Medicarpin exhibits multiple pharmacological activities, including antitumor and antibacterial effects. However, its extraction from natural plant sources is limited, and chemical synthesis is complex and costly. Therefore, developing an economical, green, and sustainable medicarpin production method is of great significance. In this study, we achieved the de novo synthesis of medicarpin in engineered Saccharomyces cerevisiae. Specifically, we overexpressed and mutated endogenous yeast genes involved in the upstream shikimate pathway and aromatic amino acid biosynthesis pathway, which are essential for flavonoid synthesis. Additionally, we constructed the downstream flavonoid biosynthetic pathway in engineered yeast strains by integrating heterologous genes derived from plants and bacteria. Consequently, the synthesis of p-coumaric acid, liquiritigenin, daidzein, and formononetin was successfully achieved in a series of engineered strains, with medicarpin ultimately synthesized in the strain of GlaN22. After 168 h of cultivation, the medicarpin titer of GlaN22 reached 3.13 ± 0.68 μg/L. Further optimization via double-copy integration of some key biosynthetic genes resulted in strains of GlaN25 and GlaN26, which produced 76.23 ± 9.43 μg/L and 157.55 ± 17.05 μg/L of medicarpin, respectively. This work demonstrates the successful de novo production of medicarpin in engineered yeasts, providing a foundation for the green and sustainable biomanufacturing of high-value isoflavonoid compounds derived from traditional Chinese herbs.

Certain microbes can enhance the utilization and nutritional value of defatted cottonseed meal, an oilseed processing by-product. In this study, 11 microbial strains with strong gossypol-degrading activity were identified. The interactions among these 11 gossypol-resistant strains were examined using supernatant cross-feeding assays. Based on these interactions, 28 synthetic microbial communities (SynComs) were constructed. Evaluation of the fermentation performance of these SynComs revealed four core functional strains of YZ-1 (Pichia kudriavzevii LNTJQ-1), YZ-3 (Wickerhamomyces anomalus YJQ-1), YZ-6 (Candida tropicalis TJQ-4), and YZ-7 (Saccharomyces cerevisiae LNTJQ-3). Among the tested SynComs, SC5 (composed of YZ-1, YZ-3, and YZ-7) was identified as the optimal consortium. SC5 degraded free gossypol by 93.82% (Reducing from 1068.00 mg/kg to 66.00 mg/kg), while increasing crude protein content by 11.08% and total amino acid content by 7.98% based on dry matter. In summary, the screening of gossypol degradation microbes and construction of SynComs improved the nutritional value and utilization of defatted cottonseed meal, providing a feasible solution for developing defatted cottonseed meal as an animal feed resource.

Chronic kidney disease (CKD) characterized by the progressive loss of renal, represents a significant global health challenge. Central to CKD progression is kidney fibrosis, an irreversible process marked by the accumulation of extracellular matrix proteins. The development of effective antifibrotic therapies is thus crucial for improving patient outcomes. We conducted a comprehensive analysis of bulk RNA sequencing data from unilateral ureteral obstruction (UUO) and folic acid (FA)-induced nephropathy mice models, combined with single-cell RNA sequencing (scRNA-seq) to explore cellular heterogeneity and molecular mechanisms of kidney fibrosis. Differential gene expression analysis, gene co-expression network (CN) analysis, time-series clustering, and cell marker analysis were employed to identify core fibrosis-related genes. Our analyses revealed a set of 37 core fibrosis-related genes which are largely associated with inflammation and immune response and contributed to the production of extracellular matrix (ECM), with Ckap4 standing out as a key marker of kidney fibrosis. In vivo experiments demonstrated that knockdown of Ckap4 significantly reduced kidney fibrosis in UUO mice, as evidenced by decreased collagen deposition and improved renal function. Additionally, the repurposed small molecule drugs, especially CGP-60474, showed promising antifibrotic effects, further highlighting the potential of Ckap4 as a therapeutic target.

Cocoa butter is the main raw material for chocolate and other food products. However, cocoa butter production is constrained by land availability and environmental factors. Oleaginous yeasts offer a promising alternative. In this study, 103 yeast strains were isolated and screened for their lipid accumulation capacity. Among them, Papiliotrema laurentii MYL-1 produced high-level cocoa butter equivalent (CBE), accounting for 45.3% of total triacylglycerols. Under nitrogen limitation with an optimal C/N ratio of 80:1, MYL-1 achieved 58.2% fatty acids of dry cell weight, 14.9 g/L biomass, and 8.7 g/L fatty acid titer. Fed-batch cultivation in a 5-L bioreactor yielded 24.6 g/L lipids with a productivity of 0.17 g/L/h, and a balanced C16:0/C18:0 ratio near 1:1, enhancing the suitability for CBE production.

