Utility of Thermostable Xylanases of Mycothermus thermophilus in Generating Prebiotic Xylooligosaccharides

Direct enzymatic hydrolysis of solid wheat straw with endo-xylanases: Effect of the temperature on the hemicellulose release and the product profile modulation

Prebiotics are non-digestible compounds that promote intestinal microbiota growth and/or activity. Xylooligosaccharides (XOS) are new prebiotics derived from the hemicellulose fraction of lignocellulosic materials. Challenges in using those materials as sources for prebiotic compounds lie in the hemicellulose extraction efficiency and the safety of those ingredients. In this sense, this work aims to optimize hemicellulose extraction and XOS production through direct enzymatic hydrolysis of alkali pre-treated wheat straw without undesired byproducts. By increasing the temperature of the enzymatic step from 40 °C to 65 °C we achieved an improvement in the extraction yield from 55 % to 80 %. Products with different degrees of polymerization were also noticed: while XOS ≤ X6 where the main products at 40 °C, a mixture of long arabinoxylan derived polymers (ADPo) and XOS ≤ X6 was obtained at 65 °C, irrespective of the extraction yield. Thus, a modulatory effect of temperature on the product profile is suggested here. Among the XOS ≤ X6 produced, X2-X3 were the main products, and X4 was the minor one. At the end of the hydrolysis, 146.7 mg XOS per gram of pre-treated wheat straw were obtained.

Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches

There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.

One-step fermentation for producing xylo-oligosaccharides from wheat bran by recombinant Escherichia coli containing an alkaline xylanase

Background

One-step fermentation is a cheap way to produce xylo-oligosaccharides (XOS), where production of xylanases and XOS is integrated into a single process. In spite of cost advantage, one-step fermentation is still short in yield so far due to the limited exploration. To cope with this issue, production of XOS from wheat bran by recombinant Escherichia coli through one-step fermentation was investigated in this study.

Results

An endo-β-1,4-xylanase gene belonging to glycoside hydrolase family 11 of Bacillus agaradhaerens was employed to construct recombinant E. coli. This xylanase showed maximal activity at 60 °C and pH 8.0–8.5. Its activity retained more than 60% after incubation at 70 °C for 4 h, showing a good stability. The recombinant E. coli BL21(DE3) could secreted xylanases that directly hydrolyzed de-starched wheat bran to XOS in fermentation medium. The XOS generated from hydrolysis consisted of xylose, xylobiose and xylotriose accounting for 23.1%, 37.3% and 39.6%, respectively. Wheat bran concentration was found to be the most crucial factor affecting XOS production. The XOS concentration reached 5.3 mg/mL at 10% loading of wheat bran, which is higher than those of previous researches. Nitrogen source type could also affect production of XOS by changing extracellular xylanase activity, and glycine was found to be the best one for fermentation. Optimal fermentation conditions were finally studied using response surface optimization. The maximal concentration emerged at 44.3 °C, pH 7.98, which is affected by characteristics of the xylanase as well as growth conditions of E. coli.

Conclusions

This work indicates that the integrated fermentation using recombinant E. coli is highly competitive in cost and final concentration for producing XOS. Results can also provide theoretical basis for large-scale production and contribute to the wide adoption of XOS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-022-00736-8.

Tetracycline hydrochloride-stressed succession in microbial communities during aerobic composting: Insights into bacterial and fungal structures

Available information that whether antibiotics affect the succession in microbial communities during aerobic composting remains limited. Thus, this work investigated the dynamic changes in bacterial and fungal structures during aerobic composting amended with tetracycline hydrochloride (TCH: 0, 50, 150 and 300 mg kg^-1). Composting phases significantly affected bacterial and fungal communities, but only fungi strongly responded to antibiotics, while bacteria did not. Firmicutes, Proteobacteria, Bacteroidota and Actinobacteriota were primary bacterial phylum. Neocallimastigomycota was dominant fungal phylum at temperature-heating phase, then Basidiomycota and Ascomycota became main fungal phylum at thermophilic and temperature-colling phases. Low TCH concentration promoted Chytridiomycota growth, while high TCH concentration inhibited mostly fungal activity in TCH-amended composting. Nitrogen species were critical factors controlling the succession in bacterial and fungal communities during composting process. These results cast a new light on understanding about microbial function during aerobic composting.

