World journal of microbiology & biotechnology最新文献

{"title":"Reusable combinatorial libraries with high diversity for efficient multi-gene expression optimization in Escherichia coli.","authors":"Dongyuan Cheng, Qingyu Zhang, Zhimin Ou, Zhinan Xu","doi":"10.1007/s11274-025-04501-9","DOIUrl":"10.1007/s11274-025-04501-9","url":null,"abstract":"<p><p>Efficient multi-gene expression in Escherichia coli is critical for advancing metabolic engineering and synthetic biology. However, existing strategies for combinatorial optimization remain labor-intensive and low-throughput. In addressing this challenge, a high-throughput platform was developed, encompassing the engineering of standardized genetic elements (promoters and 5' UTRs) with fluorescent reporters (e.g. eGFP, mCherry, TagBFP) to quantify expression variability. Libraries of single-, dual-, and tri-gene (dual-plasmid) constructs were assembled via Golden Gate, validated by IPTG induction, and applied to lycopene biosynthesis by replacing fluorescent genes with crtE, crtI, and crtB using Gibson assembly. The optimized tri-gene library was used to generate E. coli BL21(DE3) strains exhibiting variable levels of lycopene production, thereby demonstrating the platform's capacity to balance multi-gene pathways. Subsequent quantitative analysis by qPCR confirmed the uniformity of promoter-UTR combinations across the plasmid library. This modular platform, featuring reusable libraries and a dual-plasmid system, enables rapid exploration of multi-gene expression landscapes, offering a scalable tool for metabolic engineering and multi-enzyme co-expression.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"291"},"PeriodicalIF":4.2,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761539","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":"Functional and safety profiles of microbial communities in milk of ranched and nomadic goats and their predictive role in mycotoxin reduction.","authors":"Muiz O Akinyemi, Mariska S Kleyn, Mona Abdelmaksoud, Deidré A B Van Wyk, Rasheed A Adeleke, Chibundu N Ezekiel","doi":"10.1007/s11274-025-04507-3","DOIUrl":"10.1007/s11274-025-04507-3","url":null,"abstract":"","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"292"},"PeriodicalIF":4.2,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12316834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Laminaria Japonica hydrolysate as a novel biostimulant for enhancing DHA accumulation in Aurantiochytrium limacinum.","authors":"Jia-Xue Lin, Ying Wang, Shao-Geng Zhao, Bei-Chen Huang, Yue Zhang, Zhi-Qiang Wang, Sheng-Jie Li, Qian Liu, Yan Ma, Jing-Run Ye, Hai-Ying Wang, Zhi-Peng Wang","doi":"10.1007/s11274-025-04511-7","DOIUrl":"10.1007/s11274-025-04511-7","url":null,"abstract":"<p><p>Aurantiochytrium limacinum is recognized as an ideal candidate to produce docosahexaenoic acid (DHA). However, elevating the biomass and lipid yield on a large scale is still a challenge. In this study, a simple and feasible strategy for enhancing DHA accumulation based on Laminaria japonica hydrolysate (LPH) addition has been developed. The addition of 40 mL/L LPH enhanced the accumulation of biomass and lipid of A. limacinum by 31.48% and 49.48%, respectively. Meanwhile, the DHA production was increased by 40.78%. By investigating the effects on DHA and biomass accumulation hormones in LPH, gibberellin 3, abscisic acid, and salicylic acid were characterized as the key factor. With the addition of LPH, the upregulated genes were enriched in pathways including fatty acid biosynthesis, metabolism, and the tricarboxylic acid cycle. In particular, key genes involved in fatty acid synthesis, such as ACC1 and FAS2, were significantly upregulated. In this study, LPH was identified as a novel additive with practical application value due to its readily available and low-cost raw ingredients.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"290"},"PeriodicalIF":4.2,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144745306","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":"Biopigments production from sugarcane bagasse hemicellulosic hydrolysate using cells of Monascus ruber immobilized in polyurethane foam.","authors":"Gabriel Leda de Arruda, Maria Teresa F R Raymundo, Layde Teixeira de Carvalho, Silvio S da Silva, Júlio C Santos","doi":"10.1007/s11274-025-04497-2","DOIUrl":"10.1007/s11274-025-04497-2","url":null,"abstract":"<p><p>The complete use of all fractions of agro-industrial by-products is essential to promote sustainability and consolidated bioprocesses in biorefineries. Among the biomass fractions, hemicellulose is still underutilized and could be used to produce high value bioproducts, as fungal biopigments, emerging biomolecules with potential applications in different industrial sectors. Besides raw material, cultivation strategies such as the use of immobilized cells can be interesting for industrial applications, presenting advantages by favoring downstream steps and reuse of cells in repeated or continuous bioprocesses. In this study, the production of biopigments by Monascus ruber immobilized in polyurethane foam was evaluated as a strategy to valorize a xylose-rich sugarcane bagasse hemicellulosic hydrolysate. An experimental design was