Fecal microbiome dynamics in sows and piglets following the replacement of antibiotics with Bacillus probiotics during the transition and lactation periods under tropical conditions

Background In tropical environments, probiotics are increasingly explored as alternatives to antibiotics in sow diets, aiming to stabilize gut microbiota and mitigate antimicrobial resistance. This study investigated the temporal dynamics of the fecal microbiome in sows and piglets following dietary supplementation with Bacillus sp. probiotics during the transition and lactation periods under tropical conditions. A total of 150 fecal samples were analyzed using 16S rRNA gene sequencing. Sixty samples were obtained from 20 sows at day 0 (entry into the farrowing pen), day 7 (farrowing), and day 28 (weaning), while 90 samples were collected from 30 piglets at 3, 7, and 21 days of age. Sows (n = 10) and piglets (n = 15) were assigned to either CONTROL or TREATMENT groups. The TREATMENT group received Bacillus sp. probiotics (1.1 × 10⁹ CFU/kg) in both sow feed and creep feed, whereas the CONTROL group received standard feed. No antibiotics were included in either diet. Alpha diversity, beta diversity, and taxonomic profiles were compared across time points. Results In sows, microbial richness (Chao1 index and observed features) was higher in the CONTROL group on days 7 and 28 ( p  < 0.05). In piglets, the Shannon and Chao1 indices were lower in the CONTROL group at day 21 ( p  < 0.05). In both sows and piglets, no significant differences were detected in overall microbial community composition between groups ( p  > 0.05). No significant differences in the relative abundance of dominant phyla in sows (e.g., Firmicutes, Bacteroidota, Spirochaetota, and Proteobacteria) were detected across the three time points (days 0, 7, and 28) in the CONTROL group ( p  > 0.05). However, in the TREATMENT group, the abundance of Bacteroidota on day 7 was higher than on day 0 ( p  = 0.025), but did not differ from that on day 28 ( p  > 0.05). The abundance of Spirochaetota was reduced on both day 7 ( p  = 0.014) and day 28 ( p  = 0.002) compared with day 0. Regarding the natural dynamics of fecal microbiota in piglets, at the phylum level, Bacteroidetes was less abundant on day 3 (29.4%) compared with day 7 (34.9%) ( p  = 0.001) and day 21 (30.0%) ( p  = 0.049). Proteobacteria was more abundant on day 3 (10.1%) than on day 7 (4.6%) ( p  = 0.007) and day 21 (3.5%) ( p  = 0.003). At the genus level, Bacteroides abundance was greater in the TREATMENT group at day 21 compared with the CONTROL group (7.5% vs. 3.7%, p  = 0.028). Across ages, in both the CONTROL and TREATMENT groups, Bacteroides , Clostridium , Enterococcus , Escherichia–Shigella , Lactobacillus , and Streptococcus declined, whereas Christensenellaceae_R-7_group , Prevotella , and Oscillospiraceae UCG-002 increased ( p  < 0.05). Conclusion Bacillus sp. supplementation influenced microbial richness and the relative abundance of specific taxa in sows and piglets but did not markedly alter overall gut community structure. In sows, Bacillus sp. supplementation led to changes in the relative abundance of dominant phyla, whereas in piglets it influenced the abundance of dominant genera. Compared with the relatively stable sow microbiome in terms of richness and diversity, the developing piglet microbiome exhibited more dynamic shifts. These changes likely reflect microbial maturation toward greater diversity, richness, and taxonomic complexity by 21 days of age, both with and without Bacillus sp. supplementation.