Recent advancements in prebiotic oligomers synthesis via enzymatic hydrolysis of lignocellulosic biomass

Interest in functional food, such as non-digestible prebiotic oligosaccharides is increasing day by day and their production is shifting toward sustainable manufacturing. Due to the presence of high carbohydrate content, lignocellulosic biomass (LCB) is the most-potential, cost-effective and sustainable substrate for production of many useful products, including lignocellulose-derived prebiotic oligosaccharides (LDOs). These have the same worthwhile properties as other common oligosaccharides, such as short chain carbohydrates digestible to the gut flora but not to humans mainly due to their resistance to the low pH and high temperature and their demand is constantly increasing mainly due to increased awareness about their potential health benefits. Despite several advantages over the thermo-chemical route of synthesis, comprehensive and updated information on the conversion of lignocellulosic biomass to prebiotic oligomers via controlled enzymatic saccharification is not available in the literature. Thus, the main objective of this review is to highlight recent advancements in enzymatic synthesis of LDOs, current challenges, and future prospects of sustainably producing prebiotic oligomers via enzymatic hydrolysis of LCB substrates. Enzyme reaction engineering practices, custom-made enzyme preparations, controlled enzymatic hydrolysis, and protein engineering approaches have been discussed with regard to their applications in sustainable synthesis of lignocellulose-derived oligosaccharide prebiotics. An overview of scale-up aspects and market potential of LDOs has also been provided.

Characterization of Two α-l-Arabinofuranosidases from Acetivibrio mesophilus and Their Synergistic Effect in Degradation of Arabinose-Containing Substrates

Arabinofuranosidases are important accessory enzymes involved in the degradation of arabinose-containing poly- and oligosaccharides. Two arabinofuranosidases from the recently described novel anaerobic cellulolytic bacterium Acetivibrio mesophilus, designated AmAraf51 and AmAraf43, were heterologously expressed in Escherichia coli and biochemically characterized. AmAraf51 not only removed arabinose moieties at O-3, O-2 and terminal O-5 positions of arabinose-containing oligosaccharides, but also exhibited exo-β-xylosidase side activity. In comparison, AmAraf43 preferably cleaved 1,3-linkages from arabinosyl disubstitutions. AmAraf51 and AmAraf43 demonstrated maximum activity at 70 °C and 57 °C, respectively. Judging from the genetic context and substrate specificity, AmAraf51 may decompose internalized arabino/xylo-oligosaccharides. The embedding of the AmAraf43 gene between genes for several putative xylanolytic enzymes, along with its enzymatic properties suggests that AmAraf43 cleaves arabinose decorations from heteroxylans extracellularly. The enzymes revealed completely converse activity profiles towards arabinan/arabinoxylan: AmAraf51 displayed strong activity on arabinan, while AmAraf43 prefers arabinoxylan. AmAraf51 dramatically stimulated the saccharification level of wheat arabinoxylan (WAX-RS) and sugar beet arabinan when administered along with xylanase M_Xyn10 or arabinanase PpAbn43, respectively. For WAX-RS degradation, the yield of arabinose and xylose was boosted 13.77-fold and 4.96-fold, respectively. The bifunctional activity, thermostability and high catalytic efficiency make AmAraf51 an interesting candidate for industrial applications.

Highly-Efficient Release of Ferulic Acid from Agro-Industrial By-Products via Enzymatic Hydrolysis with Cellulose-Degrading Enzymes: Part I-The Superiority of Hydrolytic Enzymes Versus Conventional Hydrolysis

Historically Triticum aestívum L. and Secale cereále L. are widely used in the production of bakery products. From the total volume of grain cultivated, roughly 85% is used for the manufacturing of flour, while the remaining part is discarded or utilized rather inefficiently. The limited value attached to bran is associated with their structural complexity, i.e., the presence of cellulose, hemicellulose, and lignin, which makes this material suitable mostly as a feed supplement, while in food production its use presents a challenge. To valorize these materials to food and pharmaceutical applications, additional pre-treatment is required. In the present study, an effective, sustainable, and eco-friendly approach to ferulic acid (FA) production was demonstrated through the biorefining process accomplished by non-starch polysaccharides degrading enzymes. Up to 11.3 and 8.6 g kg⁻¹ of FA was released from rye and wheat bran upon 24 h enzymatic hydrolysis with multi-enzyme complex Viscozyme^® L, respectively.