carried out and showed the optimum xylose/glucose ratio obtained was similar to the values usually found in sugarcane bagasse hemicellulosic hydrolysates. Then, the kinetic profile of the in situ immobilization of the fungus (simultaneous cell growth and adsorption) in polyurethane indicated an inoculum preparation time of 8 days of growth/immobilization before the process conducted in hydrolysate-based medium. The use of immobilized cells resulted in the production of biopigments with maximum values of 13.1 AU, 11.87 AU, and 11.32 AU of yellow, orange and red biopigments, respectively, in medium based on detoxified hydrolysate. The obtained results can contribute to the valorization of agro-industrial by-products as an alternative source of substrates, as well as to future research to explore the potential of immobilizing filamentous fungi in bioprocesses, such as the reuse of cells and continuous systems for production of biopigments.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"289"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733507","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":"Bioprecipitation of calcium carbonate by Antarctic endolithic bacteria: biotechnological applications.","authors":"Susana Patricia Lotero Arcila, Gabriel Neumann Magalhães, Reinaldo Santos Shimabuku Junior, Edna Possan, Pablo Henrique Nunes, Alysson Wagner Fernandes Duarte, Luiz Henrique Rosa, Michel Rodrigo Zambrano Passarini","doi":"10.1007/s11274-025-04476-7","DOIUrl":"10.1007/s11274-025-04476-7","url":null,"abstract":"<p><p>Calcium carbonate is a chemical compound used in several industries due to its properties and versatility and can be obtained by extraction from sedimentary rocks. Endolithic Antarctic microbes can precipitate several minerals, including calcium carbonate. In this sense, this work evaluated the crystals produced from precipitated calcium carbonate by bacteria isolated from rocks collected in Deception Island and King George Island, maritime Antarctica. Qualitative screenings were performed to select bacteria that precipitate calcium carbonate, using acidic and basic culture media. The presence of carbonate was verified with hydrochloric acid. Scanning electron microscopy (SEM), equipped with an energy dispersive X-ray detector (EDS), was used to confirm the formation of calcium crystals. A total of 48 bacteria were isolated, most of which belonged to the genera Arthrobacter, Pseudomonas, Bacillus, and Stenotrophomonas, identified by MALDI-TOF and biochemical methodology. Of them, 45 were able to form crystals on the microbial biofilm in solid medium and also produced effervescence in the areas where the crystals formed, confirming the presence of carbonate. Thirteen isolates were able to produce calcium, confirmed by SEM. Bacillus and Stenotrophomonas were the best calcium carbonate producers. This is the first report of the evaluation of calcium carbonate bioprecipitation by endolithic bacterial strains recovered from rocks collected on Deception Island and King George Island, Antarctica. Calcium carbonate bioprecipitation can be considered an innovative strategy for microbial bioprospecting in Antarctica targeting future biotechnological applications in several sectors, including civil engineering and cosmetics.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"275"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733508","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":"Combined application of Sphingobacterium sp. PNL1 and myo-inositol enhanced the remediation ability of BDE-209-contaminated soil by promoting plant growth, reducing oxidative stress, improving photosynthetic efficiency and degrading BDE-209 in soil.","authors":"Jing Ji, Runzhong Wang, Baoying Ma, Tiange Li, Chunfeng Guan","doi":"10.1007/s11274-025-04500-w","DOIUrl":"10.1007/s11274-025-04500-w","url":null,"abstract":"<p><p>As a polybrominated diphenyl ether (PBDE) flame retardant, BDE-209 has attracted attention because of its extensive accumulation in soil and toxic effect on plant growth. Plant promoting rhizosphere bacteria (PGPR) assisted phytoremediation is widely recognized for removing contaminants from soils. In this study, Sphingobacterium sp. PNL1, isolated from soil, exhibited both tolerance to BDE-209 and plant-growth-promoting (PGP) traits, including production of 1-aminocyclopropane-1-carboxylic acid deaminase, indole-3-acetic acid, ammonia, and siderophore. Notably, the addition of the biological growth factor myo-inositol (MI) enhanced the PGP traits and adhesion capacity of strain PNL1 under BDE-209 stress. Therefore, this study proposed a strategy of combined use of MI and PGPR to assist phytoremediation and highlighted the effect of this combined application on rice seedling growth and soil BDE-209 remediation under BDE-209 stress. The results revealed that the combined application of PNL1 and MI could significantly mitigate the negative effects of BDE-209 on rice, including increased photosynthetic efficiency and reduced oxidative stress, promoting rice seedling growth. Also, the combined use of PNL1 strain and MI enabled the removal rate of soil BDE-209 to reach 64.06%, which was 38.87% higher than that the group without additional addition. Furthermore, the combined treatment could regulate soil enzyme activities (soil urease, sucrase and alkaline phosphatase) and increase the relative abundance of beneficial rhizosphere bacteria (Firmicutes, Myxococcota, etc.), thereby creating a more favorable microenvironment for plant growth. In conclusion, the combined use of PNL1 and MI effectively alleviated BDE-209 stress in rice seedlings and improved the efficiency of soil remediation, providing an eco-friendly method for treating BDE-209 soil contamination.