Microbial Cell Factories最新文献

{"title":"Combinatorial optimization engineering for the high-level production of shikimic acid in Escherichia coli.","authors":"Changyang Yang, Yang Li, Mingxiong Liu, Hongxin Fu, Jufang Wang","doi":"10.1186/s12934-026-03016-8","DOIUrl":"https://doi.org/10.1186/s12934-026-03016-8","url":null,"abstract":"<p><p>Shikimic acid is a crucial precursor for the production of indole derivatives and chiral drugs, and the biomanufacturing offers reduced cost and simplified process compared to traditional plant extraction. Current research on industrial-scale production of shikimic acid achieves notable progress, yet the limitations associated with high production cost, complex operation process, and excessive byproduct formation still persist. To tackle these difficulties, this study aimed at establishing a high-efficient shikimic acid-producer through systematic modification and fermentation optimization in Escherichia coli. First, the route for the synthesis of shikimic acid was divided into three modules (i.e., sugar uptake, bioproduct synthesis, and metabolite catabolism), of which the disruption of glucose uptake system, reinforcement of bioproduct synthesis, and block of its catabolism rewired metabolic fluxes and provided the possibility for efficient synthesis. Next, series of systematic engineering involving in deleting pyruvate bypass, reinforcing the pentose phosphate (PP) pathway, and adjusting promoter strength promoted precursor supply and avoided metabolic overflow. The best strain EC022 generated 5.27 g/L of shikimic acid, highlighting the significance of precursor availability. Then, fermentation conditions including substrate concentration, inoculation size, cultivation temperature, induction time, and C/N ratio were comprehensively optimized, which boosted the bioproduction to 8.70 g/L in the optimized conditions. Finally, a final titer of 61.87 g/L shikimic acid was achieved in a 7 L bioreactor. This study developed an efficient shikimic acid-producer with industrial potential through metabolic engineering and bioprocess optimization.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seven inducible promoters for Zymomonas mobilis.","authors":"Gerrich Behrendt","doi":"10.1186/s12934-026-03013-x","DOIUrl":"10.1186/s12934-026-03013-x","url":null,"abstract":"<p><p>Zymomonas mobilis is an ethanologenic Alphaproteobacterium with many interesting characteristics for fundamental research and applied microbial engineering. Although genetic engineering has been established for Z. mobilis since the 1980s, a rich set of inducible transcriptional regulators is still unavailable. In this work, seven different chemically inducible promoters have been systematically tested for their functionality in Z. mobilis. In particular, for the first time, NahR-P_salTTC, VanR^AM-P_vanCC, CinR^AM-P_cin and LuxR-P_luxB have been characterized in Z. mobilis, alongside the commonly used regulator-promoter pairs TetR-P_tet and LacI-P_{lacT7A1_O3O4}, and the less commonly used XylS-P_m. All promoters investigated in this work are compatible with the Golden Gate modular cloning framework Zymo-Parts. Characterization was carried out with a shuttle vector backbone based on pZMO7, which has so far been rarely used for applications in Z. mobilis but is stable without selection and generates high and uniform levels of expression. From the experimental results presented, it can be concluded that VanR^AM-P_vanCC and CinR^AM-P_cin are particularly promising for broad use in the Z. mobilis community.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reprogramming probiotic for uric acid modular degradation and hyperuricemia treatment by synthetic biology regulation.","authors":"Jingyu Zhou, Xinyu Cheng, Liping Chen, Yongzhong Wang, Qiang Ding","doi":"10.1186/s12934-026-03022-w","DOIUrl":"https://doi.org/10.1186/s12934-026-03022-w","url":null,"abstract":"<p><p>Hyperuricemia has emerged as the fourth most prevalent metabolic disorder, necessitating the development of safer and more effective therapeutic strategies. In this study, we constructed a recombinant probiotic strain expressing the PucL and PucM enzymes, which demonstrated a uric acid degradation rate of 65% in vitro. To enhance this activity, we performed modular optimization by employing