Metatranscriptomic insights into the effect of Lactiplantibacillus plantarum inoculation on fermentation metabolism, bacterial community function and antibiotic resistome of corn silage
TL;DR
The results show that L. plantarum inoculation improved fermentation characteristics by reducing acetic acid accumulation and preserving water-soluble carbohydrates and was associated with differences in the late-stage dominant taxa and functional gene transcription but did not increase the active antibiotic resistome under controlled laboratory conditions.
Abstract
Lactic acid bacteria inoculants are widely applied in silage production; however, it remains unclear how Lactiplantibacillus plantarum inoculation shapes temporal changes in microbial function during ensiling, and whether it accelerates normal successional process or is associated with changes in antibiotic resistome dynamics. In this study, we applied an integrated metatranscriptomic approach combining microbial community profiling, differential expression analysis, carbohydrate-active enzyme (CAZy) profiling, and resistome characterization to analyze whole-crop corn silage inoculated with L. plantarum at fresh material (day 0), early fermentation (day 3), and late fermentation (day 90). The results indicated that inoculation was associated with higher expression of central carbon genes, including >30-fold induction of ackA at day 3 and 44 differentially expressed genes at day 90, together with higher residual water-soluble carbohydrates and reduced late-stage acetic acid accumulation. Nitrogen-related gene expression underwent marked temporal restructuring, shifting from broad early enrichment of glnA and denitrification-linked genes to targeted late-stage enrichment of nirA involved in nitrite assimilation. In LP-treated silage, we did not detect statistically significant temporal differences in CAZyme family-level transcript abundance between day 3 and day 90, whereas 56.4% of families shifted significantly over time in control silage. An existing core resistome was dominated by tet(C), APH (3’)-Ia, bacA, and tet(M), collectively accounting for 85%–94% of total ARG abundance across all treatments. Resistome configuration was determined mainly by fermentation time rather than LP inoculation. Notably, LP-driven gene expression changes did not increase the actively transcribed antibiotic resistome under the tested conditions, suggesting that the microbial community shifted without expanding the detected resistome profile. Overall, these results show that L. plantarum inoculation improved fermentation characteristics by reducing acetic acid accumulation and preserving water-soluble carbohydrates and was associated with differences in the late-stage dominant taxa and functional gene transcription but did not increase the active antibiotic resistome under controlled laboratory conditions. These results support the potential application of this inoculant in laboratory-scale silage production, although further validation across different forage types, strains, and field conditions is warranted.