Carlos A Adarme-Duran, Elianna Castillo, Pedro F B Brandão
{"title":"Cadmium removal and indole acetic acid production by ureolytic bacteria isolated from rhizosphere soils.","authors":"Carlos A Adarme-Duran, Elianna Castillo, Pedro F B Brandão","doi":"10.1007/s11274-025-04482-9","DOIUrl":"10.1007/s11274-025-04482-9","url":null,"abstract":"<p><p>This work reports the isolation of 54 ureolytic bacteria with microbiologically induced carbonate precipitation (MICP) activity from Theobroma cacao L. rhizosphere soils with Cd concentration ranging from 0.49 to 21.29 mg kg<sup>- 1</sup>. Analysis of the 16 S rRNA gene showed the isolates belong to the genera Serratia, Pseudomonas, Comamonas, Klebsiella, Bacillus, Citrobacter, Flavobacterium, Delftia, and Stenotrophomonas. They showed ureolytic activity between 0.31 and 1.01 µmol NH<sub>4</sub><sup>+</sup> mL<sup>- 1</sup> h<sup>- 1</sup> and produced the phytohormone indole acetic acid (IAA). Interestingly, Cd was observed to increase ureolytic activity and did not affect the IAA production of various isolates. Cadmium removal in solution ranged from 4.4 to 87.0% after 48 h. Strains Serratia sp. 89a, Klebsiella sp. 76 h, and Stenotrophomonas sp. 67w exhibited the best performance (> 80%). Cadmium removal through MICP by the genera Delftia, Flavobacterium, and Klebsiella is reported for the first time. Results suggest the isolated bacteria have the potential for Cd bioremediation and could be used to alleviate metal-induced stress through IAA production.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"302"},"PeriodicalIF":4.2,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144800419","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}
Garima Singh, Shriti Shreya, Saurabh Yadav, Yusuf Akhter
{"title":"S292L mutation in Rv1258c efflux pump drives pyrazinamide efflux and a novel inhibitor designed for co-therapy to improve MDR-TB treatment outcomes.","authors":"Garima Singh, Shriti Shreya, Saurabh Yadav, Yusuf Akhter","doi":"10.1007/s11274-025-04510-8","DOIUrl":"10.1007/s11274-025-04510-8","url":null,"abstract":"","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"300"},"PeriodicalIF":4.2,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144795672","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":"Discovery and characterization of bioactive compounds from Limnophila aromatica: nevadensin and related flavonoids as potent antimicrobial agents.","authors":"Thanaporn Maswanna, Cherdsak Maneeruttanarungroj","doi":"10.1007/s11274-025-04523-3","DOIUrl":"10.1007/s11274-025-04523-3","url":null,"abstract":"<p><p>Limnophila aromatica, a traditional medicinal plant, has been previously reported to possess notable antimicrobial properties. However, the specific bioactive constituents responsible for this activity remain largely unidentified. This study aimed to isolate, identify, and evaluate the antibacterial potential of compounds from a 100% ethanolic extract of L. aromatica. The crude ethanolic extract exhibited the highest antibacterial activity against Methicillin-resistant Staphylococcus aureus (MRSA) and was subsequently subjected to Diaion HP-20 column chromatography, followed by preparative HPLC. Seven major peaks were identified using UV-Vis spectra, LC-QTOF-MS, and NMR analyses. The antibacterial efficacy of these isolated compounds was assessed using disc diffusion and broth microdilution assays against Bacillus subtilis, S. aureus, MRSA, Escherichia coli, and Pseudomonas aeruginosa. The isolated compounds were identified as norethindrone acetate, isothymusin, nevadensin, gardenin B, 5,3'-dihydroxy-7,8,2'-trimethoxyisoflavone, jasmolin II, and oleanolic acid. Nevadensin, the predominant compound (79.55%), demonstrated potent bactericidal activity against B. subtilis, S. aureus, and MRSA. Jasmolin II and gardenin B also exhibited promising antibacterial effects. Although the disc diffusion assay was limited by compound diffusion, the broth microdilution method confirmed significant MIC values, ranging from 0.59 to 2.86 mg/ml while the MBC values ranged from 0.59 to 12.72 mg/ml. This study highlights nevadensin and other flavonoids from L. aromatica as potential candidates for the development of alternative antibacterial therapies, particularly against drug-resistant Gram-positive bacteria.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"301"},"PeriodicalIF":4.2,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144795671","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}
Ning Zhang, Yajun Li, Zhenzhen Jiang, Hanghai Zhou, Ming Zhou, Ruichang Zhang, Xing Ren, Chunfang Zhang, Xuefeng Wei
