Exploring microbial community structure and metabolic gene clusters during silage fermentation of paper mulberry, a high-protein woody plant

•This is the first report on metabolic gene clusters in paper mulberry silage.•Ensiling causes a shift in dominant bacteria from Gram-negative to Gram-positive.•Enterobacter and Lactobacillus species determine silage fermentation quality.•PacBio sequencing reveals microbial dynamics during silage fermentation.•Paper mulberry can be used to prepare high-quality nutrient-rich silage. To develop a new high-protein woody forage resource for livestock to alleviate feed shortages in the tropics, we applied PacBio single-molecule, real-time (SMRT) sequencing to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms associated with paper mulberry (PM) silage fermentation. High levels of microbial diversity and abundance were observed in PM raw material, and these levels decreased with the progression of silage fermentation. During woody ensiling, the dominant bacteria shifted from pathogenic Gram-negative Proteobacteria to beneficial Gram-positive Firmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in terminal silages. Global and overview maps, carbohydrate metabolism and amino-acid metabolism were the important microbial metabolic pathways that impacted the final fermentation product of silage. PacBio SMRT sequencing revealed specific microbial-related information concerning silage. PM is rich in nutrients and macro mineral contents, which are preserved well during ensiling, indicating that PM silage can serve as a new woody resource suitable for ruminants.