Selection of a reasonable herbage mowing height is a crucial but easy-to-overlook problem for promoting cleaner production for a feed company. To evaluate the effects of mowing height at harvest on the fermentation products, microbial community, co-occurrence networks, functionality and pathogenic contamination risk of hybrid Pennisetum (HP) silage, HP harvested at two mowing heights (45 cm, F45; 15 cm, F15) were spontaneously ensiled (S45 and S15) for 2, 4, 8, 16, 32 and 64 days. The decrease of the mowing height significantly (P < 0.05) increased the water soluble carbohydrate content (145–162 g/kg dry matter), and numerically increased Enterobacter cloacae (0.02%–0.47%), Klebsiella oxytoca (0.00%–0.12%) and Serratia marcescens (0.00%–0.05%) levels. After ensilage, S45 and S15 presented lactic fermentation with high lactic acid concentration and Lactiplantibacillus proportion, low pH value and absent butyric acid. Both mowing height and storage length affected the complexity of bacterial co-occurrence networks. The decrease of mowing height significantly (P < 0.05) reduced the bacterial KEGG carbohydrate metabolism before ensilage, but there were no significant (P > 0.05) differences in this crucial functionality between mowing heights after ensilage. Ensilage promoted the key Glycolysis pathway and related enzymes (glucose-6-phosphate isomerase, 1-phosphofructokinase, pyruvate kinase, L-lactate dehydrogenase) associated with lactic acid synthesis, but suppressed undesirable lysine, valine, leucine and isoleucine degradation pathways. In bacterial phenotype analysis, regardless of storage length, low mowing height (F15 or S15) had significantly (P < 0.05) higher proportions of ‘Contains Mobile Elements’ and ‘Potentially Pathogenic’ than high mowing height (F45 or S45). These results concluded that although both mowing heights appeared to present the parameters of desirable fermentation, the risk of microbial contamination and pathogens from low mowing heights was not eliminated by 64-day ensilage. Therefore, a relatively high mowing height, e.g. 45 cm, is recommended to ensure the cleanliness, hygiene and safety of HP silage.
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