Synthetic biology enables mushrooms to meet emerging sustainable challenges.

With the increasing sustainability challenges, synthetic biology is offering new possibilities for addressing the emerging problems through the cultivation and fermentation of mushrooms. In this perspective, we aim to provide an overview on the research and applications mushroom synthetic biology, emphasizing the need for increased attention and inclusion of this rapidly advancing field in future mushroom technology over China and other countries. By leveraging synthetic biology, mushrooms are expected to play a more versatile role in various area, including traditional fields like circular economy, human wellness and pharmaceutics, as well as emerging fields like vegan meat, mushroom-based materials and pollution abatement. We are confident that these efforts using synthetic biology strategies have the potential to strengthen our capacity to effectively address sustainable challenges, leading to the development of a more sustainable social economy and ecology.

The health effects of artificial sweeteners: Towards personalized quantification and prediction through gut microbiome.

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World Health Organization's first-ever release of a fungal priority pathogens list: A reply action proposal for the prevention and treatment of fungal pathogens.

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Heterologous biosynthesis of medicarpin using engineered Saccharomyces cerevisiae.

Medicarpin is an important bioactive compound with multiple medicinal activities, including anti-tumor, anti-osteoporosis, and anti-bacterial effects. Medicarpin is associated with pterocarpans derived from medicinal plants, such as Sophora japonica, Glycyrrhiza uralensis Fisch., and Glycyrrhiza glabra L. However, these medicinal plants contain only low amounts of medicarpin. Moreover, the planting area for medicarpin-producing plants is limited; consequently, the current medicarpin supply cannot meet the high demands of medicinal markets. In this study, eight key genes involved in medicarpin biosynthesis were identified using comparative transcriptome and bioinformatic analyses. In vitro and in vivo enzymatic reaction confirmed the catalytic functions of candidate enzymes responsible for the biosynthesis of medicarpin and medicarpin intermediates. Further engineering of these genes in Saccharomyces cerevisiae achieved the heterologous biosynthesis of medicarpin using liquiritigenin as a substrate, with a final medicarpin yield of 0.82 ± 0.18 mg/L. By increasing the gene copy numbers of vestitone reductase (VR) and pterocarpan synthase (PTS), the final medicarpin yield was increased to 2.05 ± 0.72 mg/L. This study provides a solid foundation for the economic and sustainable production of medicarpin through a synthetic biology strategy.

Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows.

Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 â„ƒ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 â„ƒ. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.

Advancing Insights into Probiotics during Vegetable Fermentation.

Fermented vegetables have a long history and are enjoyed worldwide for their unique flavors and health benefits. The process of fermentation improves the nutritional value, taste, and shelf life of foods. Microorganisms play a crucial role in this process through the production of metabolites. The flavors of fermented vegetables are closely related to the evaluation and succession of microbiota. Lactic acid bacteria (LABs) are typically the dominant bacteria in fermented vegetables, and they help inhibit the growth of spoilage bacteria and maintain a healthy gut microbiota in humans. However, homemade and small-scale artisanal products rely on spontaneous fermentation using bacteria naturally present on fresh vegetables or from aged brine, which may introduce external microorganisms and lead to spoilage and substandard products. Hence, understanding the role of LABs and other probiotics in maintaining the quality and safety of fermented vegetables is essential. Additionally, selecting probiotic fermentation microbiota and isolating beneficial probiotics from fermented vegetables can facilitate the use of safe and healthy starter cultures for large-scale industrial production. This review provides insights into the traditional fermentation process of making fermented vegetables, explains the mechanisms involved, and discusses the use of modern microbiome technologies to regulate fermentation microorganisms and create probiotic fermentation microbiota for the production of highly effective, wholesome, safe, and healthy fermented vegetable foods.

Advancements in the Biotransformation and Biosynthesis of the Primary Active Flavonoids Derived from Epimedium.

