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

The influence of low-temperature resistant lactic acid bacteria on the enhancement of quality and the microbial community in winter Jerusalem Artichoke (Helianthus tuberosus L.) silage on the Qinghai-Tibet Plateau

Jerusalem Artichoke (Helianthus tuberosus L.), an emerging "food and fodder" economic crop on the Qinghai-Tibet Plateau. To tackle problems such as incomplete fermentation and nutrient loss occurring during the low-temperature ensilage of Jerusalem Artichokes in the plateau's winter, this study inoculated two strains of low-temperature resistant lactic acid bacteria, Lactobacillus plantarum (GN02) and Lactobacillus brevis (XN25), along with their mixed components, into Jerusalem Artichoke silage material. We investigated how low-temperature resistant lactic acid bacteria enhance the quality of low-temperature silage fermentation for Jerusalem Artichokes and clarify its mutual feedback effect with microorganisms. Results indicated that inoculating low-temperature resistant lactic acid bacteria significantly reduces the potential of hydrogen and water-soluble carbohydrates content of silage, while increasing lactic acid and acetic acid levels, reducing propionic acid, and preserving additional dry matter. Inoculating the L. plantarum group during fermentation lowers pH and propionic acid levels, increases lactic acid content, and maintains a dry matter content similar to the original material. Bacterial community diversity exhibited more pronounced changes than fungal diversity, with inoculation having a minor effect on fungal community diversity. Within the bacteria, Lactobacillus remains consistently abundant (>85%) in the inoculated L. plantarum group. At the fungal phylum and genus levels, no significant changes were observed following fermentation, and dominant fungal genera in all groups did not differ significantly from those in the raw material. L. plantarum exhibited a positive correlation with lactic acid and negative correlations with pH and propionic acid. In summary, the inoculation of L. plantarum GN02 facilitated the fermentation process, preserved an acidic silage environment, and ensured high fermentation quality; it is a suitable inoculant for low-temperature silage in the Qinghai-Tibet Plateau.

Microbial network and fermentation modulation of Napier grass and sugarcane top silage in southern Africa

IMPORTANCE

Feed shortage in the tropics is a major constraint to the production of livestock products such as milk and meat. In order to effectively utilize of local feed resources, the selected lactic acid bacteria (LAB) strain was used to prepare Napier grass and sugarcane top silage. The results showed that the two silages inoculated with LAB formed a co-occurrence microbial network dominated by Lactiplantibacillus during the fermentation process, regulated the microbial community structure and metabolic pathways, and improved the silage fermentation quality. This is of great significance for alleviating feed shortage and promoting sustainable production of livestock.

Silage preparation and sustainable livestock production of natural woody plant

As the global population increases and the economy grows rapidly, the demand for livestock products such as meat, egg and milk continue to increase. The shortage of feed in livestock production is a worldwide problem restricting the development of the animal industry. Natural woody plants are widely distributed and have a huge biomass yield. The fresh leaves and branches of some woody plants are rich in nutrients such as proteins, amino acids, vitamins and minerals and can be used to produce storage feed such as silage for livestock. Therefore, the development and utilization of natural woody plants for clean fermented feed is important for the sustainable production of livestock product. This paper presents a comprehensive review of the research progress, current status and development prospects of forageable natural woody plant feed resources. The nutritional composition and uses of natural woody plants, the main factors affecting the fermentation of woody plant silage and the interaction mechanism between microbial co-occurrence network and secondary metabolite are reviewed. Various preparation technologies for clean fermentation of woody plant silage were summarized comprehensively, which provided a sustainable production mode for improving the production efficiency of livestock and producing high-quality livestock product. Therefore, woody plants play an increasingly important role as a potential natural feed resource in alleviating feed shortage and promoting sustainable development of livestock product.

Cellulase-lactic acid bacteria synergy action regulates silage fermentation of woody plant

BACKGROUND

Feed shortage is an important factor limiting livestock production in the world. To effectively utilize natural woody plant resources, we used wilting and microbial additives to prepare an anaerobic fermentation feed of mulberry, and used PacBio single-molecule real-time (SMRT) sequencing technology to analyse the "enzyme-bacteria synergy" and fermentation mechanism.