{"title":"Construction and application of an efficient diesel degrading bacterial consortium for oily wastewater bioremediation.","authors":"Ning Zhang, Yajun Li, Zhenzhen Jiang, Hanghai Zhou, Ming Zhou, Ruichang Zhang, Xing Ren, Chunfang Zhang, Xuefeng Wei","doi":"10.1007/s11274-025-04520-6","DOIUrl":"10.1007/s11274-025-04520-6","url":null,"abstract":"<p><p>The treatment of oil-contaminated wastewater represents a significant environmental challenge. In this study, five highly efficient diesel-degrading bacterial strains were successfully isolated from oily wastewater, which was designated as Pseudomonas sp. ZC1, Vibrio sp. ZL2, Acinetobacter sp. ZY3, Citrobacter sp. GO5, and Enterobacter cloacae GM6. To construct an efficient bacterial consortium based on these five strains, the optimized strain combination of 26 different consortia composed of two, three, four, and five bacterial strains was conducted. The results suggested that a consortium comprising three strains (ZL2, ZY3, and GM6) showed the highest diesel degradation efficiency of 89.66% on day 3, while other strain combinations exhibited lower degradation rates and tended to require more time to achieve comparable efficiency. The orthogonal experiments further determined the optimal inoculation ratios of 1.0%, 0.5%, and 1.5% for strains ZL2, ZY3, and GM6 improved diesel degradation efficiency to 93.65% by day 3. The application of this consortium in the oily wastewater bioremediation confirmed its degrading capacity for n-alkanes (C8-C40) and polycyclic aromatic hydrocarbons (PAHs). This study highlights the excellent performance of the engineered bacterial consortium in the bioremediation of petroleum-contaminated wastewater, demonstrating its potential for scaling up to pilot and full-scale applications.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"299"},"PeriodicalIF":4.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790195","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":"Bifidobacteria in antibiotic-associated dysbiosis: restoring balance in the gut microbiome.","authors":"Rajashree Jena, Namita Ashish Singh, Nafees Ahmed, Prasanta Kumar Choudhury","doi":"10.1007/s11274-025-04517-1","DOIUrl":"10.1007/s11274-025-04517-1","url":null,"abstract":"<p><p>Antibiotic-associated dysbiosis disrupts the gut's microbial balance, leading to reduced diversity, overgrowth of antibiotic-resistant strains, and compromised gut homeostasis. This can result in inflammation, increased intestinal permeability, impaired immunity, and heightened susceptibility to infections. In this context, probiotics have been highlighted as a promising remedy in alleviating this antibiotic-induced gut microbiome aberrations with subsequent decrease of the detrimental effects. Bifidobacteria, a prominent bacterial group with promising probiotic attributes, have shown effectiveness in restoring the gut microbiome by strong adherence to the colon's mucosal lining and enhancing the immune response through increased anti-inflammatory cytokines. They also play a crucial role as key producers of acetic acid, which supports butyric acid-producing bacteria essential for colonocyte health during dysbiosis. The synergistic use of bifidobacteria with other probiotic species or prebiotic substrates has further enhanced their survival, colonization capacity, and overall impact on gut microbial restoration. Advanced metagenomic analyses have begun to reveal strain-specific functions, paving the way for personalized probiotic therapies tailored to an individual's unique microbiome profile. Despite encouraging progress, critical research gaps persist, particularly regarding strain-specific efficacy, formulation stability, long-term outcomes, underlying mechanisms, systemic interactions, and the distinct and specific role of bifidobacteria. Addressing these gaps through targeted clinical investigations is essential to fully harness their therapeutic potential and develop optimized strategies for restoring the microbial balance in the gut microbiome.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"297"},"PeriodicalIF":4.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790194","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}
Carlos García-Ausencio, Fernando Guzmán-Chávez, Romina Rodríguez-Sanoja, Sergio Sánchez
{"title":"Promiscuity of lanthipeptide enzymes: new challenges and applications.","authors":"Carlos García-Ausencio, Fernando Guzmán-Chávez, Romina Rodríguez-Sanoja, Sergio Sánchez","doi":"10.1007/s11274-025-04505-5","DOIUrl":"10.1007/s11274-025-04505-5","url":null,"abstract":"<p><p>Lanthipeptides are a group of peptides synthesized by ribosomes that undergo post-translational modifications and have significant potential for medical and biotechnological applications. Various bacterial strains produce these peptides, and their synthesis involves the structural modification of precursor compounds through specialized enzymes present within a biosynthetic gene cluster (BGC) of the producing organisms. These enzymes are particularly notable for their capacity to modify non-cognate substrates, allowing for the installation of lanthionine rings on precursor peptides and enabling further modifications, such as methylation, reduction, and oxidation, to enhance the biological properties of specific peptides. The inherent flexibility of lanthipeptide enzymes-an important characteristic of this class of proteins-can be utilized to create peptides with improved bioactive and physicochemical properties. This review synthesizes recent advances in the application of promiscuous enzymes for the synthesis of bioactive peptides, emphasizing the diverse classes identified to date.