Expression of a Recombinant Lentinula edodes Xylanase by Pichia pastoris and Its Effects on Ruminal Fermentation and Microbial Community in in vitro Incubation of Agricultural Straws

Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research Techniques, Functional Analysis, and Prospects

Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry.

Regulation of intestinal flora in patients with chronic atrophic gastritis by modified Chai Shao Liu Jun Zi decoction based on 16S rRNA sequencing

Chai Shao Liu Jun Zi decoction (CSLJZD) is an effective Chinese medicine for the treatment of chronic atrophic gastritis (CAG). However, the effect of CSLJZD on the intestinal flora of patients with CAG remains unclear. We used 16S rRNA gene sequencing to investigate the regulatory effects of CSLJZD on intestinal microflora in patients with CAG. Eight patients with CAG were randomly selected as the model group and 8 healthy medical examiners as the control group; the treatment group comprised patients with CAG after CSLJZD treatment. High-throughput sequencing and bioinformatics analysis of the V3V4 region of the 16S rRNA gene of intestinal bacteria obtained from the intestinal isolates of fecal specimens from all participants were performed separately. A rarefaction curve, species accumulation curve, Chao1 index, and ACE index were calculated to assess the alpha diversity. Principal component analysis (PCA), non-metric multi-dimensional scaling, and the unweighted pair group method with arithmetic mean were used to examine beta diversity. The LEfSe method was used to identify the differentially expressed bacteria. Differential function analysis was performed using PCA based on KEGG function prediction. Rarefaction and species accumulation curves showed that the sequencing data were reasonable. The Chao1 and ACE indices were significantly increased in patients with CAG compared with those in the healthy group. Following CSLJZD and vitacoenzyme treatment, Chao1 and ACE indices decreased. The PCA, non-metric multi-dimensional scaling, and unweighted pair group method with arithmetic mean results showed that the CAG group was distinct from the healthy and treatment groups. The LEfSe results showed that the abundances of the genus Bilophila, family Desulfovibrionaceae, order Desulfovibrionales and genus Faecalibacterium were significantly higher in the healthy group. The abundance of genus Klebsiella, order Deltaproteobacteria, genus Gemmiger, and other genera was significantly higher in the treatment group. Treatment with CSLJZD had a therapeutic effect on the intestinal flora of patients with CAG.

A Glycosyl Hydrolase 30 Family Xylanase from the Rumen Metagenome and Its Effects on In Vitro Ruminal Fermentation of Wheat Straw

The challenge of wheat straw as a ruminant feed is its low ruminal digestibility. This study investigated the impact of a xylanase called RuXyn, derived from the rumen metagenome of beef cattle, on the in vitro ruminal fermentation of wheat straw. RuXyn encoded 505 amino acids and was categorized within subfamily 8 of the glycosyl hydrolase 30 family. RuXyn was heterologously expressed in Escherichia coli and displayed its highest level of activity at pH 6.0 and 40 °C. RuXyn primarily hydrolyzed xylan, while it did not show any noticeable activity towards other substrates, including carboxymethylcellulose and Avicel. At concentrations of 5 mM, Mn2+ and dithiothreitol significantly enhanced RuXyn's activity by 73% and 20%, respectively. RuXyn's activity was almost or completely inactivated in the presence of Cu2+, even at low concentrations. The main hydrolysis products of corncob xylan by RuXyn were xylopentose, xylotriose, and xylotetraose. RuXyn hydrolyzed wheat straw and rice straw more effectively than it did other agricultural by-products. A remarkable synergistic effect was observed between RuXyn and a cellulase cocktail on wheat straw hydrolysis. Supplementation with RuXyn increased dry matter digestibility; acetate, propionate, valerate, and total volatile fatty acid yields; NH3-N concentration, and total bacterial number during in vitro fermentation of wheat straw relative to the control. RuXyn's inactivity at 60 °C and 70 °C was remedied by mutating proline 151 to phenylalanine and aspartic acid 204 to leucine, boosting activity to 20.3% and 21.8% of the maximum activity at the respective temperatures. As an exogenous enzyme preparation, RuXyn exhibits considerable potential to improve ruminal digestion and the utilization of wheat straw in ruminants. As far as we know, this is the first study on a GH30 xylanase promoting the ruminal fermentation of agricultural straws. The findings demonstrate that the utilization of RuXyn can significantly enhance the ruminal digestibility of wheat straw by approximately 10 percentage points. This outcome signifies the emergence of a novel and highly efficient enzyme preparation that holds promise for the effective utilization of wheat straw, a by-product of crop production, in ruminants.

