The use of PacBio SMRT technology to explore the microbial network and fermentation characteristics of woody silage prepared with exogenous carbohydrate additives

Abstract

Aims: To effectively use woody plant resources to prepare silage for ruminants, Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing was applied to study the microbial network and fermentation characteristics of paper mulberry (PM) silage prepared with corn meal (CM) and rice bran (RB) as exogenous additives. Methods and Results: PM is rich in nutrients and contains more than 26% crude protein in dry matter. After ensiling, the microbial diversity and abundance in PM, CM and RB decreased due to the anaerobic environment and acidic conditions. The CM-treated PM silage accelerated the conversion of the dominant microbial community from harmful bacteria to lactic acid bacteria and promoted lactic acid fermentation. When RB was used to treat PM silage, Enterobacter and Clostridium species became the main bacterial community during ensiling, leading to butyric acid fermentation and protein decomposition. Compared with RB, CM increased the amount of fermentation substrates, changed the microbial community structure and affected metabolic pathways (global metabolism, carbohydrate metabolism and amino acid metabolism), which improved the flavour and quality of the PM silage. Conclusions: The CM addition of improved the fermentation quality of PM silage, with PM + CM being the ideal combination. The SMRT sequencing technology could accurately obtain specific details of the microbial networks and fermentation characteristics. Our results indicate that PM can be used as a potential high-protein silage in animal production. Significance and Impact of the Study: In tropics, the effective use of abundant natural biomass resources such as woody plants to prepare silage for feed preservation can solve the problem of restricting livestock production due to the shortage of feed in the dry season. SMRT sequencing technology was used to accurately analyze the microbial network and fermentation characteristics of woody silage prepared with CM as an exogenous additive to improve the fermentation quality of silage.

Microbial Co-occurrence Network and Fermentation Information of Natural Woody-Plant Silage Prepared With Grass and Crop By-Product in Southern Africa

“…In the KEGG analysis, carbohydrate metabolism was the most important metabolic category in gliricidia materials and silage. Pyruvate metabolism, glycolysis, and butyrate metabolism were predominant components of the carbohydrate metabolic pathways, consistent with the main silage metabolism pathway reported by Du et al (2021b). In this study (Figure 6), silage had a higher proportion of carbohydrate metabolism pathways than did the corresponding material, reflecting the community dynamics and metabolic activities of the major LAB.…”

“…The dominant species in the NG and CS materials was M. trichothecenolyticum, a Gram-positive and aerobic or weakly anaerobic non-spore-producing and acid-fast species. In contrast, the abundance of L. plantarum was low in all materials, indicating that WP were similar to forage and crop by-products; WP typically have a low abundance of LAB but a high abundance of undesirable bacteria before ensiling (Tian et al, 2020;Du et al, 2021b). Therefore, measures to control the microbial community are needed to improve silage fermentation.…”

Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry

“…4 CCS was obtained from the P_CCS module using the parameter Min Complete Passes = 2 and Min Predicted Accuracy = 0. After examining for poly (A) signal and 5′ and 3′ adaptors, only the CCS with all three signals was considered as a FLNC read ( Du et al, 2021 ). Unmerged subreads were also examined for the three signals, and those with three signals were incorporated into the final FLNC read set.…”

“…As an alternative, PacBio single-molecule real-time sequencing (SMRT) technology can be used to construct libraries with different inserts and has an advantage of ultra-long read lengths (5–8 kb). SMRT technology has been widely applied to multiple species ( Minoche et al, 2015 ; Du et al, 2021 ). SMRT has also been applied in combination with Illumina sequencing in many studies ( Xu et al, 2015 ; Li et al, 2017 ; Qian et al, 2020 ).…”

Effects of Paper Mulberry Silage on the Growth Performance, Rumen Microbiota and Muscle Fatty Acid Composition in Hu Lambs

“…Hu sheep are widely farmed in southern China because of their high reproductive performance (Multiple fetuses) [3]. However, the main constraint for further improvement of lamb products is the lack of adequate and high-quality feed stuff [4,5]. Large amounts of forage are consumed by cattle and sheep, and the global trade of fodder has been limited due to the pandemic of COVID-19.…”