three ribosome binding sites (RBSs) of different strengths-RBS 29, RBS 31, and RBS T7-to tune the expression levels of pucL and pucM, resulting in highly efficient uric acid degradation. Further improvement was achieved by overexpressing the uric acid transporter gene ygfU and the hydrogen peroxide-degrading catalase gene katG, leading to significant uric acid degradation. Furthermore, the engineered Escherichia coli Nissle 1917 strain was evaluated in a mouse model of hyperuricemia; treatment with the optimized probiotic reduced serum uric acid levels to 39.11 mg/L, representing a 15.98% decrease compared with the control group. Further analysis revealed that this engineered bacterium ameliorates hyperuricemia by modulating the Firmicutes-to-Bacteroidetes ratio, increasing microbial diversity, and promoting the growth of beneficial genera. Collectively, this study establishes an engineered probiotic cell factory for uric acid degradation and demonstrates a proof-of-concept for the microbial remediation of hyperuricemia.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-cultivation dynamics of the filamentous microorganisms Aspergillus niger and Streptomyces coelicolor in shake flasks.","authors":"Tolue Kheirkhah, Fangxing Zhang, Fabia Jaeger, Alexander Gantenbein, Peter Neubauer, Heiko Briesen, Stefan Junne","doi":"10.1186/s12934-026-03015-9","DOIUrl":"10.1186/s12934-026-03015-9","url":null,"abstract":"<p><strong>Background: </strong>The co-cultivation of filamentous fungi and actinobacteria is challenging due to their complex growth interactions. This study investigates how key parameters, such as inoculation strategy, glutamic acid concentration, hydrodynamic stress, and dissolved oxygen, influence the growth dynamics between Aspergillus niger and Streptomyces coelicolor in shake flask co-cultures. Recognizing the crucial role of macromorphology in filamentous microorganisms, an automated image analysis pipeline was developed to quantitatively assess the heterogeneity and reproducibility of each population.</p><p><strong>Results: </strong>Simultaneous growth was achieved when both microorganisms were inoculated in pelleted form, whereas spore inoculation led to complete A. niger dominance. At 1:2 and higher inoculation ratios (fungus to bacteria), S. coelicolor could compete effectively. While A. niger growth-maintained dominance at 136 and 250 rpm (1:1), S. coelicolor growth outcompeted the fungus at 60 rpm, a shift attributed to a reduced oxygen transfer rate. Notably, only the highest shear forces (250 rpm) produced homogeneous, reproducible fungal pellet populations. Overall, bottom-baffled flasks enhanced reproducibility compared to non-baffled flasks.</p><p><strong>Conclusion: </strong>It is possible to regulate the growth of S. coelicolor and A. niger in a co-culture by the aforementioned parameters. Among these, the inoculation ratio is most important to achieve different dynamics. A quantitative analysis of morphology development while optimising inoculation strategies provides a foundation for designing co-culture experiments that achieve balanced and reproducible growth.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel bacterial consortium isolated from long-term plastic-contaminated soil exhibits efficient biodegradation of polyvinyl chloride microplastics.","authors":"Nawal Magdy, Mahmoud S Maher, Ahmed Mohamed Soliman, Tarek A A Moussa, Hoda M Shehata","doi":"10.1186/s12934-026-03011-z","DOIUrl":"https://doi.org/10.1186/s12934-026-03011-z","url":null,"abstract":"<p><strong>Background: </strong>Polyvinyl chloride (PVC) is one of the most widely used synthetic polymers globally, and its continuous accumulation in natural ecosystems has emerged as a critical environmental and public health concern. Recently, microbial degradation has been recognized as an efficient and eco-friendly strategy for mitigating plastic pollution. Despite increasing interest, knowledge of bacteria capable of efficiently degrading PVC microplastics (PVC-MPs) remains limited. This gap highlights the urgency of exploring novel bacterial candidates for effective PVC biodegradation.