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

Abstract

To 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

Impacts of Low Temperature and Ensiling Period on the Bacterial Community of Oat Silage by SMRT

“…Shorter sequences with relatively low taxonomical resolution have limited the classification of microorganisms in the community to the genus level [ 13 ]. The method of PacBio single molecule, real time sequencing technology (SMRT) could classify the bacteria into species level because of its relatively high taxonomic resolution [ 14 , 15 ], which could help us seek the certain species adapted to low temperature. Unfortunately, until now, relevant studies are seldom.…”

New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods

“…Thus, microbial fermentation can be regarded as a potential technology for the release of certain bioactive compounds from natural resources [ 7 ]. Simultaneously, fermentation processes involve initial digestion of foods to improve absorption thereof in the human body [ 8 ]. Moreover, they enrich food with such ingredients as proteins, sugars, vitamins, and amino acids.…”

Replacing Alfalfa with Paper Mulberry in Total Mixed Ration Silages: Effects on Ensiling Characteristics, Protein Degradation, and In Vitro Digestibility

“…Since the quantity of alfalfa can no longer meet the requirements of dairy farms, the contradiction between demand and supply has increased sharply [ 1 ]. Finite access to high-quality forage decreases milk and meat production for livestock industry, undermines health and welfare of animals, and contributes to loss of economic benefits for farmers [ 2 ]. Therefore, exploring locally produced, high yielding, alternative forage resource to ensure satisfactory animal production becomes an urgent problem to be solved.…”

“…As one of China’s top ten targeted poverty alleviation projects, over 300,000 hectares of RY are cultivated in China [ 3 ]. It is rich in crude protein (CP) and contains highly digestible fiber and minerals [ 2 ]. Multiple biologically active ingredients are also associated with its antioxidant and anti-inflammatory functions in ruminants [ 3 , 4 ].…”

“…Over-production would be discarded in the field, causing squandering of resources [ 6 ]. Recently, the conservation of RY as silage has proven to be effective for overcoming the gap between annual animal production and seasonal imbalance [ 2 ]. Nevertheless, similar to other high-protein forages (e.g., legume forages), the fermentation quality of ensiled RY is usually unsatisfactory, as indicated by extensive proteolysis, high butyric acid content, and unfavorable odor [ 6 , 7 ].…”