RESULTS

The fresh branches and leaves of mulberry have high levels of moisture and nutrients, and also contain a diverse range of epiphytic microorganisms. After ensiling, the microbial diversity decreased markedly, and the dominant bacteria rapidly shifted from Gram-negative Proteobacteria to Gram-positive Firmicutes. Lactic acid bacteria (LAB) emerged as the dominant microbial population, resulting in increased in the proportion of the carbohydrate metabolism and decreased in the proportion of the amino acid and "global and overview map" (GOM) metabolism categories. The combination of cellulase and LAB exhibited a synergistic effect, through which cellulases such as glycanase, pectinase, and carboxymethyl cellulase decomposed cellulose and hemicellulose into sugars. LAB converted these sugars into lactic acid through the glycolytic pathway, thereby improving the microbial community structure, metabolism and fermentation quality of mulberry silage. The GOM, carbohydrate metabolism, and amino acid metabolism were the main microbial metabolic categories during ensiling. The presence of LAB had an important effect on the microbial community and metabolic pathways during silage fermentation. A "co-occurrence microbial network" formed with LAB, effectively inhibiting the growth of harmful microorganisms, and dominating the anaerobic fermentation process.

CONCLUSIONS

In summary, PacBio SMRT was used to accurately analyse the microbial network information and regulatory mechanism of anaerobic fermentation, which provided a scientific basis for the study of woody silage fermentation theory. This study reveals for the first time the main principle of the enzyme-bacteria synergy in a woody silage fermentation system, which provides technical support for the development and utilization of woody feed resources, and achieves sustainable livestock production.

Effects of Different Types of LAB on Dynamic Fermentation Quality and Microbial Community of Native Grass Silage during Anaerobic Fermentation and Aerobic Exposure

Silage of native grasses can alleviate seasonal forage supply imbalance in pastures and provide additional sources to meet forage demand. The study aimed to investigate the effects of Lactobacillus plantarum (LP), Lactobacillus buchneri (LB), and Lactobacillus plantarum in combination with Lactobacillus buchneri (PB) on the nutritional quality, fermentation quality, and microbial community of native grass silage at 2, 7, 15, and 60 days after ensiling and at 4 and 8 days after aerobic exposure. The results showed that dry matter content, crude protein content, the number of lactic acid bacteria, and lactic acid and acetic acid content increased and pH and ammonia nitrogen content decreased after lactic acid bacteria (LAB) inoculation compared with the control group (CK). LP had the lowest pH and highest lactic acid content but did not have greater aerobic stability. LB maintained a lower pH level and acetic acid remained at a higher level after aerobic exposure; aerobic bacteria, coliform bacteria, yeast, and molds all decreased in number, which effectively improved aerobic stability. The effect of the compound addition of LAB was in between the two other treatments, having higher crude protein content, lactic acid and acetic acid content, lower pH, and ammonia nitrogen content. At the phylum level, the dominant phylum changed from Proteobacteria to Firmicutes after ensiling, and at the genus level, Lactiplantibacillus and Lentilactobacillus were the dominant genera in both LAB added groups, while Limosilactobacillus was the dominant genus in the CK treatment. In conclusion, the addition of LAB can improve native grass silage quality by changing bacterial community structure. LP is beneficial to improve the fermentation quality in the ensiling stage, LB is beneficial to inhibit silage deterioration in the aerobic exposure stage, and compound LAB addition is more beneficial to be applied in native grass silage.

Effect of different regions on fermentation profiles, microbial communities, and their metabolomic pathways and properties in Italian ryegrass silage

Introduction

Italian ryegrass is less studied in northern China due to high-quality forage grass has not been fully utilized. Full utilization of high-quality forage grass helps to alleviate the shortage of forage grass in winter and spring season and guarantee stable development of livestock production. Consequently, this study was aimed to evaluate the effects of different regions in northern China on the fermentative products, bacterial community compositions, and metabolic pathways and metabolites of Italian ryegrass silage.

