candidatus Arthromitus and Ruminococcus, and late-stage prevalence of lactic acid bacteria such as Lactobacillus and Streptococcus. Functional prediction indicated carbohydrate and amino acid metabolism as the predominant microbial functions. Quantification of ecological processes revealed that homogeneous selection constituted the dominant mechanism, overwhelmingly governed microbiota assembly, with stochastic processes playing a minor, breed-specific role. The CG breed exhibited a pattern of rapid, directional succession, culminating in a stable and phylogenetically conserved community. This suggests that host genetic factors may exert strong and consistent deterministic selection, which could thereby facilitate the formation of specialized microbiota. In contrast, the GY breed displayed a more gradual and variable assembly process, resulting in a community with higher temporal turnover and greater phylogenetic plasticity. Overall, the findings reveal that inter-breed diversity is not merely compositional but extends to the underlying ecological rules governing community succession. Meanwhile, these findings suggest that inter-breed diversity may be shaped by host genetic factors, which in turn mold the temporal assembly and functional features of the early gut microbiota, providing insights into precision nutritional management and health optimization for local poultry breeds.