Abstract This study combined applied PICRUSt2 and BugBase tools to evaluate the effects of these two strains on the fermentation characteristics, microbial community, potential microbial risk and hygienic quality of whole-crop corn (WCC) silage. Fresh WCC harvested at the dough stage was ensiled with distilled water (CON), Leuconostoc lactis (LS) and Weissella confusa (WA) for 2, 4, 8, 15 and 30 days. After ensiling, all WCC silages presented desirable fermentation with high lactic acid and Lactobacillus proportions, low pH and ammonia nitrogen levels and absent butyric acid. Ensiling decreased the complexity of bacterial co-occurrence networks, and the Lc. lactis and W. confusa inoculation further decreased the complexity. The inoculation of W. confusa suppressed the most pathogenic pathways and related modules associated with zoonosis. In bacterial phenotype predicted analysis, although CON had lower proportions of ‘Potentially pathogenic’ than fresh material, this undesirable phenotype declined to negligible levels via LS and WA inoculation. Even for well-fermented WCC silages, the risk of pathogens remained after 30 days of ensiling. Therefore, WA could be developed as a promising fast start-up inoculant for reducing pathogenic contamination and improving hygienic quality of silage. Graphical Abstract
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