Optimal apple pomace proportion yields a deterministically assembled bacterial community, improving cotton straw fermentation quality

Cotton straw and apple pomace are underutilized due to their respective limitations of high lignocellulose content and high moisture content. The co-fermentation of cotton straw and apple pomace offers a promising strategy for agricultural by-product utilization, though related research remains limited. This study investigated how apple pomace proportion regulates bacterial community assembly and subsequently affects bacterial community composition and fermentation quality of cotton straw fermented feed.Fermentation trials were conducted with cotton straw to apple pomace ratios ranging from 10:0 to 5:5 (on a dry matter basis). Compared with the control (100% cotton straw), apple pomace supplementation improved fermentation quality. In all apple pomace-added groups, the pH dropped below 4.6. The addition of apple pomace inhibited harmful bacteria such as Enterobacter; as its proportion increased, the dominant genus shifted from Lactiplantibacillus to Limosilactobacillus. Additionally, bacterial community assembly transitioned from stochastic to deterministic and back to stochastic dominance as the pomace proportion rose. When the proportion of apple pomace reached 30%, both the bacterial composition and metabolic profile tended to stabilize. Notably, the P4 (cotton straw: apple pomace = 7:3) group achieved the highest comprehensive score, with deterministic processes dominating community assembly and enriching beneficial bacteria such as Limosilactobacillus.In summary, an appropriate proportion of apple pomace promotes the enrichment of beneficial bacteria via deterministic processes and regulates the metabolome, thereby improving fermentation quality.