</p><p><strong>Methodology: </strong>In this study, soil samples collected from plastic-contaminated sites were utilized to isolate PVC-degrading bacteria using enrichment culture techniques. Bacterial isolates showing potential interaction with PVC were selected and molecularly identified. In addition, their efficacy in degrading PVC-MPs was further confirmed through a combination of analytical and spectroscopic techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and gas chromatography-mass spectrometry (GC-MS).</p><p><strong>Results: </strong>The two isolates identified as Stutzerimonas sp. NH2 and Glutamicibacter nicotinae NH27 displayed markedly different PVC biodegradation efficiencies. Strain NH2 achieved a PVC-MPs weight loss of 23.41 ± 0.93%, whereas strain NH27 exhibited a lower degradation efficiency of 5.87 ± 2.16%. Notably, the consortium composed of both strains in equal volumes resulted in a greater PVC-MPs weight loss of 26.84 ± 0.94%, representing a significant increase in PVC-MPs degradation compared with each strain alone (p < 0.05). SEM analysis revealed pronounced morphological alterations on PVC surfaces following bacterial exposure, including cracks, fissures, and grooves. FTIR spectra demonstrated a substantial reduction in the intensities of some functional groups, which could be attributed to PVC degradation. TGA analysis showed a measurable decline in thermal stability, further suggesting chemical structural modifications due to bacterial activity. Additionally, GC-MS analysis detected potential degradation products, providing clear chemical evidence of bacterial-driven PVC degradation.</p><p><strong>Conclusion: </strong>This study reports, for the first time, the potential involvement of Stutzerimonas sp. NH2 and Glutamicibacter nicotinae NH27 in the transformation of PVC microplastics. The findings also provide initial insights into the combined activity of these two strains on PVC-MPs, supported by multiple physicochemical analyses. These results contribute to the growing understanding of microbial interactions with PVC microplastics and highlight the potential of these bacteria for future bioremediation studies.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low inducer concentrations at 10 °C promotes soluble recombinant expression of Aedes aegypti mosquito midgut proteases in E. coli.","authors":"Daniel Fong, Neomi Millan, My Anh Le, Elizabeth Moreno-Galvez, Kevin Derisier, Abigail G Ramirez, Kaelyn Pluta, Kimberly Houghton, Alberto A Rascón","doi":"10.1186/s12934-026-03012-y","DOIUrl":"https://doi.org/10.1186/s12934-026-03012-y","url":null,"abstract":"<p><strong>Background: </strong>Soluble recombinant expression of Aedes aegypti mosquito midgut proteases in Escherichia coli prove to be difficult. These enzymes depend on disulfide bond formation for structural stability. Initial attempts in BL21(DE3) were unsuccessful due to a reducing cytoplasm. The use of T7 SHuffle cells (with a more oxidizing cytoplasm) led to soluble expression. However, other factors had to be altered (use of richer media and lower (< 25 °C) growth temperature). Not all mosquito proteases were equally soluble. Therefore, given the importance of IPTG in initiating transcription and translation, we set out to determine if low IPTG concentrations (< 0.1 mM) at 10 °C would increase soluble production of midgut proteases. Additionally, we investigated the effect of the small molecule osmolyte betaine on the soluble expression of midgut proteases.</p><p><strong>Results: </strong>For this study, the focus was on Aedes aegypti Late Trypsin (AaLT), Early Trypsin (AaET), Serine Protease I (AaSPI), Serine protease V (AaSPV), and Juvenile Hormone Associated 15 (JHA15). The colder bacterial growth, along with low IPTG, slows the rate of transcription/translation of T7 RNA polymerase. Lower expression of T7 RNA polymerase, along with slower transcription activity at 10 °C, prevents rapid simultaneous translation of midgut proteases thereby promoting soluble expression. In addition, we found that different growth periods also varied among the proteases. Soluble expression for AaLT and AaET was maximal at 52 h post-induction, 72 h for JHA15, and 168 h for AaSPI and AaSPV. Surprisingly, for AaET, temperature was the only important factor. The addition of betaine to the growths had a more pronounced effect at higher (> 0.05 mM) IPTG.