Epimedium is a classical Chinese herbal medicine, which has been used extensively to treat various diseases, such as sexual dysfunction, osteoporosis, cancer, rheumatoid arthritis, and brain diseases. Flavonoids, such as icariin, baohuoside I, icaritin, and epimedin C, are the main active ingredients with diverse pharmacological activities. Currently, most Epimedium flavonoids are extracted from Epimedium plants, but this method cannot meet the increasing market demand. Biotransformation strategies promised huge potential for increasing the contents of high-value Epimedium flavonoids, which would promote the full use of the Epimedium herb. Complete biosynthesis of major Epimedium flavonoids by microbial cell factories would enable industrial-scale production of Epimedium flavonoids. This review summarizes the structures, pharmacological activities, and biosynthesis pathways in the Epimedium plant, as well as the extraction methods of major Epimedium flavonoids, and advancements in the biotransformation and complete microbial synthesis of Epimedium flavonoids, which would provide valuable insights for future studies on Epimedium herb usage and the production of Epimedium flavonoids.

Significance of sTREM-1 and sST2 combined diagnosis for sepsis detection and prognosis prediction.

The diagnosis of sepsis still lacks a practical and reliable gold standard. The purpose of this study was to confirm the effect of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) combined with soluble suppression of tumorigenicity 2 (sST2) in the diagnosis of sepsis through the correlation between sTREM-1, sST2, and sequential organ failure assessment (SOFA) scores. Baseline data of 91 patients with sepsis in the intensive care unit were collected, sTREM-1 and sST2 were detected, and the correlation between markers and SOFA score was analyzed. Besides, the prognostic value of baseline and postadmission indicators for sepsis was analyzed with death as the outcome. The results showed that the expressions of sST2 and sTREM-1 in death group and survival group were higher than those in the survival group (p < 0.05). Correlation analysis showed that sST2, sTREM-1, and the joint diagnosis model had a high correlation with SOFA score (p < 0.05), but poor correlation with Acute Physiology and Chronic Health Evaluation Ⅱ score (p > 0.05). Among them, joint diagnosis model has the highest correlation. Receiver operating characteristic curve analysis showed that combined diagnosis had higher area under curve values. sTREM-1/sST2 can be better used in the diagnosis of sepsis than the single biomarker detection, and the combination of the above two biomarkers has potential application value in the detection and prognosis prediction of sepsis.

An enriched ammonia-oxidizing microbiota enables high removal efficiency of ammonia in antibiotic production wastewater.

High ammonia concentration hinders the efficient treatment of antibiotic production wastewater (APW). Developing effective ammonia oxidation wastewater treatment strategies is an ideal approach for facilitating APW treatment. Compared with traditional nitrification strategies, the partial nitrification process is more eco-friendly, less energy-intensive, and less excess sludge. The primary limiting factor of the partial nitrification process is increasing ammonia-oxidizing bacteria (AOB) while decreasing nitrite-oxidizing bacteria (NOB). In this study, an efficient AOB microbiota (named AF2) was obtained via enrichment of an aerobic activated sludge (AS0) collected from a pharmaceutical wastewater treatment plant. After a 52-day enrichment of AS0 in 250 mL flasks, the microbiota AE1 with 69.18% Nitrosomonas microorganisms was obtained. Subsequent scaled-up cultivation in a 10 L fermenter led to the AF2 microbiota with 59.22% Nitrosomonas. Low concentration of free ammonia (FA, < 42.01 mg L-1) had a negligible effect on the activity of AF2, and the nitrite-nitrogen accumulation rate (NAR) of AF2 was 98% when FA concentration was 42.01 mg L-1. The specific ammonia oxidation rates (SAORs) at 30 °C and 15 °C were 3.64 kg NH4+-N·kg MLVSS-1·d-1 and 1.43 kg NH4+-N·kg MLVSS-1·d-1 (MLVSS: mixed liquor volatile suspended solids). The SAOR was 0.52 kg NH4+-N·kg MLVSS-1·d-1 when the NaCl concentration was increased from 0 to 20 g L-1, showing that AF2 functioning was stable in a high-level salt environment. The ammonia oxidation performance of AF2 was verified by treating abamectin and lincomycin production wastewater. The NARs of AF2 used for abamectin and lincomycin production wastewater treatment were >90% and the SAORs were 2.39 kg NH4+-N·kg MLVSS-1·d-1 and 0.54 kg NH4+-N·kg MLVSS-1·d-1, respectively, which was higher than the traditional biological denitrification process. In summary, AF2 was effective for APW treatment via enhanced ammonia removal efficiency, demonstrating great potential for future industrial wastewater treatment.

Harnessing synthetic biology for mushroom farming.

