Exploring the microbial community structure and metabolic gene clusters during silage fermentation of paper mulberry, and developing the high-protein woody plant as ruminant feed

Abstract

ABSTRACTTo develop a new high-protein woody forage resource for livestock, we applied PacBio single-molecule, real-time (SMRT) sequencing technology to explore the community structure, species diversity, and metabolic gene clusters of nature microbes associated with paper mulberry (PM) silage fermentation. The microbial diversity and abundance were rich in PM raw material and decreases with the progress of silage fermentation. Woody ensiling is process that the dominant bacteria shifted from Gram-negative pathogenic Proteobacteria to Gram-positive beneficial Firmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in the terminal silages. Global and overview maps, carbohydrate metabolism and amino acid metabolism were the important microbial metabolic pathways that impact final fermentation product of silage. PM is rich in nutrients and preserved well during ensiling, indicating PM can develop as new woody resources suitable for ruminants. PacBio SMRT sequencing revealed specific microbial-related information about silage.IMPORTANCE In the tropics, there is often a shortage of forage during the dry season. Failure to obtain high-quality feed will reduce the milk and meat production of ruminants. Therefore, it is essential to maximize the use of land and biomass resources through strategic development of alternative feed. Paper mulberry (PM) is a perennial deciduous tree in tropics, with a variety of nutrients and biologically active ingredients, and it adapts to various soils and climates, with high production capacity, and low cultivation costs. In order to develop new potential woody forage, we firstly used PacBio single-molecule real-time (SMRT) sequencing technology to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms related to the fermentation of silage. PacBio SMRT revealed information about specific microorganisms related to silage, indicating PM can prepare as good-quality silage, and will become a new potential woody feed resources for livestock.View Full Text