</p><p><strong>Conclusions: </strong>Low IPTG at 10 °C slows the rate of transcription/translation of recombinantly expressed mosquito proteases in bacteria. By preventing rapid accumulation in the cell, prevents aggregation, and ultimately inclusion body formation. Betaine works better at higher IPTG concentrations, but more studies are needed to better understand how this osmolyte stabilizes proteins during recombinant bacterial expression. Nonetheless, this study provides a blueprint for researchers who have never attempted IPTG concentrations < 0.05 mM to recombinantly express proteins in bacteria.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pleurotus ostreatus L-asparaginase's use in food safety and biotechnology: from processing assistance to bioactive agent.","authors":"Yehia A-G Mahmoud, Mohamed Bedaiwy, Maha M Salem, Samar Shamla, Omyma A Awadallah","doi":"10.1186/s12934-026-03007-9","DOIUrl":"https://doi.org/10.1186/s12934-026-03007-9","url":null,"abstract":"<p><strong>Background and aim: </strong>L-ASNase has attracted attention in many biomedical and food safety applications. Therefore, this study was designed to identify a novel and promising candidate for the sustainable biosynthesis of extracellular L-ASNase from P. ostreatus AUMC 16015 grown on various agricultural substrates under solid-state fermentation (SSF). Also, the enzyme's wide-ranging bioactivities were examined, involving its antioxidant, anti-inflammatory, and antitumor properties, while evaluating its potential applications in food processing.</p><p><strong>Results: </strong>Optimal P. ostreatus AUMC 16015 L-ASNase production was 56.47 U/mL, which was attained under SSF conditions where the enzyme yield increased by 2.46-fold compared to pre-optimization conditions. Enzyme high purity was validated by a single distinct band at approximately 48 kDa on both SDS-PAGE and native PAGE analyses. The enzyme demonstrated high substrate specificity (K_m = 7.7 mM; V_max = 167.78 U/mL). Functionally, it exhibited strong antioxidant activity (2,2-diphenyl-1-picrylhydrazyl) (DPPH) IC₅₀ = 48.28 µg/mL) and a robust anti-hemolytic effect (95.9% at 1000 µg/mL). L-ASNase exhibited its most potent inhibitory effect against Caco-2 cells at an IC₅₀ of 5.49 ± 0.03 µg/mL, followed by MCF-7, which showed a slightly higher IC₅₀ of 5.86 ± 0.08 µg/mL. Furthermore, L-ASNase significantly mitigated potato chips acrylamide formation, achieving a 9.6-fold decrease after 120 min of treatment. Additionally, Gas chromatography-mass spectrometry (GC-MS) showed that the potato's chemical profile was significantly changed by L-ASNase treatment, with the introduction of numerous bioactive substances and the elimination of some potentially dangerous components.</p><p><strong>Conclusion: </strong>The biochemical activity of the purified L-ASNase suggested potential biomedical and food applications. This study is a trial for cost-effective enzyme production and supports a circular bioeconomy by converting waste into useful bioproducts. Future work should focus on scaling up production and testing its effects in living organisms to unlock this enzyme's full commercial and medical potential.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13141449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription factor MtCLR-2 regulates cellulase production via direct modulation of Mtegl2 and Mtbgl1 expression in Myceliophthora thermophila.","authors":"Yapeng Lai, Juan Wang, Ning Xie, Gang Liu, Donnabella C Lacap-Bugler","doi":"10.1186/s12934-026-02976-1","DOIUrl":"https://doi.org/10.1186/s12934-026-02976-1","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synechocystis sp. PCC 6803 shows high cell cycle dynamics reflected by an extraordinary genome copy number variation.","authors":"Jacky Till, Juan López-Gálvez, Florian Schattenberg, Matthias Schmidt, Susann Müller, Jörg Toepel, Bruno Bühler","doi":"10.1186/s12934-026-02982-3","DOIUrl":"10.1186/s12934-026-02982-3","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced secretion of thermostable phytases from Myceliophthora thermophila by Komagataella phaffii.","authors":"Ronja Gratzer, Magdalena Merkaš, Andrej Nikolikj, Andreas Winkler, Martina Geier, Anton Glieder, Anita Emmerstorfer-Augustin","doi":"10.1186/s12934-026-02988-x","DOIUrl":"https://doi.org/10.1186/s12934-026-02988-x","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}