Lentinula edodes lignocellulolases and lipases produced in Macaúba residue and use of the enzymatic extract in the degradation of textile dyes

Agro-industrial residue and textile effluents have caused environmental damage to soil and water bodies. The production of fungal enzymes using agro-industrial residues and the use of these enzymes in the degradation of textile dyes can be a viable alternative to reduce these environmental damages. Lentinula edodes is a white rot fungus with high nutritional value that produces edible mushrooms and enzymes of commercial interest. Thus, the objectives of this study were to produce, purify, and biochemically characterize the lignocellulolytic enzymes and lipases produced for L. edodes in Macaúba coconut and to evaluate their potential for the degradation of textile dyes. The L. edodes UFV 73 had maximum enzymatic activity at 37 days of incubation. After the purification steps, the laccase, manganese peroxidase (MnP), cellulase, and, xylanase yields were 489.01, 264.2, 105.02, and 9.5%. The optimum temperature of cellulase activity did not change from 4 to 60 °C. The MnP, laccase, and lipase had activity directly proportional to the increase in temperature, while the cellulase and xylanase activity did not change. The optimum pH varied among analyzed enzymes. All the enzymes analyzed are according to Michaelis-Menten kinetics. The lignocellulolytic enzymes were stable up to 8 h of incubation and lipase had a reduction of activity after one hour. The discoloration rate of indigo dye by partially purified enzymatic extract (PPPE) was 40%, which shows its potential for degradation of dyes from textile industries.

Solid-State Fermentation with White Rot Fungi (Pleurotus Species) Improves the Chemical Composition of Highland Barley Straw as a Ruminant Feed and Enhances In Vitro Rumen Digestibility

Lignin degradation is important for enhancing the digestibility and improving the nutritive quality of ruminant feeds. White rot fungi are well known for their bioconversion of lignocellulosic biomass. The objective of this paper was to evaluate whether Lentinus sajor-caju, Pleurotus ostreatus, Phyllotopsis rhodophylla, Pleurotus djamor, Pleurotus eryngii, and Pleurotus citrinopileatus treatments altered the chemical compositions of highland barley straw constituents and enhanced their nutritional value as a ruminant feed. All white rot fungi significantly increased the relative crude protein (CP), ethyl ether extract (EE), starch, soluble protein (SP), and non-protein nitrogen (NPN) contents but decreased the ash, neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and acid detergent insoluble protein (ADFIP) contents. In addition, L. sajor-caju treatment increased (p < 0.001) the levels of PA, PB2, PB3, CA, CB1, CB2, and CNSC, but reduced (p < 0.001) the PC and CC in the solid-state fermentation of highland barley straw. Maximum ligninlysis (50.19%) was optimally produced in the presence of 1.53% glucose and 2.29% urea at 22.72 ℃. The in vitro dry matter digestibility and total volatile fatty acid concentrations of fermented highland barley straw, as well as the fermentability, were optimized and improved with L. sajor-caju, which degraded the lignocellulose and improved the nutritional value of highland barley straw as a ruminant feed.

Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep

BACKGROUND

The nutrient availability of roughages could affect the dietary utilization efficiency of ruminants even in isocaloric and isonitrogenous diets. Here, we analyzed the bacterial composition and their metabolic pathways in the gastrointestinal tracts (GITs) of Hu sheep fed with wheat straw (WS) instead of alfalfa (AL) in isocaloric and isonitrogenous diets, trying to explore the reasons from the perspective of GITs bacterial network structure changes.