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"269"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733510","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":"Microbiota-driven epigenetic modifications in gastrointestinal cancer: Implications for pathogenesis and therapeutic strategies.","authors":"Haniye Rahimi-Kolour, Hedyeh Sadat Eshaghi, Elahe Shams, Fatemeh Sanjabi, Stefania Nobili, Hamideh Raeisi, Amir Sadeghi, Ehsan Nazemalhosseini-Mojarad, Nayeralsadat Fatemi","doi":"10.1007/s11274-025-04457-w","DOIUrl":"10.1007/s11274-025-04457-w","url":null,"abstract":"<p><p>The gastrointestinal (GI) tract hosts a complex microbiota that plays a crucial role in maintaining health and contributing to disease, including cancer. This narrative review explores the role of gut microbiota in driving epigenetic modifications associated with GI cancers. We highlight key bacterial phyla such as Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria, and explain how their representative species, including Fusobacterium nucleatum, Bacteroides fragilis, Lactobacillus sp., and Escherichia coli, influence host gene expression through mechanisms such as DNA methylation, histone modification, and regulation of non-coding RNAs. Microbial metabolites, including short-chain fatty acids (SCFAs) like butyrate and secondary bile acids, affect the activity of epigenetic regulators such as DNA methyltransferases and histone deacetylases and have been implicated in the development of colorectal, gastric, liver, pancreatic, and esophageal cancers. By integrating recent scientific findings, this review underscores the potential of targeting microbiota-driven epigenetic pathways to improve prevention and treatment strategies for GI cancers.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"288"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733529","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":"Recent advances in the study of the properties and applications of lactic acid bacteria.","authors":"Viktor Stabnikov, Iryna Kovshar, Olena Stabnikova","doi":"10.1007/s11274-025-04499-0","DOIUrl":"10.1007/s11274-025-04499-0","url":null,"abstract":"<p><p>This review highlights recent developments in the study of the properties and applications of lactic acid bacteria (LAB). The involvement of LAB in human life has a long history, especially in food production, where their ability to lactic acid fermentation has been crucial in extending the shelf life of perishable raw materials. However, in recent decades, the role of lactic acid bacteria has steadily expanded covering new areas of biotechnology, particularly, in the development of biosynthetic products that find application in a wide range of areas. Certain strains of lactic acid bacteria are recognized as probiotics, and their incorporation into food products promotes the development of functional foods that offer enhanced health benefits to consumers. Traditionally, LAB have been used in food preservation. Beyond their technological functions, they contribute to extending the shelf life of fermented products by inhibiting spoilage and pathogenic microorganisms through the production of antimicrobial compounds like bacteriocins and reuterin. Additionally, LAB are recognized as producers of valuable secondary metabolites, such as exopolysaccharides and polyhydroxyalkanoates, as well as primary metabolites, including enzymes and gamma-aminobutyric acid. They also show potential in the biosynthesis of metal nanoparticles and the development of innovative packaging materials. This review aimed to highlight the wide range of potential applications for lactic acid bacteria, with a focus on novel and emerging trends in their biotechnological utilization.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"287"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733546","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":"Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.","authors":"Syed Atif Hasan Naqvi, Ummad Ud Din Umar, Ateeq Ur Rehman","doi":"10.1007/s11274-025-04461-0","DOIUrl":"10.1007/s11274-025-04461-0","url":null,"abstract":"<p><p>Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"285"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733506","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":"AI-enhanced bioprocess technologies: machine learning implementations from upstream to downstream operations.","authors":"Deepankar Sharma, Kavita Singh","doi":"10.1007/s11274-025-04494-5","DOIUrl":"10.1007/s11274-025-04494-5","url":null,"abstract":"","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"278"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733505","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}