Recent advances in synthetic biology have transformed mushroom farming from a focus on traditional cultivation to comprehensive applications based on cutting-edge biotechnologies. Synthetic biology has promising applications in this field, including precision breeding, mining biosynthetic gene clusters, developing mushroom chassis cells, and constructing cell factories for high value-added products.

Facultative symbionts are potential agents of symbiont-mediated RNAi in aphids.

Aphids are major crop pests, and they can be controlled through the application of the promising RNA interference (RNAi) techniques. However, chemical synthesis yield of dsRNA for RNAi is low and costly. Another sustainable aphid pest control strategy takes advantage of symbiont-mediated RNAi (SMR), which can generate dsRNA by engineered microbes. Aphid host the obligate endosymbiont Buchnera aphidicola and various facultative symbionts that not only have a wide host range but are also vertically and horizontally transmitted. Thus, we described the potential of facultative symbionts in aphid pest control by SMR. We summarized the community and host range of these facultative symbionts, and then reviewed their probable horizontal transmitted routes and ecological functions. Moreover, recent advances in the cultivation and genetic engineering of aphid facultative symbionts were discussed. In addition, current legislation of dsRNA-based pest control strategies and their safety assessments were reviewed.

Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota.

Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.

Advances in the human skin microbiota and its roles in cutaneous diseases.

Skin is the largest organ in the human body, and the interplay between the environment factors and human skin leads to some skin diseases, such as acne, psoriasis, and atopic dermatitis. As the first line of human immune defense, skin plays significant roles in human health via preventing the invasion of pathogens that is heavily influenced by the skin microbiota. Despite being a challenging niche for microbes, human skin is colonized by diverse commensal microorganisms that shape the skin environment. The skin microbiota can affect human health, and its imbalance and dysbiosis contribute to the skin diseases. This review focuses on the advances in our understanding of skin microbiota and its interaction with human skin. Moreover, the potential roles of microbiota in skin health and diseases are described, and some key species are highlighted. The prevention, diagnosis and treatment strategies for microbe-related skin diseases, such as healthy diets, lifestyles, probiotics and prebiotics, are discussed. Strategies for modulation of skin microbiota using synthetic biology are discussed as an interesting venue for optimization of the skin-microbiota interactions. In summary, this review provides insights into human skin microbiota recovery, the interactions between human skin microbiota and diseases, and the strategies for engineering/rebuilding human skin microbiota.

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning.

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, no medical treatment has been approved for the treatment of NAFLD. In our previous study, we found that PKLR could be a potential target for treatment of NALFD. Here, we investigated the effect of PKLR in in vivo model and performed drug repositioning to identify a drug candidate for treatment of NAFLD. METHODS: Tissue samples from liver, muscle, white adipose and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptomics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were both tested in in vitro and in vivo models to evaluate their toxicity and efficacy. FINDINGS: The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in the liver as well as in other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drug candidates were identified as potential inhibitor of PKLR using our drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and we found that these drugs attenuate the hepatic steatosis without side effect on other tissues. INTERPRETATION: In conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical studies. FUNDING: ScandiEdge Therapeutics and Knut and Alice Wallenberg Foundation.

Developments in Fatty Acid-Derived Insect Pheromone Production Using Engineered Yeasts.

The use of traditional chemical insecticides for pest control often leads to environmental pollution and a decrease in biodiversity. Recently, insect sex pheromones were applied for sustainable biocontrol of pests in fields, due to their limited adverse impacts on biodiversity and food safety compared to that of other conventional insecticides. However, the structures of insect pheromones are complex, and their chemical synthesis is not commercially feasible. As yeasts have been widely used for fatty acid-derived pheromone production in the past few years, using engineered yeasts may be promising and sustainable for the low-cost production of fatty acid-derived pheromones. The primary fatty acids produced by Saccharomyces cerevisiae and other yeasts are C16 and C18, and it is also possible to rewire/reprogram the metabolic flux for other fatty acids or fatty acid derivatives. This review summarizes the fatty acid biosynthetic pathway in S. cerevisiae and recent progress in yeast engineering in terms of metabolic engineering and synthetic biology strategies to produce insect pheromones. In the future, insect pheromones produced by yeasts might provide an eco-friendly pest control method in agricultural fields.