RESULTS

We employed 16S rRNA gene sequencing in combination with the Kruskal-Wallis test, Spearman correlation analysis, and other statistical methods to describe the microbiota composition in the GITs of Hu sheep. The results showed after the roughage was replaced from AL to WS, the most positive response occurred in the rumen microbiota, resulting in a more obvious microbiological and functional redundancy phenomenon. Whereas extended biogeographic studies of the GITs bacterial community found opposite results for the hindgut microbiota and metabolism networks compared to the forestomach. The abundance of fiber-degrading bacteria such as Prevotella, Oscillospiraceae NK4A214 group, and Treponema was significantly increased in GITs, but low-efficiency crude fiber degradation inhibited energy use efficiency, the pentose phosphate pathway, gluconeogenesis, and volatile acid synthesis. In addition, dietary shifting from AL to WS decreased the abundance of beneficial bacteria such as the Lachnospiraceae NK3A20 group and Alistipes, thereby enhancing the underlying inflammatory response.

CONCLUSIONS

These findings suggest that feeding untreated WS affected the structure and function of the bacterial network in the GITs due to limited total digestible nutrients, and in particular increases the complexity of the rumen bacterial network, and limit the abundance of bacteria involved in the crude fiber degradation in the hindgut.

Production, purification, characterization and application of two novel endoglucanases from buffalo rumen metagenome

BACKGROUND

Lignocellulose biomass is the most abundant and renewable material in nature. The objectives of this study were to characterize two endoglucanases TrepCel3 and TrepCel4, and determine the effect of the combination of them (1.2 mg TrepCel3, 0.8 mg TrepCel4) on in vitro rumen fermentation characteristics. In this study, three nature lignocellulosic substrates (rice straw, RS; wheat straw, WS; leymus chinensis, LC) were evaluated for their in vitro digestibility, gas, NH3-N and volatile fatty acid (VFA) production, and microbial protein (MCP) synthesis by adding enzymatic combination.

METHODS

Two endoglucanases' genes were successfully expressed in Escherichia coli (E. coli) BL21 (DE3), and enzymatic characteristics were further characterized. The combination of TrepCel3 and TrepCel4 was incubated with lignocellulosic substrates to evaluate its hydrolysis ability.

RESULTS

The maximum enzymatic activity of TrepCel3 was determined at pH 5.0 and 40 °C, while TrepCel4 was at pH 6.0 and 50 °C. They were stable over the temperature range of 30 to 60 °C, and active within the pH range of 4.0 to 9.0. The TrepCel3 and TrepCel4 had the highest activity in lichenan 436.9 ± 8.30 and 377.6 ± 6.80 U/mg, respectively. The combination of TrepCel3 and TrepCel4 exhibited the highest efficiency at the ratio of 60:40. Compared to maximum hydrolysis of TrepCel3 or TrepCel4 separately, this combination was shown to have a superior ability to maximize the saccharification yield from lignocellulosic substrates up to 188.4% for RS, 236.7% for wheat straw WS, 222.4% for LC and 131.1% for sugar beet pulp (SBP). Supplemental this combination enhanced the dry matter digestion (DMD), gas, NH3-N and VFA production, and MCP synthesis during in vitro rumen fermentation.

CONCLUSIONS

The TrepCel3 and TrepCel4 exhibited the synergistic relationship (60:40) and significantly increased the saccharification yield of lignocellulosic substrates. The combination of them stimulated in vitro rumen fermentation of lignocellulosic substrates. This combination has the potential to be a feed additive to improve agricultural residues utilization in ruminants. If possible, in the future, experiments in vivo should be carried out to fully evaluate its effect.

Characterization of a novel bifunctional enzyme from buffalo rumen metagenome and its effect on in vitro ruminal fermentation and microbial community composition

To efficiently use lignocellulosic materials in ruminants, it is crucial to explore effective enzymes, especially bifunctional enzymes. In this study, a novel stable bifunctional cellulase-xylanase protein from buffalo rumen metagenome was expressed and characterized, CelXyn2. The enzyme displayed optimal activity at pH 6.0 and 45 °C. The residual endoglucanase and xylanase activities were 90.6% and 86.4% after a 60-min pre-incubation at 55 °C. Hydrolysis of rice straw, wheat straw, sheepgrass and sugar beet pulp by CelXyn2 showed its ability to degrade both cellulose and hemicellulose polymers. Treatment with CelXyn2 improved the hydrolysis of agricultural residues with an evident increase in production of total gas, lactate and volatile fatty acids. The results of 16S rRNA and real-time PCR showed that the effect on in vitro ruminal microbial community depended on fermentation substrates. This study demonstrated that CelXyn2 could strengthen lignocellulose hydrolysis and in vitro ruminal fermentation. These characteristics of CelXyn2 distinguish it as a promising candidate for agricultural application.