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"298"},"PeriodicalIF":4.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12328550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790196","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":"Gold nanocluster-based biosensing for rapid detection of carbapenem-resistant organisms in bloodstream infections.","authors":"Rahul Harikumar Lathakumari, Leela Kakithakara Vajravelu, Poornima Baskar Vimala, Vishnu Priya Panneerselvam, Dakshina M Nair, Jayaprakash Thulukanam, Ashwin Kumar Narasimhan","doi":"10.1007/s11274-025-04490-9","DOIUrl":"10.1007/s11274-025-04490-9","url":null,"abstract":"<p><p>Carbapenem resistance in Gram-negative bacteria poses a critical global health challenge, particularly in the context of bloodstream infections (BSIs) where treatment options are severely limited and diagnostic delays can be fatal. Existing methods for detecting carbapenem resistant organisms (CROs) often lack the speed, sensitivity, and specificity required for timely clinical intervention, and currently, no validated approach exists for direct detection from blood samples. In this study, we introduce a novel diagnostic strategy utilizing bovine serum albumin-stabilized gold nanoclusters (BSA-AuNCs), which exhibit a strong fluorescence emission and average size of 2.9 nm. This method enabled rapid detection of carbapenem resistance among 400 Gram-negative clinical isolates, with 97 confirmed resistant by both phenotypic and genotypic analyses. Real-time PCR revealed NDM and VIM as the most common resistance genes, followed by OXA-48, IMP, and KPC. The BSA-AuNC assay detected as few as 10 CFU/mL in cultured isolates within 1.5 h, achieving 100% positive and negative predictive values. Remarkably, when applied directly to centrifuged blood samples, the assay maintained a high sensitivity of 95.8% with a detection limit of 1000 CFU/mL in under 2 h, outperforming the Carba NP test, which showed only 85.56% sensitivity. These findings highlight the potential of BSA-AuNCs as a rapid, sensitive, and culture-independent tool for early identification of carbapenem-resistant organisms in BSIs, offering critical support for timely and effective clinical decision-making.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"294"},"PeriodicalIF":4.2,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769133","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}
Amit Srivastava, Eetika Chot, Vipin Gupta, Nirjara Singhvi, Pratyoosh Shukla
{"title":"Stress genomics of the toxigenic cyanobacteria: environmental and biotechnological perspectives.","authors":"Amit Srivastava, Eetika Chot, Vipin Gupta, Nirjara Singhvi, Pratyoosh Shukla","doi":"10.1007/s11274-025-04509-1","DOIUrl":"10.1007/s11274-025-04509-1","url":null,"abstract":"<p><p>The genomic investigation of toxigenic cyanobacteria reveals unique features of potential genes, proteins, and genomic regions associated with varied functions critical for their survival and stress tolerance. Cyanobacteria are prevalent photoautotrophic microorganisms forming harmful blooms in aquatic environments, with significant public health and ecological implications. Despite the availability of complete genome sequences, the stress genomics of these harmful cyanobacteria remains understudied. This review highlights the genomic \"arsenal\" of these resilient species, emphasizing their stress adaptation mechanisms and potential vulnerabilities. Understanding this molecular basis is essential for developing targeted strategies to mitigate their impact. The insights gained from the genomic analysis could be leveraged to express unexploited stress-related genes for enhanced stress tolerance in industrial applications. Additionally, the review underscores the importance of redirecting research focus towards the functional genomics of bloom-forming strains to uncover novel pathways and strategies for their selective eradication and to improve the productivity of beneficial cyanobacterial strains under fluctuating environmental conditions. Finally, this review is an effort towards creating an important genomic resource for such toxic cyanobacteria.