Microbial succession and molecular ecological networks response to the addition of superphosphate and phosphogypsum during swine manure composting

This study assessed the effects of superphosphate (SPP) and phosphogypsum (PPG) on the bacterial and fungal community succession and molecular ecological networks during composting. Adding SPP and PPG had positive effects on the bacterial richness and diversity, negative effects on the fungal richness and diversity. The microbial diversity and richness were higher in PPG than SPP. Non-metric multidimensional scaling analysis clearly separated SPP and PPG from the control treatment with no additives. The dominant genera comprised Turicibacter, Bacillus, norank_o_SBR1031, Thermobifida, norank_f_Limnochordaceae, Truepera, Thermopolyspora, Mycothermus, Dipodascus, Thermomyces, and unclassified_p_Ascomycota. In all treatments, the major bacterial species differed clearly in the later thermophilic, cooling, and maturation composting stages, whereas the main fungal species varied significantly in the thermophilic stage. The changes in the dominant microorganisms in SPP and PPG may have inhibited or promoted the degradation of organic matter during various composting stages. Adding SPP and PPG led to more complex bacterial networks and less complex fungal networks, where SPP had more adverse effects on the fungal networks than PPG. SPP and PPG could potentially alter the co-occurrence patterns of the bacterial and fungal communities by changing the most influential species. SPP and PPG changed the composition and succession of the microbial community by influencing different physiochemical properties during various composting stages where the pH was the main explanatory factor. Overall, this study provides new insights into the effects of SPP and PPG on the microbial community and its interactions during composting.

Enhancement of catalytic performance of a metagenome-derived thermophilic oligosaccharide-specific xylanase by binding module removal and random mutagenesis

Xylo-oligosaccharide (XO) is a promising pre-biotic with applications in food, feed and healthcare products. XO can be produced by enzymatic digestion of xylan with xylanase. In this study, we aimed to improve the biochemical properties relevant to catalysis and kinetics of X11, a thermophilic glycosyl hydrolase (GH) family 11 endo-β-1,4-xylanase derived from a metagenomic library isolated from sugarcane bagasse, under high-temperature conditions preferred for XO synthesis. Removal of a carbohydrate-binding module (X11C) resulted in 6.5 fold greater catalytic efficiency. X11C was further improved by a Pro71Thr mutation in the X11P variant obtained from a random mutagenesis library, which exhibited 15.9 fold greater catalytic efficiency compared with wild-type X11 under the enzyme's optimal conditions of 80°C and pH 6.0. Homology modeling suggested that the improved performance of X11P could be attributed to formation of an extra H-bond between Thr71 and Ser75, which stabilizes the key catalytic residue Glu180 at the active pocket and β-sheet layers and agrees with the respective increase in melting temperature (T_m) where X11P >X11C >X11 as determined by differential scanning fluorimetry. The X11P variant was tested for hydrolysis of beechwood xylan, which showed X6 as the major product followed by X3 and X4 XOs. The highest yield of 5.5 g total XOs product/mg enzyme was observed for X11P, equivalent to 3.7 fold higher than that of wild-type with XO production of >800 mg/g xylan. The X11P enzyme could be developed as a thermophilic biocatalyst for XO synthesis in biorefineries.

Effect of extraction methods on the physicochemical, structural, functional, and antioxidant properties of the dietary fiber concentrates from male date palm flowers

The current study evaluates the effect of both aqueous and alkaline extraction methods on the physicochemical, structural, functional, and antioxidant properties of dietary fibers (DF) from male date palm flowers (MDPF). The DF extracted by the alkali treatment (ADF) display a higher DF content as well as lower protein and lipid content than the DF resulting from watery extraction (WDF). The scanning electron microscopy, the Fourier-transform infrared spectroscopy, and the X-ray diffraction show that the alkaline treatment contributes to a slight modification of the structural characteristics of ADF leading to better purity and functional properties. The oil holding capacity and the antioxidant activity of ADF have improved compared to the WDF, which makes this concentrate a promoting functional ingredient and a natural antioxidant. Therefore, these findings confirm the wealth of both concentrates in DF, especially ADF, as well as their potential of functional and antioxidant properties, which emphasize their suitability to be used in food applications as functional ingredients. PRACTICAL APPLICATIONS: Nowadays, studies on the extraction of DF from vegetable waste are of considerable interest in the face of the rising global demand for dietetic food. The male date palm flowers (MDPF), an agricultural waste generated during the period of pollination, are valuable natural sources of DF and antioxidants. The insoluble DF of MDPF could be essential in a balanced diet as they could fight against obesity by creating a feeling of satiety. The presence of antioxidants, which are known for preventing or slowing cell damage caused by free radicals, could contribute to the improvement of the antioxidant properties of the formulated food. The functional properties of DF concentrates from MDPF are able to solve the technical problems of agri-food industries when used as food ingredients. The use of DF from MDPF, consequently, contributes to the minimization of waste and provides value addition to the by-product considered as waste in agricultural processing.