Probiotic effect of ferulic acid esterase-producing Lactobacillus plantarum inoculated alfalfa silage on digestion, antioxidant, and immunity status of lactating dairy goats

A feeding experiment was conducted to determine the effects of inoculating alfalfa silage with a ferulic acid esterase-producing inoculum on feed digestibility, rumen fermentation, antioxidant, and immunity status of lactating dairy goats. Twenty dairy goats were distributed into 2 experimental groups consisting of control diet (Lp MTD/1, including Lactobacillus plantarum MTD/1 inoculated silage) against diet containing silage treated with ferulic acid esterase-producing L. plantarum A1 (Lp A1). Alfalfa silage inoculated with a ferulic acid esterase-producing Lp A1 had better fermentation quality than the Lp MTD/1 inoculation. The application of Lp A1 improved silage antioxidant capacity as indicated by greater total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and glutathion peroxidase (GSH-Px) activities in Lp A1 treated silage versus Lp MTD/1 treatment. Compared with Lp MTD/1 treated group, inoculation of silage with Lp A1 increased apparent total tract digestibility of dietary dry matter, organic matter and crude protein, and ruminal concentrations of total volatile fatty acids, acetate, propionate and isobutyrate as well. The results of current study also demonstrated improved antioxidant capacity and immune performance of dairy goats with Lp A1 inoculation. Feeding Lp A1-treated silage increased dairy goats' serum antioxidase activity, such as T-AOC, SOD, GSH-Px and catalase, and the serum concentration of immunoglobulin A, while decreased tumor necrosis factor α, interleukin (IL)-2 and IL-6. In addition, compared with Lp MTD/1, diet containing alfalfa silage inoculated with Lp A1 endowed dairy goats' milk with greater fat and protein contents, improved dairy goat milk quality without affecting feed efficiency.

Characterization of yeast cell surface displayed Lentinula edodes xylanase and its effects on the hydrolysis of wheat

The current study displayed a xylanase from Lentinula edodes on the surface of Pichia pastoris (sdLeXyn) and investigated its properties and effects on the wheat hydrolysis. Fluorescence microscope results showed that sdLeXyn was successfully anchored and displayed on the surface of P. pastoris X-33 cells. The highest activity of sdLeXyn was obtained at pH 3.0 and 50 °C. The sdLeXyn exhibited anti-high temperature property and showed broad temperature adaptability (>55% of the highest activity at 20-80 °C). The sdLeXyn was very stable at room temperature and could remain functionally stable at 50 °C for 3 h. The K_m value was greater in sdLeXyn than that in free recombinant L. edodes xylanase. The sdLeXyn exhibited well resistance to Mn²⁺, Zn²⁺, Ca²⁺, Na⁺, Cu²⁺, Mg²⁺, K⁺, Ni²⁺ (1 mM and 5 mM) except Cu²⁺, which reduced the sdLeXyn activity by 54.5% at 5 mM dosage. The activity of sdLeXyn was increased by 42.6% by 5 mM Mn²⁺, 5 mM DTT, Trition X-100, and Tween 20 did not affect the activity of sdLeXyn, but SDS and EDTA slightly reduced it by 12.8% and 14.6%, respectively. The sdLeXyn could resist the degradation of pepsin, efficiently hydrolyzed wheat and reduced the viscosity of wheat hydrolysate. Current data indicate that the sdLeXyn has a potential as a feed additive to improve the utilization of wheat in poultry production.

