Integrating Machine Learning to Identify Key Microbiota of Gut Community Changes Across Different Stages in Dahe Black Pigs

Growth stage is a key factor influencing the composition and richness of the porcine gut microbiota. The stage-specific alterations in gut microbiota of indigenous Chinese pig breeds and cultivated breeds remain to be elucidated. This study conducted 16S rRNA sequencing analysis on fecal microbiota from Dahe black pigs across distinct growth stages. Samples included lactating sows, suckling piglets, weaned piglets, pigs weighing 50-100 kg, pigs weighing 120-150 kg, and pigs weighing > 200 kg. The results indicated that <i>Escherichia shigella</i> (12.4% vs. 16.2%), <i>Lactobacillus</i> (5.9% vs. 6.3%), and <i>Rikenellaceae RC9 gut group</i> (3.9% vs. 4.2%) were dominant genera shared between lactating sows and suckling piglets. The relative abundance of <i>Eubacterium brachy group</i> was significantly higher in lactating sows, whereas <i>Flavonifractor</i> was significantly lower compared to suckling piglets (<i>p</i> < 0.05). Compared to pigs weighing > 120 kg, lactating sows exhibited 22 differentially abundant genera, including <i>Escherichia shigella</i>, <i>Cloacibacillus</i>, <i>Fusobacterium</i>, <i>Faecalibacterium</i>, and <i>Prevotella</i> (<i>p</i> < 0.05). In suckling piglets, Firmicutes and Bacteroidota constituted 47.4% and 27.3% of the microbiota, respectively. Their relative abundance increased with body weight, reaching 52.6% and 33.3% in pigs weighing > 200 kg. Proteobacteria decreased from 17.3% in suckling piglets to 2.0% in >200 kg pigs. Spirochaetota declined from 2.5% in suckling piglets to 0.9% in weaned piglets and then increased to 6.9% in >200 kg pigs. <i>Lactobacillus</i> peaked at 15.7% in weaned piglets, while <i>Escherichia shigella</i> reached its maximum (16.2%) in suckling piglets, both gradually declining thereafter. <i>Streptococcus</i> abundance remained relatively stable (1.1% in suckling piglets; 4.5% in weaned piglets). <i>Prevotellaceae NK3B31 group</i> registered 2.9% in suckling piglets, increased to 7.1% in weaned piglets, and then declined to 2.6% in >200 kg pigs. <i>Mitsuokella</i>, <i>Bilophila</i>, <i>Succinivibrio</i>, <i>Romboutsia</i>, and <i>Desulfovibrio</i> were identified as the top five genera discriminating suckling and weaned piglets. Similarly, <i>Lachnospiraceae XPB1014 group</i>, <i>Clostridium sensu stricto 1</i>, <i>Turicibacter</i>, <i>Quinella</i>, and <i>p 1088 a5 gut group</i> were key discriminators between weaned piglets and 50-100 kg pigs. These identified microbial taxa represent potential candidate targets for modulating the developmental timing of growth phases in pigs, offering possibilities for either advancing or delaying specific physiological timepoints.