Methods

The Italian ryegrass was harvested from three regions (Ordos-WK; Hohhot-AK; Ulanqab-SYK) and ensiled for 60 days. Single molecule real-time (SMRT) sequencing and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) were used to analyze bacterial communities and metabolites, respectively.

Results

After 60 d of fermentation, the SYK group had the lowest pH (4.67), the highest lactic acid contents (95.02 g/kg DM) and largest lactic acid bacteria populations (6.66 log₁₀ cfu/g FM) among the treatment groups. In addition, the SYK group had the highest abundance of Lactiplantibacillus plantarum (63.98%). In SYK group, isoquinoline alkaloid biosynthesis was the significantly enriched (p < 0.05) and high-impact value (0.0225) metabolic pathway. In AK group, tryptophan metabolism the was the significantly enriched (p < 0.001) and high-impact value (0.1387) metabolic pathway. In WK group, citrate cycle (TCA cycle) was the significantly enriched (p < 0.001) and high-impact value (0.1174) metabolic pathway. Further, Lactiplantibacillus plantarum was positively correlated with cinnamic acid, tetranor 12-HETE, D-Mannitol, (2S)-2-amino-4-methylpentanoic acid L-Leucine, guanine, isoleucyl-aspartate and 3,4-Dihydroxyphenyl propanoate, but negatively correlated with isocitrate and D-mannose.

Discussion

In conclusion, this study can improve our understanding of the ensiling microbiology and metabolomics in different regions to further regulate the fermentation products and promote livestock production.

Effects of growth stage on the fermentation quality, microbial community, and metabolomic properties of Italian ryegrass (Lolium multiflorum Lam.) silage

Introduction

This study aimed to investigate the effects of different growth stages (booting period-SYK; initial flowering-SCK; full flowering-SSK) on the fermentation quality, microbial community, metabolic pathways and metabolomic characteristics of Italian ryegrass silage.

Methods

Single molecule real-time (SMRT) sequencing and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) were used to analyze bacterial communities and metabolites, respectively.

Results

After 60 d of fermentation, SYK had the lowest pH and the highest lactic acid content, which were significantly different from the other groups. The bacteria with the highest abundance in SYK, SCK and SSK groups were Lactiplantibacillus plantarum (63.98%), Weissella minor (28.82%) and Levilactobacillus brevis (64.81%), respectively. In addition, among the main differential metabolites in different growth stages, the number of amino acids was the most, and the corresponding metabolic pathways were mainly amino acid metabolic pathways. The biosynthesis of phenylalanine, tyrosine and tryptophan was significantly enriched (p<0.01) at booting stage and full flowering stage. Purine metabolism and ABC transporter pathway were significantly enriched at the initial flowering (p<0.001). Lactiplantibacillus plantarum had a negative correlation with xanthine and ganoderic acid F. Weissella minor had a positive correlation with D-Mannose and ganoderic acid F. Levilactobacillus brevis had a positive correlation with xanthine, and Latilactobacillus sakei had a positive correlation with cinnamic acid, D-Mannose, 2-Hydroxycinnamic acid and uridine.

Discussion

In conclusion, this study reveals the interaction mechanisms between ryegrass raw materials at different growth stages and epiphytic microorganisms during ensiling fermentation, providing new ideas for screening functional lactic acid bacteria, and laying a theoretical foundation for the production of safe and high-quality silage.

Characteristics of lactic acid bacteria, microbial community and fermentation dynamics of native grass silage prepared in Inner Mongolian Plateau

Introduction

To prepare high-quality silage, we studied the chemical composition, silage fermentation, characterization, and identification of lactic acid bacteria (LAB) associated with the silage fermentation of native grass on the Inner Mongolian Plateau.

Methods

LAB were isolated from fresh native grass and their silage, and silages were prepared using a small-scale fermentation system with 2-3 cm length in plastic bags.