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"295"},"PeriodicalIF":4.2,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769135","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":"Postbiotics: an insightful review of the latest category in functional biotics.","authors":"Ayodeji Amobonye, Brynita Pillay, Felicity Hlope, Stella Tofac Asong, Santhosh Pillai","doi":"10.1007/s11274-025-04483-8","DOIUrl":"10.1007/s11274-025-04483-8","url":null,"abstract":"<p><p>Postbiotics have recently emerged as one of the latest functional food products due to the ever-evolving landscape for microbiome-targeted health interventions. Postbiotics, along with other functional biotics, viz., probiotics, prebiotics and synbiotics, confer their health benefits mainly via the modulation of the gut microbiota. Postbiotics are considered more promising than probiotics as they elicit similar effects, despite being inactivated, thus relegating concerns of strain activity and stability that have been raised about probiotics. This review attempts to provide critical insights into postbiotics by firstly revising its definition to create a streamlined framework for further discourse on the interplay between postbiotics, nutrition, microbiota, and health. Similarly, this review establishes the nexus between postbiotics and probiotics while highlighting that postbiotics can also be derived from other microbes apart from lactobacilli such as yeasts and fungi. Furthermore, an overview of the extraction and production of postbiotics are presented as well as the biochemistry of short-chain fatty acids, enzymes, peptides, polysaccharides, peptidoglycans and teichoic acids, which have all been identified as postbiotic components. Finally, their bioactivities (antioxidant, anti-inflammatory, antidiabetic, immunomodulatory, anti-hypertensive, antimicrobial) and the patent landscape of postbiotics are evaluated to promote its innovative applications in the food, veterinary, pharmaceutical and cosmetic industries. Having identified major gaps and areas of improvement, it is believed that this critical review will serve as a guide in the increasing effort to advance the industrial potential of postbiotics.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"293"},"PeriodicalIF":4.2,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12317891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769134","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}
Edna Mary Varghese, Jositta George, Anagha Hareendran, Athira Anilkumar, Adharsh A Y Narayanan, Jesmy James, Vyshakh Thykoottathil, Aswathi Prasad, Lakshmipriya Perincherry, Bony Cyriac, M S Jisha
{"title":"Dynamics of rice microbiome: insights into functional diversity, environmental influences, response to stress, and applications.","authors":"Edna Mary Varghese, Jositta George, Anagha Hareendran, Athira Anilkumar, Adharsh A Y Narayanan, Jesmy James, Vyshakh Thykoottathil, Aswathi Prasad, Lakshmipriya Perincherry, Bony Cyriac, M S Jisha","doi":"10.1007/s11274-025-04515-3","DOIUrl":"10.1007/s11274-025-04515-3","url":null,"abstract":"<p><p>Rice is the primary diet for the vast majority of the world's population. Since rice is a mainstay of the diet for most Asians, research must be prioritized to boost rice productivity. Scientific advances have unveiled various techniques for sustainable rice production. One promising strategy is understanding plant-microbe interactions, which significantly affect plant health, growth, and productivity. In addition to its agricultural significance, the rice plant harbors a diverse microbiome within its rhizosphere, phyllosphere, and endosphere, which plays a crucial role in its growth, health, and resilience to stress. This review examines the intricate interactions within the rice microbiome, highlighting its functional diversity and critical roles in nutrient cycling, pathogen control, and stress alleviation. Soil properties, environmental circumstances, and agronomic methods are crucial determinants influencing microbial community composition and functionality. Additionally, the rice microbiome demonstrates dynamic alterations under stress conditions, adapting to biotic and abiotic challenges. The mechanisms involved in the rice microbial community assembly and shifts under various stress situations are also dealt. Lastly, the progress in microbiome research, the prospects for microbiome-based therapies in rice cultivation, and the difficulties in applying these insights into field applications are highlighted. Therefore, a deeper understanding of the microbial shifts during various stress conditions and extensive studies on the functional aspects of rice microbiome, attained through this review, present transformative prospects for improving agricultural resilience, productivity, and sustainability amid global environmental and food security issues.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 8","pages":"296"},"PeriodicalIF":4.2,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769132","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}