This review provides a mechanistic synthesis of extracellular vesicles (EVs) in fermented foods, highlighting their emerging role as key bioactive mediators beyond traditional metabolites. EVs originate from both fermentative microorganisms and raw materials, carrying diverse cargos that enable intercellular and cross-kingdom communication. During fermentation, EV characteristics are dynamically modified through microbial-raw material interactions and environmental factors, which regulate EV biogenesis, cargo composition, and functional activity. Mechanistically, fermented food-derived EVs modulate host signaling pathways, thereby influencing immune responses and intestinal barrier function.

Ginkgo biloba contains diverse natural products. This study employed microbial fermentation to alter phytochemical profiles in Ginkgo biloba leaves (GBL). Four microorganisms—Lactobacillus plantarum SCTM-1, Saccharomyces cerevisiae GLLB-3, Aspergillus niger ZYDC-1, and Aspergillus cristasukae LNAC-1—were used individually and in a consortium (YXSL: L. plantarum + S. cerevisiae). All the microbial fermentation changes the GBL metabolite profiles, including total polyphenols, flavonoids, and polysaccharides. Especially, compared to unfermented GBL, YXSL increased total polyphenols, flavonoids, and polysaccharides by 76.0 %, 170.6 %, and 20.9 %, respectively. Metabolomic analysis identified 116 differentially expressed secondary metabolites, mainly in plant secondary metabolite, phenylpropanoid, and flavonoid biosynthesis pathways. YXSL specifically enhanced flavonoid production via microbial biotransformation, with crocetin content increasing 104.5 % through hydrolysis of crocin. This work highlights microbial potential to boost GBL’s bioactive components and provides a basis for improving phytochemical yields via fermentation.

Isoflavones such as daidzein and genistein are naturally occurring compounds found in plants such as legumes. They have diverse pharmacological activities, making them valuable in the food, pharmaceutical, and cosmetic industries. Currently, isoflavones are mainly obtained through the extraction of plant biomass. Chemical synthesis is challenging for most isoflavones due to the complexity of their structures. The limited supply of isoflavones cannot meet the market demands. Advances in synthetic biology have provided a sustainable and efficient solution for the production of isoflavones, with yeasts often serving as the microbial chassis for biosynthesis. This review summarizes the pharmacological properties of specific isoflavones, their biosynthetic pathways, and the technical strategies used in engineered yeasts for isoflavone production. In addition, the development of synthetic biology and state-of-the-art biotechnological strategies for the environmentally friendly production of bioactive isoflavones is discussed.

Lactiplantibacillus plantarum, one of the lactic acid bacteria (LAB), has shown numerous probiotic properties and health benefits to humans, particularly in the fight against obesity. Identification and characterization of effective L. plantarum strains and understanding their health effects are essential for developing effective probiotic-based therapies for chronic diseases like obesity and diabetes. By screening various environmental samples, 17 L. plantarum strains were isolated. The acid and bile salt tolerance, short-chain fatty acids (SCFAs) production, cholesterol-lowering effect, and antioxidant performance of these L. plantarum strains were evaluated. The health effects of L. plantarum ZNFL-1 were assessed in high-fat diet-feeding mice by monitoring mice weight gain, adipose tissue, blood glucose, and lipid, and investigating the changes of the mice gut microbiota. The representative L. plantarum strain ZNFL-1 exhibited significant tolerance to acid and bile salts. Its supplementation significantly reduced cholesterol levels and exhibited antioxidant properties. In high-fat diet-feeding mice, L. plantarum ZNFL-1 intervention, especially at higher doses, reduced body weight gain, inhibited adipose tissue accumulation, and improved gut microbiota dysbiosis. This study identified L. plantarum ZNFL-1, which has notable anti-obesity effects in mice fed with a high-fat diet. These anti-obesity effects were achieved by increasing levels of beneficial bacteria and decreasing potentially harmful ones. Additionally, L. plantarum ZNFL-1 alleviated dysbiosis induced by a high-fat diet and improved symptoms associated with obesity by regulating lipid metabolism.