Results

The dominant species of native grasses used were Stipa baicalensis, Leymus chinensis, Cleistogenes squarrosa, Melissilus ruthenicus and Pulsatilla turczaninovii, which contained 47.83-59.43 % moisture, 55.12-67.74 % neutral detergent fiber (NDF), and 8.72-14.55 crude protein (CP), and these nutrients did not change greatly during ensiling. Good preservation with a relatively low pH (below 4.44) and high (p < 0.05) lactic acid content (>0.58) was obtained after ensiling. Based on the morphological and biochemical characteristics, these isolates were divided into 12 groups (A-L). All isolate strains were gram-positive and catalase-negative bacteria that produce lactic acid from glucose. Group A-K were cocci, while group L was rod-shaped. Group A-E formed D-lactic acid, but group H-K formed L-lactic acid, and other groups formed DL-lactic acid. Group A-E were heterofermentative, and Group F-L were homofermentative types of LAB. According to the 16S rRNA gene sequences analysis, strains were identified as genus Leuconostoc (A, B, and C), Weissellla (D, E), Pediococcus (F, G), Enterococcus (H, I, J and K), and Lactiplantibacillus (L). Enterococcus (E.) faecium (29.17%, percentage of total isolates) and Pediococcus (P.) acidilactici (18.75%) were the most frequently occurring dominant species.

Discussion

This study suggests that the native grasses contained abundant LAB species, and they can be used as good-quality silages in animal husbandry. In addition, the strains P. acidilactici and E. faecium were the most frequently isolated from native grass silages as dominant species which can be a potentially excellent inoculant for native grass silage.

Current approaches on the roles of lactic acid bacteria in crop silage

Lactic acid bacteria (LAB) play pivotal roles in the preservation and fermentation of forage crops in spontaneous or inoculated silages. Highlights of silage LAB over the past decades include the discovery of the roles of LAB in silage bacterial communities and metabolism and the exploration of functional properties. The present article reviews published literature on the effects of LAB on the succession, structure, and functions of silage microbial communities involved in fermentation. Furthermore, the utility of functional LAB in silage preparation including feruloyl esterase-producing LAB, antimicrobial LAB, lactic acid bacteria with high antioxidant potential, pesticide-degrading LAB, lactic acid bacteria producing 1,2-propanediol, and low-temperature-tolerant LAB have been described. Compared with conventional LAB, functional LAB produce different effects; specifically, they positively affect animal performance, health, and product quality, among others. In addition, the metabolic profiles of ensiled forages show that plentiful probiotic metabolites with but not limited to antimicrobial, antioxidant, aromatic, and anti-inflammatory properties are observed in silage. Collectively, the current knowledge on the roles of LAB in crop silage indicates there are great opportunities to develop silage not only as a fermented feed but also as a vehicle of delivery of probiotic substances for animal health and welfare in the future.

Effects of different additives on the bacterial community and fermentation mode of whole-plant paper mulberry silage

The purpose of this study was to investigate the effects of inoculation with two lactic acid bacteria (LAB) strains (Lacticaseibacillus rhamnosus and Lentilactobacillus buchneri) and the addition of four corn flour proportions (0, 3, 6, and 9%) in different treatments, on the composition and function of the bacterial community in whole-plant paper mulberry silage. The different treatments promoted Lactiplantibacillus, Lentilactobacillus, and Lacticaseibacillus growth, but the microbial species responsible for fermentation differed among the treatments. High species diversity and various Gram-negative bacteria, such as Flavitalea sp., Pantoea agglomerans, Acinetobacter pittii, Turicibacter sanguinis, and Ralstonia pickettii, were found in the uninoculated LAB treatments. A beneficial bacterium, Lactobacillus johnsonii, was discovered for the first time in whole-plant paper mulberry silage. LAB inoculation simplifies the microbial community structure, and beneficial Lactobacillus as a key species aggregates in the inoculated treatment group. However, L. rhamnosus inoculation alone may have limited bacteriostatic activity against in whole-plant paper mulberry silage. Compared with silage lacking corn flour, amino sugar and nucleotide sugar metabolism, galactose metabolism, the phosphotransferase system and the pentose phosphate pathway metabolic activity were increased in corn flour-containing silage. Whole-plant paper mulberry can be used as a high-quality silage to provide high-quality feed resources for sustainable ruminant livestock production. Moreover, additive use is necessary for preparing paper mulberry silage.

