Dynamics of fermentation profile, bacterial communities and their functional characteristics in red clover

Abstract The bacterial community is important for shaping the fermentation characteristics of silage. This study aimed to investigate the fermentation characteristics, bacterial community and predicted functional characteristics of red clover ( Trifolium pratense L.) silage. First-cutting red clover was collected at the early bloom stage, wilted for 5 h and then ensiled in 10 litre-capacity silos. Triplicate silos were sampled after 1, 3, 7, 15, 30 and 60 days of ensiling, respectively. The bacterial communities on days 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional characteristics were analysed based on the KEGG using Tax4Fun. After 60 days of ensiling, red clover silage was fermented well, as indicated by high lactic acid (~77.3 g/kg DM), and low concentrations of butyric acid (~3.73 g/kg DM) and ammonia nitrogen (~55.0 g/kg TN). During the initial stage of ensiling, fructose and glucose were more preferred than sucrose for microbes. The predominant genus Lactococcus (0.542) on day 3 was replaced by Lactobacillus (0.553) on day 60. The metabolism of amino acids, energy, cofactors and vitamins was inhibited, while the metabolism of nucleotides and carbohydrates was enhanced after ensiling. High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of red clover silage not only for distinct bacterial compositions but also for specific functional traits. Our results could provide a comprehensive insight into bacterial community and their functional profiles to further improve the silage quality.