Rapid advancements in sequencing technologies in the past decade have driven the widespread adoption of amplicon metagenome. However, current amplicon data analysis software/pipelines often require manual intervention spanning multiple steps, necessitating a clear understanding of parameters and hindering inexperienced users from automating their workflows. Here, we introduce Dix-seq, a fully containerized tool for rapid, automated, and scalable amplicon data analysis. With one single command, Dix-seq can process raw amplicon sequences down to various statistical and visualization results, generate html-based reports, and retrospective logfiles. Dix-seq utilizes a single parameter sheet file to drastically simplify its command line interface, making it much more approachable by inexperienced users while improving study reproducibility. The modular design of Dix-seq enables rapid adoption of new methods and databases into its software frame. Currently, more than 21 algorithms, software, and third-party procedures have been integrated into eight modules in Dix-seq, while more are coming down the line. This approach also allows experienced users to fine-tune the workflow, facilitating customized analysis. Benchmarks performed on datasets from real-world case studies demonstrated Dix-seq’s capabilities in generating publish-ready figures integrated with statistical information and extracting biologically meaningful patterns. Furthermore, it remained highly effective at detecting variance upon simulated sequencing depth drop, the results remained robust down to a depth of 11000 and 1000 in all and certain fronts, such as phylogenetic diversity and Pearson correlation, respectively. In summary, Dix-seq is a convenient yet highly customizable tool for amplicon data analysis, making it an ideal choice for both entry-level and experienced users.

Omega-amino fatty acids (ω-AmFAs) are non-natural organic molecules with amino and carboxyl groups located at the ends of unbranched carbon chains. They are widely used in the synthesis of polymers such as polyesters and polyamides, as well as in the production of chemical products such as biofuels and pharmaceutical intermediates. In recent years, the production of such materials and other chemicals via the fermentation of renewable resources using engineered microorganisms has become a hot spot of research, as examples of emerging green and low-carbon technologies. Traditional petrochemical synthesis methods of nylon monomers often face problems such as environmental pollution, increased energy consumption and high cost. By contrast, the catalytic production of ω-AmFAs from fatty acids such as oleic acid, ricinoleic acid and lauric acid found in vegetable oils using a multienzyme cascade has the unique advantages of being environmentally friendly and having high process economics. This paper reviews multienzyme synthesis strategies of ω-AmFAs used as nylon monomers.

Cottonseed is a valuable source of high-quality proteins and oils. Defatted cottonseed meal (DCSM), a by-product of cottonseed oil extraction, holds significant potential as a sustainable protein resource. This review outlines the chemical composition, structural features, and unique properties of cottonseed, with a focus on its inherent antinutritional factors, such as gossypol. Strategies for enhancing the utilization of DCSM as a protein source are systematically evaluated, including physical, chemical, and biological methods used to eliminate or reduce antinutritional components. Among these, microbial fermentation, particularly solid-state fermentation, is highlighted as a promising, eco-friendly approach for detoxification and nutritional improvement. This review further discusses critical factors influencing the removal of anti-nutritional compounds, such as pretreatment methods, fermentation parameters, and microbial strains. The efficacy of probiotic strains (e.g., Bacillus and yeasts) in enhancing the protein digestibility, amino acid profiles, and functional properties of DCSM is discussed. Additionally, recent advances in the application of fermented cottonseed protein in foods (e.g., animal feed, functional peptides, and food additives) and non-food sectors (e.g., biofuels and bioplastic) are explored. The integration of probiotic-driven fermentation processes is proposed as a strategy to exploit the full nutritional and economic potential of DCSM, paving the way for its broader and sustainable use in foods and non-food applications.

Tiger nut (Cyperus esculentus L.) is widely recognized as both an oil crop and a high-quality forage. However, the comprehensive utilization of tiger nut meal (TNM) remains underexplored. This study investigates the potential of solid-state fermentation with selected microorganisms to convert TNM into a high-nutritional-value animal feed. After evaluation, fermentation of TNM with Saccharomyces cerevisiae GLLB−3, or the mixture of S. cerevisiae GLLB−3 and Lactiplantibacillus plantarum SCTM−1 (EMIX group) improves the nutrient profiles of TNM. Post-fermentation, the contents of crude protein, crude fiber, total phosphorus, and amino acids increased. Especially, the crude protein content in TNM fermented with S. cerevisiae GLLB−3 increased by 34.71%, whereas TNM fermented with EMIX exhibited a 27.77% increase. Additionally, essential amino acids except histidine showed significant increases, ranging from 6.82% to 119.49%. The fermentation not only enhances TNM’s nutritional values but also contributes to a more balanced amino acid composition suitable for animal feed production. Simultaneously, fermentation of TNM with two Aspergillus strains changes amino acid and other nutrient profiles. The analysis of the fermented products revealed significant increases in the contents of crude protein, crude fiber, total phosphorus, and amino acids. Notably, the levels of eight essential amino acids were substantially elevated, indicating a marked improvement in the nutritional quality of the fermented products as compared to the raw materials. This study demonstrates probiotic fermentation can effectively enhance the nutritional profile of TNM, highlighting it as a promising approach for the comprehensive utilization of tiger nut by-products.

