{"title":"Novel degenerate PCR primers targeting the β-galactosidase gene for broad-spectrum identification of lactose-degrading bacteria.","authors":"Canting Shen, Qinglong Shu","doi":"10.1007/s11274-025-04601-6","DOIUrl":"https://doi.org/10.1007/s11274-025-04601-6","url":null,"abstract":"<p><p>β-galactosidase (EC 3.2.1.23), a pivotal enzyme in lactose degradation, is widely distributed across numerous bacterial species. This study aimed to develop degenerate primers with high specificity and universality, using the β-galactosidase gene as a molecular marker to identify diverse lactose-degrading bacteria in environmental samples. High-quality β-galactosidase gene sequences belonging to glycoside hydrolase family 2 were retrieved from the NCBI and CAZY databases for sequence alignment and phylogenetic analysis. Through extensive screening and optimization of full-length sequences, a pair of primers was successfully designed for detecting environmental β-galactosidase genes. The newly developed primers were validated using four types of DNA samples, revealing the diversity of lactose-degrading bacterial communities: Human feces (2 phyla, 5 genera), Rat feces (3 phyla, 3 genera), Mouse feces (2 phyla, 6 genera), and soil (6 phyla, 13 genera). By optimizing sequences of representative strains based on the full-length target gene, this study successfully developed novel degenerate primers, providing a reference strategy for addressing the challenge of primer design for highly variable gene families. Additionally, a new molecular probe targeting the β-galactosidase gene was developed to identify diverse lactose-degrading bacteria in environmental samples. To the best of our knowledge, this is the first report of universal primers targeting the β-galactosidase gene for detecting lactose-degrading microbial communities in environmental samples.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"359"},"PeriodicalIF":4.2,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Larissa M M Mattos, Davi A Andrade, Alan N S Alves, Victória T Ferreira, Simone S C Oliveira, Bruna B Segat, André L S Santos, Adolfo Horn, Christiane Fernandes, Marcos D Pereira
{"title":"Iron, manganese, and copper complexes protect saccharomyces cerevisiae from methyl methanesulfonate-induced genotoxicity and oxidative stress.","authors":"Larissa M M Mattos, Davi A Andrade, Alan N S Alves, Victória T Ferreira, Simone S C Oliveira, Bruna B Segat, André L S Santos, Adolfo Horn, Christiane Fernandes, Marcos D Pereira","doi":"10.1007/s11274-025-04595-1","DOIUrl":"https://doi.org/10.1007/s11274-025-04595-1","url":null,"abstract":"<p><p>Methyl methanesulfonate (MMS) is a well-known classical alkylating agent that induces DNA damage, mutagenesis, and cell dysfunction. Alternatives to mitigate the damage caused by MMS are essential for understanding DNA repair mechanisms and developing approaches to reduce mutagenic and cytotoxic effects of alkylating agents. This study explores the potential of synthetic antioxidants containing iron (1), manganese (2), or copper (3) to protect Saccharomyces cerevisiae from MMS-induced damage. The wild type strain, BY4741, and its isogenic DNA-repair mutants rad9Δ and rad54Δ strains were used to investigate whether these complexes effectively mitigate yeast susceptibility, mitochondrial dysfunction, intracellular oxidation, and mutagenesis caused by MMS. The results demonstrate that all complexes significantly enhanced the survival rates of all fungal strains, indicating their protective role against MMS-induced DNA damage. Additionally, MMS exposure increased mitochondrial dysfunction, intracellular oxidation, and canavanine-based mutagenesis, which was subsequently reduced by the treatment with the complexes, indicating their ability to mitigate oxidative stress and genotoxicity caused by MMS. Among the tested compounds, complex 3 conferred the greatest protective effect against MMS-induced cellular damage, followed by complexes 2 and 1, establishing a consistent order of efficacy: 3 > 2 > 1. These findings demonstrate that the coordination compounds employed in this study effectively protected S. cerevisiae against MMS-induced toxicity, highlighting their potential role in enhancing cellular defense against genotoxic agents.