Biochemical Characterization of Xylanases from Streptomyces sp. B6 and Their Application in the Xylooligosaccharide Production from Viscose Fiber Production Waste

Enzymatic hydrolysis of xylan represents a promising way to produce xylooligosaccharide (XOS), which is a novel ingredient in functional food. However, the recalcitrance of xylan in natural lignocellulosic biomass entails effective and robust xylanases. In the present study, we reported the isolation of a thermophilic Streptomyces sp. B6 from mushroom compost producing high xylanase activity. Two xylanases of Streptomyces sp. B6 belonging to GH10 (XynST10) and GH11 (XynST11) families were thus identified and biochemically characterized to be robust enzymes with high alkaline- and thermostability. Direct hydrolysis of neutralized viscose fiber production waste using XynST10 and XynST11 showed that while XynST10 produced 23.22 g/L XOS with a degree of polymerization (DP) of 2-4 and 9.27 g/L xylose, XynST11 produced much less xylose (1.19 g/L) and a higher amounts of XOS with a DP = 2-4 (28.29 g/L). Thus, XynST11 holds great potential for the production of XOS from agricultural and industrial waste.

Xylooligosaccharide Modulates Gut Microbiota and Alleviates Colonic Inflammation Caused by High Fat Diet Induced Obesity

Obesity leads to colonic inflammation and may increase the risk of colorectal cancer. Xylooligosaccharide (XOS) exhibits strong antioxidant and excellent antibacterial properties, and can be utilized by gut microbes to maintain the ecological balance of the intestinal tract. In this study, we explored how XOS modulates the microbiota and regulates high fat diet (HFD) induced inflammation. We measured the changes in body weight and visceral coefficients in rats fed a high-fat diet. We also measured the expression levels of inflammatory factors in the plasma and colonic tissues of the rats using the enzyme-linked immunosorbent assay and real-time quantitative polymerase chain reaction. We analyzed the composition of fecal microorganisms and short chain fatty acid (SCFA) content using 16S rDNA and GC-MS. We found that XOS significantly counteracted HFD induced weight gain. Moreover, the plasma levels of monocyte chemoattractant protein-1, tumor necrosis factor (TNF-α) and lipopolysaccharide decreased in the XOS-treated rats. XOS treatment decreased TNF-α mRNA expression and increased occludin mRNA expression in the rat colon. We observed a reduction in the overall microbial abundance in the feces of the XOS-treated rats, although the proportion of Bacteroidetes/Firmicutes increased significantly and the number of beneficial bacteria increased in the form of dominant microbes. We found that both SCFA-producing bacteria and SCFA content increased in the gut of the XOS-treated rats. We identified a correlation between the abundance of Prevotella and Paraprevotella and SCFA content. Taken together, we propose that XOS can alleviate colonic inflammation by regulating gut microbial composition and enhancing SCFA content in the gut.

Thermozymes: Adaptive strategies and tools for their biotechnological applications

In today's scenario of global climate change, there is a colossal demand for sustainable industrial processes and enzymes from thermophiles. Plausibly, thermozymes are an important toolkit, as they are known to be polyextremophilic in nature. Small genome size and diverse molecular conformational modifications have been implicated in devising adaptive strategies. Besides, the utilization of chemical technology and gene editing attributions according to mechanical necessities are the additional key factor for efficacious bioprocess development. Microbial thermozymes have been extensively used in waste management, biofuel, food, paper, detergent, medicinal and pharmaceutical industries. To understand the strength of enzymes at higher temperatures different models utilize X-ray structures of thermostable proteins, machine learning calculations, neural networks, but unified adaptive measures are yet to be totally comprehended. The present review provides a recent updates on thermozymes and various interdisciplinary applications including the aspects of thermophiles bioengineering utilizing synthetic biology and gene editing tools.