Innovative utilization of herbal residues: Exploring the diversity of mechanisms beneficial to regulate anaerobic fermentation of alfalfa

In order to increase the utilization of herbal residues, realize efficient utilization of resources, the bacterial community and anaerobic fermentation characteristics of alfalfa ensiling treated with 36 kinds of herbal residues were studied. All the herbal residues improved the anaerobic fermentation quality in different degrees, indicated by lower pH, NH₃-N and butyric acid concentrations. However, the contents of lactic and acetic acids varied widely in silage with different herbal residues. Pearson's correlation analysis showed that the improved fermentation quality was closely associated with the variation of lactic acid bacteria community. Consequently, the herbal residues could improve anaerobic fermentation quality by stimulating desirable Lactobacillus species and inhibiting undesirable microbes. This study provides new insights for efficient utilization of herbal residues.

Using PacBio SMRT Sequencing Technology and Metabolomics to Explore the Microbiota-Metabolome Interaction Related to Silage Fermentation of Woody Plant

Silage fermentation is a dynamic process involving the succession of microbial communities and changes in metabolites. Fresh branched and leaves of paper mulberry were used to prepared silage. Crop by-products including corn bran, rice bran, and wheat bran were used as exogenous additives. Pacific Biosciences single-molecule real-time (SMRT) sequencing technology and metabolomics are used to explore the interaction mechanism of microbial structure and metabolites during woody silage fermentation and to verify the principle that exogenous additives can modulate silage fermentation. Under the dual stress of anaerobic and acidic environment of silage fermentation, the microbial community changed from Gram-negative to Gram-positive bacteria, and a large amount of lactic acid and volatile fatty acid were produced, which lowered the pH value and caused the rapid death of aerobic bacteria with thin cell walls. The exogenous additives of corn bran and wheat bran accelerated the dynamic succession of lactic acid bacteria as the dominant microbial community in silage fermentation, increased the metabolic pathways of lactic acid, unsaturated fatty acids, citric acid, L-malic acid and other flavoring agents, and inhibited the growth of Clostridium and Enterobacter, thereby improving the flavor and quality of the silage. However, because rice bran contained butyric acid spore bacteria, it can multiply in an anaerobic environment, led to butyric acid fermentation, and promoted protein degradation and ammonia nitrogen production, thereby reduced the fermentation quality of woody silage. The results showed that during the silage fermentation process, the microbial community and the metabolome can interact, and exogenous additives can affect the fermentation quality of silage. SMRT sequencing technology and untargeted metabolomics revealed the microbiota-metabolome interaction during silage fermentation. Changes in the structure of the microbial community can affect the metabolic pathways, and the final metabolites can inhibit the growth of microorganisms that are not conducive to silage fermentation. Exogenous carbohydrate additives can change the fermentation substrate and affect microbial community structure, thus modulate the silage fermentation.

Characteristics of the microbiota and metabolic profile of high-temperature Daqu with different grades