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"358"},"PeriodicalIF":4.2,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Detection and Actinobacteria-based biological suppression of leaf necrosis in tea (Camellia sinensis) caused by Lasiodiplodia theobromae in India.","authors":"Shashanka Sonowal, Pranami Bharadwaj, Debajit Thakur","doi":"10.1007/s11274-025-04577-3","DOIUrl":"https://doi.org/10.1007/s11274-025-04577-3","url":null,"abstract":"<p><p>Fungal diseases are a common threat to the cultivation of tea [Camellia sinensis (L.)] in India, with Lasiodiplodia theobromae found recently to be a major cause of leaf necrosis. The objective of this work was to isolate and identify fungal pathogens from diseased tea plants and to assess the biocontrol effectiveness of Streptomyces sp. strains OR02 and PTS59 against L. theobromae strain KF16. Four fungal isolates were isolated, among which KF16 was identified as L. theobromae. Antagonistic analysis found that OR02 showed the maximum inhibition zone (24 ± 0.8 mm) and mycelial suppression (91.11%) against KF16, outperforming commercial fungicides, Mancozeb and Hexaconazole. In vitro and In vivo studies revealed that OR02 and PTS59 substantially decreased the formation of necrotic lesions and enhanced plant growth without causing any harmful effects. Improved height, leaf count, and branches were observed in OR02 treated plants, suggesting that it serves as both a biocontrol and growth-promoting agent. The study also revealed that KF16 could systematically infect newly growing leaves, emphasizing its virulence and the pressing need for sustainable control measures. These results highlight Streptomyces sp. OR02 potential as an eco-friendly substitute to chemical fungicides in the treatment of tea diseases, particularly against L. theobromae, and encourages its further development into a bioformulation for field use.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"355"},"PeriodicalIF":4.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yurong Wang, Yan Lei, Jianhui Zhang, Qiangchuan Hou, Zhuang Guo
{"title":"Differential characterization of medium-temperature Daqu from different geographical regions: bacterial profile, color, taste, and flavor.","authors":"Yurong Wang, Yan Lei, Jianhui Zhang, Qiangchuan Hou, Zhuang Guo","doi":"10.1007/s11274-025-04560-y","DOIUrl":"https://doi.org/10.1007/s11274-025-04560-y","url":null,"abstract":"<p><p>In this study, the sensory qualities of MTD from different geographical regions were comprehensively analyzed using electronic sensing technology. Moreover, the culturable Bacillus species, LAB, and other bacterial communities in these MTD samples were identified using culture methods and single-molecule real-time sequencing. The most abundant culturable species of Bacillus and LAB in MTD were Bacillus licheniformis and Pediococcus pentosaceus, respectively. The bacterial diversity was higher in MTD from the Nanyang region than in that from the Luzhou region, and its sensory quality were superior. Nevertheless, Nanyang MTD showed poorer microecological stability. Functional characterization revealed that the bacterial communities present in MTD were actively enriched in processes related to ribosome structure and biogenesis, as well as cell wall/membrane/envelope biogenesis. Notably, Thermoactinomyces daqus and Leuconostoc citreum emerged as the bacterial species with the highest relative abundance in MTD from the Luzhou and Nanyang regions, respectively, and were identified as biomarkers for the MTD from these two regions. Leuconostoc citreum, Leuconostoc mesenteroides, Pediococcus pentosaceus, Thermoactinomyces daqus, and Weissella paramesenteroides was significantly correlated with the synthesis of aromatic compounds (P < 0.05). These findings expand our knowledge of the microbiological composition and quality of MTD from various regions, offering a valuable reference for product optimization.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"354"},"PeriodicalIF":4.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Strategies for enhancing the adaptive response to oxidative stress in microbial cell factories.","authors":"Ziyun Zou, Mei-Li Sun, Kaifeng Wang, Xiao-Jun Ji","doi":"10.1007/s11274-025-04544-y","DOIUrl":"https://doi.org/10.1007/s11274-025-04544-y","url":null,"abstract":"<p><p>Reactive oxygen species (ROS), inevitable byproducts of aerobic respiration, exhibit both signaling and cytotoxic effects depending on concentration within cells. At controlled levels, ROS serve as crucial signaling molecules mediating intracellular signal transduction pathways. However, excessive accumulation triggers oxidative stress, leading to oxidative damage that disrupts protein structure and function, ultimately inducing cell death. Enhancing cellular adaptive responses to oxidative stress and mitigating intracellular ROS accumulation