GH-10 and GH-11 Endo-1,4-β-xylanase enzymes from Kitasatospora sp. produce xylose and xylooligosaccharides from sugarcane bagasse with no xylose inhibition

A novel strategy for the low-cost, high-yield co-production of xylose and xylooligosaccharides together with no xylose inhibition was developed using a novel heterologous expression of XYN10Ks_480 endo-1,4-β-xylanase with a ricin-type β-trefoil type of domain and XYN11Ks_480 endo-1,4-β-xylanase with a CBM 2 superfamily from the Kitasatospora sp in an actinomycetes expression system. Xylose is the main building block for hemicellulose xylan. Our findings demonstrated high levels of expression and catalytic activity for XYN10Ks_480 during hydrolysis of the extracted xylan of bagasse, and three types of xylan-based substrates were used to produce xylose and xylooligosaccharides. However, hydrolysis by XYN11Ks_480 produced xylooligosaccharides without xylose formation. This study demonstrated how integrating sodium hypochlorite-extracted xylan and enzymatic hydrolysis could provide an alternative strategy for the generation of XOS from lignocellulosic material.

Prebiotic compounds from agro-industrial by-products

Prebiotics are nondigestible food components that have an impact on gut microbiota composition and activity, which in turn results in the improvement of health conditions. Nowadays, the production of prebiotics from agro-industrial by-products is under investigation. In this regard, polysaccharides are usually found in these sources and their potential use as prebiotics has been studied recently since these compounds act as substrates for the human gut microbiota, and they have the potential to modulate its composition through many mechanisms. Additionally, the use of agricultural by-products is advantageous because it is a cheap and abundantly available material. This review focuses on the recent scientific literature regarding the prebiotic properties of polysaccharides from agro-industrial by-products. PRACTICAL APPLICATIONS: Currently, the maintenance of gut homeostasis is a target for the improvement of human health. This review can broaden the perspective on the utilization of agro-industrial by-products that can compete in the market with the commercial ones or act as a source for new food ingredients.

Changes in structure and function of fungal community in cow manure composting

In this study, dynamic changes in fungal communities, trophic modes and effect factors in 60 days composting of cow manure were analyzed by using high throughput sequencing, FUNGuild and Biolog FF MicroPlate, respectively. Orpinomyces (relative abundance >10.85%) predominated in feedstock, and Mycothermus became the dominating genus (relative abundance >75%) during the active phase. Aerobic composting treatment had a significant effect on fungal trophic modes with pathogenic fungi fading away and wood saprotrophs increasing over composting time. Fungal communities had the higher carbon sources utilization capabilities at the thermophilic phase and mature phase than those in the other periods. Oxidation reduction potential (ORP) significantly increased from -180 to 180 mV during the treatment. Redundancy analysis showed that the succession of fungal community during composting had a significant association with ORP (p < .05). This indicated that aerobic composting treatment not only influenced fungal community structure, but also changed fungal trophic modes and metabolic characteristics.

Thermostability improvement of a Talaromyces leycettanus xylanase by rational protein engineering

Thermophilic xylanases with high catalytic efficiency are of great interest in the biofuel, food and feed industries. This study identified a GH11 xylanase gene, Tlxyn11B, in Talaromyces leycettanus JCM12802. Recombinant TlXyn11B produced in Pichia pastoris is distinguished by high specific activity (8259 ± 32 U/mg with beechwood xylan as substrate) and excellent pH stability (from 1.0 to 10.5). The beechwood xylan hydrolysates consisted mainly of xylobiose, xylotriose and xylotetraose, thus TlXyn11B could be used for the production of prebiotic xylooligosaccharide. By using the structure-based rational approach, the N-terminal sequence of TlXyn11B was modified for thermostability improvement. Mutants S3F and S3F/D35V/I/Q/M had elevated T_m values of 60.01 to 67.84 °C, with S3F/D35I the greatest. Homology modeling and molecular dynamics (MD) simulation analysis revealed that the substituted F3 and I35 formed a sandwich structure with S45 and T47, which may enhance the overall structure rigidity with lowered RMSD values. This study verifies the efficiency of rational approach in thermostability improvement and provides a xylanase candidate of GH11 with great commercialization potential.