The superior grade Daqu (S_Daqu) and normal grade Daqu (N_Daqu) have obvious differences in flavor, fracture surface, appearance, etc., which can be accurately grouped by well-trained panel based on their sensory properties. However, the differences in microbial community diversity and metabolites between the S_Daqu and N_Daqu were still unclear. The culture-dependent method, the third generation Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) sequencing technology, and nuclear magnetic resonance (NMR) were combined to show the characteristics in microorganisms and metabolites. Results showed that the fungal counts were higher in N_Daqu while the richness of bacterial communities was higher in S_Daqu (P < 0.05). Lentibacillus, Burkholderia, Saccharopolyspora, Thermoascus, and Rasamsonia were the dominant genera of S_Daqu while Staphylococcus, Scopulibacillus, and Chromocleista were the dominant genera in N_Daqu. The content of differential acids, amino acids, and alcohols including fumarate, glucuronate, glycine, 4-carboxyglutamate, and myo-inositol in S_Daqu was higher than that in N_Daqu by ¹H NMR coupled with multivariate statistical analysis. The network analysis regarding microbes and metabolites suggested that Saccharopolyspora showed a strong positive correlation with 4-carboxyglutamate while Thermoascus and Chromocleista were highly negatively correlated with alanine and isobutyrate, respectively. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) revealed that Macrococcus and Caulobacter were regarded as bacterial biomarkers in the S_Daqu while Chromocleista was the key fungal genera in N_Daqu. Functionality prediction indicated that the bacteria in S_Daqu were largely involved in more metabolic activities including biosynthesis, degradation, detoxification, and generation of precursor metabolite and energy.

Characterization of Lactic Acid Bacteria Isolated from Banana and Its Application in Silage Fermentation of Defective Banana

To effectively utilize banana by-products, we prepared silage with defective bananas using screened lactic acid bacteria (LAB), sucrose, and tannase as additives. Eleven strains of LAB were isolated from the fruits and flowers of defective bananas, all of which were Gram-positive and catalase-negative bacteria that produced lactic acid from glucose. Among these LAB, homofermentative strain CG1 was selected as the most suitable silage additive due to its high lactic acid production and good growth in a low pH environment. Based on its physiological and biochemical properties and 16S rRNA gene sequence analysis, strain CG1 was identified as Lactiplantibacillus plantarum. Defective bananas contain 74.8−76.3% moisture, 7.2−8.2% crude protein, 5.9−6.5% ether extract, and 25.3−27.8% neutral detergent fibre on a dry matter basis. After 45 d of fermentation, the silage of deficient bananas treated with LAB or sucrose alone improved fermentation quality, with significantly (p < 0.05) lower pH and higher lactic acid contents than the control. The combination of LAB and sucrose had a synergistic effect on the fermentation quality of silage. The tannase-treated silage significantly (p < 0.05) decreased the tannin content, while the combination of tannase and LAB in silage not only decreased (p < 0.05) the tannin content, but also improved the fermentation quality. The study confirmed that defective bananas are rich in nutrients, can prepare good quality silage, and have good potential as a feed source for livestock.

Fermentation Quality, Bacterial Community, and Aerobic Stability of Perennial Recut Broussonetia papyrifera Silage with Different Additives and Wilting Time

Broussonetia papyrifera L. (paper mulberry) is an alternative woody plant, which can used to replace part of the protein feed for ruminants. Ensiling is an effective way to preserve fresh pasture and to solve the problem of stable storage and feed conversion of paper mulberry in the rapid growth period. However, low dry matter (DM), water-soluble carbohydrate, and lactic acid bacteria (LAB) reduce the quality of paper mulberry silage. This study assesses the influence of wilting time (0 h and 3.5 h; lighting: 3.43 × 104 Lux) and three additives (Enterococcus durans, CL; cellulase, CE; and formic acid, FA) on the fermentation quality, aerobic stability, and bacterial community of whole plant B. papyrifera silage. The whole plant B. papyrifera sample was mowed and wilted for 0 h and 3.5 h, and then had CL, CE, or FA added, followed by 60 days of ensiling. The results show all silage samples had high fermentation quality with pH below 4.2, ammonia-nitrogen below 100 g/kg DM, and no detectable butyric acid. The additives protected the DM and the crude protein from protease activity (p < 0.05), and CL was the most effective among them. Furthermore, wilting time influenced the silage’s bacterial communities, but overall, CL treatment had the greatest impact on bacterial communities. Wilting time and formic acid treatment significantly improved aerobic stability (p < 0.05). Enterococcus was positively correlated with lactic acid (LA), while negatively correlated with LA and Weissella (p < 0.001). Enterococcus was identified as the main driver of the whole plant paper mulberry ensiling process in the present study. In conclusion, compared to other additives, LAB is the most effective and economical to improve the fermentation quality and reduce the protein degradation of whole plant paper mulberry silage. Our findings provide a theoretical basis to improve the quality and production of paper mulberry silage.