are therefore critical strategies for maintaining cellular homeostasis. This approach significantly improves product yield and underpins its widespread application across diverse sectors, including functional foods, pharmaceuticals, and cosmeceuticals. This review first delineates the origins and multifaceted roles of ROS. Subsequently, it details strategies employed to bolster cellular oxidative stress resilience, focusing on process optimization and metabolic engineering approaches. Finally, synthesizing current research advances, existing challenges, and emerging trends, the review outlines future research directions aimed at enhancing the oxidative stress tolerance of microbial cell factories.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"356"},"PeriodicalIF":4.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jéssica Pinheiro Silva, Andrei Nicoli Gebieluca Dabul, Vera Lúcia Mores Rall, Caroline Rosa Silva, Luís Antônio Esmerino, Marcos Pileggi, Felipe Francisco Tuon, Mario de Oliveira Neto, Darlan Nakayama, Alejandra Estela Miranda, Pedro Ricardo Vieira Hamann, Igor Polikarpov
{"title":"Klebsiella aerogenes PgaB orthologue can efficiently hydrolyze Staphylococcus aureus biofilms.","authors":"Jéssica Pinheiro Silva, Andrei Nicoli Gebieluca Dabul, Vera Lúcia Mores Rall, Caroline Rosa Silva, Luís Antônio Esmerino, Marcos Pileggi, Felipe Francisco Tuon, Mario de Oliveira Neto, Darlan Nakayama, Alejandra Estela Miranda, Pedro Ricardo Vieira Hamann, Igor Polikarpov","doi":"10.1007/s11274-025-04550-0","DOIUrl":"https://doi.org/10.1007/s11274-025-04550-0","url":null,"abstract":"<p><p>Staphylococcus aureus, a gram-positive bacterium, is the prevalent cause of numerous infections. Its ability to form biofilms significantly enhances its pathogenicity, resulting in increased antibiotic resistance and evasion of the host immune response. Poly-β-(1,6)-N-acetylglucosamine (PNAG) plays a crucial role in the formation and maintenance of S. aureus biofilms. In this study, we heterologously expressed KaPgaB from Klebsiella aerogenes and evaluated its efficacy in both degrading and inhibiting S. aureus biofilm formation. Additionally, we investigated the combined effects of KaPgaB with DNase I and papain. Our results demonstrated that KaPgaB alone removed up to 81% of biofilm biomass within 4 h when used at a concentration of 0.5 mg/mL. Moreover, when the enzyme was applied sequentially with DNase I, approximately 97% of adhered biofilms were removed. We also observed significant inhibition of biofilm formation across S. aureus strains. The findings presented in this study might be useful for the development of enzymatic tools capable of degrading S. aureus PNAG-based biofilms.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"353"},"PeriodicalIF":4.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohamed Gamil Mehanna, Turky Omar Asar, Habib Changal Mudasir, Sherif Edris, Hadiah Bassam Al Mahdi, Ahmed F Bakry, Mustafa Zeyadi, Mirza Rafi Baig, Salma Naqvi, Fahad A Al-Abbasi, Omar A Al Bar, Vikas Kumar, Firoz Anwar
{"title":"Correction: Biochemical insight into gut microbial imbalance in Covid-19 and post vaccination heart attacks.","authors":"Mohamed Gamil Mehanna, Turky Omar Asar, Habib Changal Mudasir, Sherif Edris, Hadiah Bassam Al Mahdi, Ahmed F Bakry, Mustafa Zeyadi, Mirza Rafi Baig, Salma Naqvi, Fahad A Al-Abbasi, Omar A Al Bar, Vikas Kumar, Firoz Anwar","doi":"10.1007/s11274-025-04566-6","DOIUrl":"https://doi.org/10.1007/s11274-025-04566-6","url":null,"abstract":"","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"357"},"PeriodicalIF":4.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Harshvardhan Joshi, Jasmine Isar, Vidhya Rangaswamy, Anu Raghunathan
{"title":"Advances in metabolic engineering and fermentation for 3-hydroxypropionic acid biosynthesis: a comprehensive review.","authors":"Harshvardhan Joshi, Jasmine Isar, Vidhya Rangaswamy, Anu Raghunathan","doi":"10.1007/s11274-025-04554-w","DOIUrl":"https://doi.org/10.1007/s11274-025-04554-w","url":null,"abstract":"<p><p>The grand challenge in biobased Manufacturing Lies in achieving the sustainable, economically competitive conversion of renewable biomass into high-value Chemicals capable of replacing fossil-derived products. Among these, 3-hydroxypropionic acid (3-HP) has emerged as a top-tier target-an exceptionally versatile platform molecule. It finds applications in the synthesis of acrylic acid, 1,3-propanediol, and other derivatives, positioning it as a potential cornerstone for bio-based plastics. This review consolidates the latest