Microbiome and fermentation parameters in the rumen of dairy buffalo in response to ingestion associated with a diet supplemented with cysteamine and hemp seed oil

In this study, high-throughput gene amplicon sequencing was used to investigate the effects of 6 treatments [2 levels of hemp seed oil (HSO) × 3 levels of cysteamine (CS)] on bacterial and fungal communities in the rumen of 30 crossbred dairy buffalo. Our results indicate that the total numbers of bacterial and fungal taxa were unaffected regardless of diet (p > 0.05), while the total number of archaea was affected (p < 0.05) by the interaction of HSO and CS. Compared with control treatment, microbial composition of archaea was strongly influenced by CS (p < 0.05), while the addition of HSO, CS or both had a weak effect on fungus and bacteria. In addition, there was a significant increase in the lactic acid content with the addition of HSO, and the addition of CS to the feed caused a significant decrease in the ratio of acetic acid to propionic acid, compared with control treatment (p < 0.05). Correlation analysis showed that Acetobacter was significantly positively correlated with the genera Pichia, Klebsiella and Acinetobacter. pH was found to have a significant effect on the methanogens, and total volatile fatty acids (VFA) had a strong correlation with Butyrivibrio. The strong influence of CS on some methanogens shows that it may have potential in the development of methane reduction interventions.

Dietary fat and low fiber in purified diets differently impact the gut-liver axis to promote obesity-linked metabolic impairments

Selecting the most relevant control diet is of critical importance for metabolic and intestinal studies in animal models. Chow and LF-purified diet differentially impact metabolic and gut microbiome outcomes resulting in major changes in intestinal integrity in LF-fed animals which contributes to altering metabolic homeostasis. Dietary fat and low fiber both contribute to the deleterious metabolic effect of purified HF diets through both selective and overlapping mechanisms.

Construction and characterization of a chimeric enzyme of swollenin and xylanase to improve soybean straw hydrolysis

A study was carried out to produce a fusion protein (Swo-Xyn) using the Trichoderma reesei swollenin and Lentinula edodes xylanase and to investigate its characteristics and application in degrading soybean straw. In parallel, L. edodes xylanase (Xyn) alone was used as a control protein in application tests. The Swo-Xyn was recombined, expressed and produced by Pichia pastoris and had the maximum activity at 40 °C and pH 3.0 using xylan as substrate. The Swo-Xyn exhibited preferential hydrolysis of Xylan. The Swo-Xyn had slight low Km value (23.90 vs. 25.36 mg/ml) but significantly low Vmax value (162.4 vs. 227.2 μmol/mg·min) and specific activity (18.82 vs. 38.97 U/mg) relative to the Xyn. The Swo-Xyn activity was enhanced by Zn2+ in dose dependent manners with the peak activity at 30 mM of Zn2+. The Swo-Xyn could tolerate 15% of methanol, ethanol, aceton, and DMSO with >60% residual activity. The Swo-Xyn had the greater tolerance to SDS, EDTA, 2-ME than the Xyn and could be activated by DTT, Triton X-100, and Tween 20. Compared with the Xyn, the hydrolysis and sequent cellulose enzymolysis of soybean straw could be better improved by the Swo-Xyn. The Swo-Xyn should be more useful for improving the utilization of soybean straw.

Recombinant Lentinula edodes xylanase improved the hydrolysis and in vitro ruminal fermentation of soybean straw by changing its fiber structure

Soybean straw cannot be efficiently degraded and utilized by ruminants due to the complex cross-linked structure among cellulose, hemicellulose, and lignin in its cell wall. Xylanase can degrade the xylan component of hemicellulose, destroy the xylan-lignin matrix and, consequently, would theoretically improve the hydrolysis effectiveness of cellulose. Therefore, this study was performed to investigate the effects of recombinant Lentinula edodes xylanase (rLeXyn11A) on fiber structure, hydrolysis, and in vitro ruminal fermentation of soybean straw. Treatment with rLeXyn11A enhanced the hydrolysis of soybean straw with an evident increase in productions of ribose, rhamnose, and xylose. Soybean straw treated by rLeXyn11A had lower hemicellulose content and greater cellulose and lignin contents. The rLeXyn11A could remove xylan, loosen unordered fibrous networks, enhance substrate porosity, and rearrange lignin, consequently increasing the exposure of cellulose and improving the cellulase hydrolysis of soybean straw. Supplemental rLeXyn11A stimulated the dry matter digestion, volatile fatty acids production, and microbial protein synthesis during in vitro ruminal incubation. This paper demonstrated that rLeXyn11A could strengthen the cellulase hydrolysis and in vitro ruminal fermentation of soybean straw by degrading xylan and changing fiber structure, showing its potential for improving the utilization of soybean straw in ruminants.