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

To facilitate the use of woody plant (WP) as a natural biomass resource to address the shortage of feed for ruminants in the tropics, we use PacBio SMRT sequencing to explore the microbial co-occurrence network and silage fermentation of gliricidia and leucaena prepared with Napier grass (NG) and corn stover (CS) in Southern Africa. Based on dry matter, the crude protein contents of WP are as high as 25%. Compared with NG, the addition of CS speed up the dynamic succession of microorganisms in the silage fermentation process from Gram-negative bacteria to Gram-positive bacteria, and promoted Lactiplantibacillus plantarum to become the dominant community and enhanced the metabolic pathways of lactic acid and citric acid, thus improved the fermentation flavour and quality of WP silage. WP can be mixed with CS to make high-quality silage, which can alleviate the shortage of feed and promote local animal production.

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

Paper mulberry (Broussonetia papyrifera) is widely ensiled to feed sheep in southwestern China, as unconventional woody forage. Feeding lambs with paper mulberry silage (PMS) may improve certain feeding characteristics, thereby affecting the growth performance and meat quality. The aim of this study is to investigate the effects of four diets of PMS on growth performance, rumen microbial composition, and muscle fatty acids profile in Hu lambs. The results showed that 30% and 40% PMS increased the dry matter intake and average daily gain of Hu lambs compared to the control group. PMS30 and PMS40 increased the content of C24:1, and PMS40 increased the content of C20:5n-3. The content of microbial protein (MCP) was higher in PMS40 than in others, but PMS30 and PMS40 reduced the total volatile fatty acid in rumen. PMS30 significantly increased the ratio of acetic acid to propionic acid. The abundance of ruminal Christensenellaceae_R-7_group and norank_f_Eubacterium_coprostanoligenes_group was significantly higher in PMS30 and PMS40 groups. Moreover, Christensenellaceae_R-7_group had a significant positive correlation with n3-polyunsaturated fatty acid. PMS40 might lead to a relatively high content of unsaturated fatty acids in longissimus dorsi muscle by increasing the relative abundance of Christensenellaceae_R-7_group in rumen.

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

Blueberries (Vaccinium corymbosum) contain large amounts of flavonoids, which play important roles in the plant's ability to resist stress and can also have beneficial effects on human health when the fruits are eaten. However, the molecular mechanisms that regulate flavonoid synthesis in blueberries are still unclear. In this study, we combined two different transcriptome sequencing platforms, single-molecule real-time (SMRT) and Illumina sequencing, to elucidate the flavonoid synthetic pathways in blueberries. We analyzed transcript quantity, length, and the number of annotated genes. We mined genes associated with flavonoid synthesis (such as anthocyanins, flavonols, and proanthocyanidins) and employed fluorescence quantitative PCR to analyze the expression of these genes and their correlation with flavonoid synthesis. We discovered one R2R3 MYB transcription factor from the sequencing library, VcMYB1, that can positively regulate anthocyanin synthesis in blueberries. VcMYB1 is mainly expressed in colored (mature) fruits. Experiments showed that overexpression and transient expression of VcMYB1 promoted anthocyanin synthesis in Arabidopsis, tobacco (Nicotiana benthamiana) plants and green blueberry fruits. Yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay, and transient expression experiments showed that VcMYB1 binds to the MYB binding site on the promoter of the structural gene for anthocyanin synthesis, VcMYB1 to positively regulate the transcription of VcDFR, thereby promoting anthocyanin synthesis. We also performed an in-depth investigation of transcriptional regulation of anthocyanin synthesis. This study provides background information and data for studying the synthetic pathways of flavonoids and other secondary metabolites in blueberries.