breakthroughs in microbial 3-HP production, encompassing advanced strain engineering, pathway rewiring, cofactor optimization, metabolic modeling, and flux balance analysis. We critically examine strategies to overcome inherent metabolic and physiological constraints, including byproduct suppression, redox balancing, and tolerance engineering. Emerging approaches-such as dynamic regulation of metabolic flux, control of cell morphology and density, and integration of co-production pathways-are highlighted for their capacity to boost yields and process robustness. Additionally, we address the fermentation process innovations targeting enhanced productivity, substrate efficiency, minimal nutrient input, and industrially relevant titres. Collectively, these insights Chart a clear path toward the scalable, sustainable biomanufacturer of 3-HP.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"352"},"PeriodicalIF":4.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mariana Barbieri, Luana Lessa R Santos, Ana C Bahia, Susana Frases
{"title":"ITS metabarcoding of filamentous fungi in traditional biodegradation of Carapa Guianensis seeds from the Brazilian Amazon.","authors":"Mariana Barbieri, Luana Lessa R Santos, Ana C Bahia, Susana Frases","doi":"10.1007/s11274-025-04581-7","DOIUrl":"https://doi.org/10.1007/s11274-025-04581-7","url":null,"abstract":"<p><p>The relationship between microbial communities and traditional processing techniques represents a crucial intersection of cultural heritage and biological diversity. To provide the first detailed molecular characterization of this process for andiroba (Carapa guianensis) seeds, this study employed ITS1 and ITS2 metabarcoding with two primary objectives: (1) to characterize and compare the fungal communities across three distinct management systems (agroforestry, consortium, and native forest) in the Brazilian Amazon, and (2) to identify core fungal taxa and their ecological interactions. Our analysis characterized a diverse mycobiome dominated by the phylum Ascomycota, with the generaArthrinium, Aspergillus, Penicillium, andTalaromyces being most prevalent. In our dataset, ITS1 recovered more ASVs (215) than ITS2 (117), and we observed the unexpected finding of lower fungal diversity in the agroforestry system compared to the consortium system. These findings bridge traditional ecological knowledge with modern biotechnology, validating an ancestral practice while uncovering a rich fungal consortium with significant potential for future industrial applications.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"348"},"PeriodicalIF":4.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Antifungal potential of hydrothermal liquefaction wastewater in plant protection.","authors":"Emre Demirer Durak","doi":"10.1007/s11274-025-04573-7","DOIUrl":"https://doi.org/10.1007/s11274-025-04573-7","url":null,"abstract":"<p><p>This study investigates the antifungal potential of hydrothermal liquefaction (HTL) wastewater against Verticillium dahliae and its effects on the growth of pepper plants (Capsicum annuum L.). The HTL process generates wastewater containing various antimicrobial compounds, which can offer a sustainable alternative for plant protection. In this research, the biological control agent Trichoderma virens and HTL wastewater were applied both individually and in combination to assess their impact on plant growth and pathogen suppression. The results demonstrated that specific HTL wastewater treatments significantly enhanced root and shoot growth, biomass, and chlorophyll content in pepper plants. Plant growth observed in pathogen-free conditions may be related to the stimulation of plant physiology by biologically active components contained in wastewater, indicating a biostimulatory effect. Notably, the 4th wastewater mixture (wm) exhibited the highest efficacy, promoting plant development and mitigating the negative effects of V. dahliae. The combination of T. virens and wastewater also showed synergistic effects, reducing disease severity by up to 64% and improving plant biomass and structural parameters. Statistical analysis revealed significant differences among treatments, highlighting the potential of HTL wastewater as a natural and sustainable strategy for managing soil-borne pathogens. These findings suggest that integrating HTL wastewater with biocontrol agents could offer a promising approach to sustainable agriculture.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 10","pages":"349"},"PeriodicalIF":4.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}