Astragali radix: (AR, also known as Huangqi), a traditional Chinese herbal medicine, refers to the dried roots of Astragalus membranaceus var. mongholicus and Astragalus membranaceus Bunge. AR, containing flavonoids, saponins, and polysaccharides, is known for its wide array of biological activities and pharmacological effects. However, the contents of flavonoids and other bioactive components in AR are relatively low. In this study, 70 different fungal strains, including yeasts and filamentous fungi, were isolated from various traditional fermented foods. The Aspergillus cristatus and Wickerhamomyces anomalus (plus Lactiplantibacillus plantarum) were selected to ferment AR. The total phenols and total flavonoids increased after fermentation by A. cristatus and W. anomalus (plus L. plantarum). The total phenols of AR increased by 60.62% and 8.00% after fermention with A. cristatus and W. anomalus (plus L. plantarum), respectively; the total flavonoids of AR increased by 74.15% and 6.52%, respectively. Further non-targeted metabolomics analysis confirmed that fermenting with A. cristatus effectively enhanced the content of flavonoids and other bioactive compounds in AR. These suggest that A. cristatus is a promising strain for herbal fermentation to boost bioactive compounds, laying a solid foundation for the development and application of herbal medicines through fungal fermentation in the future.

Cycloastragenol is a bioactive, high-value triterpenoid derived from Astragalus membranaceus. Conventional plant-based extraction and chemical synthesis methods are expensive. To our knowledge, this is the first report on the de novo biosynthesis of cycloastragenol in yeast. The mevalonate pathway was reconstituted in yeast peroxisomes, and the engineered yeast produced 656.55 mg/L squalene. Further introduction of heterologous enzymes led the engineered yeast to produce 1.04 mg/L cycloastragenol, which demonstrated the yeast production of value-added medicinal molecules.

Background & Aims Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, not medical treatment has been approved for the treatment of the disease. In our previous study, we found PKLR could be a potential target for treatment of NALFD. Here, the aim is to investigate the effect of PKLR in in vivo model and perform drug repositioning to identify a drug candidate for treatment of NAFLD. Methods Biopsies from liver, muscle, white adipose tissue and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptmics 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 finally tested in both in vitro and in vivo models to evaluated their toxicity and efficacy. Results The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in liver as well as 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 drugs were identified as potential inhibitor of PKLR by the 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 it was demonstrated that these drugs attenuated hepatic steatosis without side effect on other tissues. Conclusion 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 experiment.

Epimedium Folium (EF) is a traditional Chinese herbal medicine, and its primary bioactive ingredients, such as icariin, are flavonoid glycosides. A rare EF flavonoid, baohuoside I, exhibits superior bioactivities and enhanced bioavailability compared to its metabolic precursor icariin. The biotransformation of icariin to baohuoside I can be effectively and specifically achieved by β-glucosidases. In this study, 33 candidate full-length β-glucosidase genes were screened from a previously built carbohydrate active enzyme (CAZyme) gene dataset derived from cow fecal microbiota. Thirteen of them exhibited β-glucosidase activity, with DCF-bgl-26 and DCF-bgl-27 showing relatively high expression levels and β-glucosidase activity. The maximum β-glucosidase activity of DCF-bgl-26 and DCF-bgl-27 was achieved at 45 °C and pH 6.0, with DCF-bgl-26 demonstrating better thermostability and pH tolerance compared to DCF-bgl-27. The activities of DCF-bgl-26 and DCF-bgl-27 were 123.2 U/mg protein and 157.9 U/mg protein, respectively, both of which are higher than those of many bacterial β-glucosidases. Structure analysis suggested that both β-glucosidases possess canonical (β/α)8-TIM barrel fold structure of GH1 family β-glucosidases. Thin-layer chromatography results showed that both enzymes could efficiently convert icariin to baohuoside I in 30 min, indicating they have potential application in the production of high value rare baohuoside I.

The human gut microbiota is a complex ecosystem that plays a crucial role in promoting the interaction between the body and its environment. It has been increasingly recognized that the gut microbiota has diverse physiological functions. Recent studies have shown a close association between the gut microbiota and the development of certain tumors, including leukemia. Leukemia is a malignant clonal disease characterized by the uncontrolled growth of one or more types of blood cells, which is the most common cancer in children. The imbalance of gut microbiota is linked to the pathological mechanisms of leukemia. Probiotics, which are beneficial microorganisms that help maintain the balance of the host microbiome, play a role in regulating gut microbiota. Probiotics have the potential to assist in the treatment of leukemia and improve the clinical prognosis of leukemia patients. This study reviews the relationship between gut microbiota, probiotics, and the progression of leukemia based on current research. In addition, utilizing zebrafish leukemia models in future studies might reveal the specific mechanisms of their interactions, thereby providing new insights into the clinical treatment of leukemia. In conclusion, further investigation is still needed to fully understand the accurate role of microbes in leukemia.

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.