Journal of microbiological methods最新文献

{"title":"Optimization of antimicrobial compound production by mangrove sediment derived Micromonospora sp. BSS-D-04 and Streptomyces sp. BSS-D-05 using response surface methodology","authors":"Dipransu Pradhan ,&nbsp;Mihir Tanay Das","doi":"10.1016/j.mimet.2025.107387","DOIUrl":"10.1016/j.mimet.2025.107387","url":null,"abstract":"<div><div>In response to the growing global health crisis caused by antibiotic resistance, actinobacteria have emerged as a promising group of microorganisms capable of producing diverse and potent bioactive compounds. India's mangrove ecosystems, known for their rich microbial biodiversity, provide a unique habitat for discovering such novel organisms. In a previous study, two actinobacterial strains, <em>Micromonospora</em> sp. BSS-D-04 and <em>Streptomyces</em> sp. BSS-D-05 were isolated from the Bichitrapur mangrove sediments along the east coast of India and were found to exhibit broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria. The present study focused on optimizing the culture conditions for enhanced production of antimicrobial compounds using Response Surface Methodology (RSM). Among the tested carbon sources, glucose and sucrose significantly improved metabolite yields. Further the Central Composite Design (CCD) analysis identified pH 8.0, temperature 37 °C, and agitation speed 140 rpm as optimal growth parameters. Under these conditions, the antibacterial activity of the strains increased up to 122 %. These findings highlight the critical role of both nutritional and physical parameters in maximizing bioactive compound production. The optimized fermentation conditions established in this study holds promise for cost-effective and scalable antimicrobial development from indigenous mangrove-derived actinobacteria.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107387"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145896616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developing machine learning classifiers for carbapenem resistance prediction in Klebsiella pneumoniae using Google's teachable machine","authors":"João V.O. Cruz ,&nbsp;Felipe G. Sacoda ,&nbsp;Vitor H. Moreau ,&nbsp;Luis G.C. Pacheco","doi":"10.1016/j.mimet.2025.107385","DOIUrl":"10.1016/j.mimet.2025.107385","url":null,"abstract":"<div><div>We developed neural network models trained with images from <em>Klebsiella pneumoniae</em> genomes, encoded <em>via</em> Chaos Game Representation, to predict carbapenem resistance. Both real (<em>n</em> = 168) and synthetic AI-generated (<em>n</em> = 200) images were used. The best-performing model, among the 72 developed, achieved up to 87.5 % accuracy on generalization datasets.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107385"},"PeriodicalIF":1.9,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145881353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterization of cephalosporin-resistant Klebsiella pneumoniae by SERS: Insights into antimicrobial resistance patterns","authors":"Benish Saif ,&nbsp;Zainab Iftikhar ,&nbsp;Haq Nawaz ,&nbsp;Muhammad Irfan Majeed ,&nbsp;Mashkoor Mohsin ,&nbsp;Rabia Saleem ,&nbsp;Najah Alwadie ,&nbsp;Sundas Sakhawat ,&nbsp;Kinza Khan ,&nbsp;Aleena Ali ,&nbsp;Rimsha Khan ,&nbsp;Riha Zulfiqar ,&nbsp;Amna Sattar ,&nbsp;Muhammad Imran","doi":"10.1016/j.mimet.2025.107388","DOIUrl":"10.1016/j.mimet.2025.107388","url":null,"abstract":"<div><div>The infectious bacteria, <em>K. pneumoniae</em> has broken another defence line by showing resistance to cephalosporin antibiotics, due to presence of extended-spectrum lactamases ESBL resistance genes. Surface-enhanced Raman spectroscopy (SERS) is used to characterize third generation cephalosporin resistant and susceptible <em>K. pneumoniae</em> strains for the purpose of identification of their characteristic SERS spectral features. For this, the silver nanoparticles (Ag-NPs) are used as a SERS substrate. The SERS spectral fingerprints of <em>K. pneumoniae</em> strains, linked directly or indirectly to resistance development against third generation cephalosporins, were differentiated by analyzing their SERS spectral data with the help of support vector machines (SVM), principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA). This can result in the effective recognition, differentiation and distinction of third generation cephalosporin resistant and susceptible strains of <em>K. pneumonia</em> bacteria which is considered crucial for selecting suitable antibiotic treatment for infections<em>.</em></div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107388"},"PeriodicalIF":1.9,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recovery of Escherichia coli and Salmonella enterica from long frozen rectal swabs using enrichment methods in a low-resource setting","authors":"Hafeez A. Adekola,&nbsp;Jacob I. Yisau,&nbsp;Ajoke O. Adagbada,&nbsp;Oluwatoyin B. Awoderu,&nbsp;Samson A. Luka,&nbsp;Adenike Aiyedogbon,&nbsp;Olusola Ajibaye,&nbsp;Toyosi Y. Raheem,&nbsp;Muinah A. Fowora,&nbsp;Emelda E. Chukwu,&nbsp;Tajudeen A. Bamidele,&nbsp;Abideen O. Salako,&nbsp;Oliver C. Ezechi","doi":"10.1016/j.mimet.2025.107382","DOIUrl":"10.1016/j.mimet.2025.107382","url":null,"abstract":"<div><div>This study evaluated bacterial recovery from rectal swabs stored at −20 °C for one month in Cary Blair medium. Enrichment methods markedly improved detection of <em>Escherichia coli</em> and <em>Salmonella enterica</em> compared to direct plating. Tryptone Soy Broth best recovered <em>E. coli</em>, while Peptone Water enhanced <em>S. enterica</em> recovery, strengthening surveillance reliability in low-resource settings.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107382"},"PeriodicalIF":1.9,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145856580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungal false positive in BioFire® FilmArray® analysis for bloodstream infection","authors":"Osamu Imataki ,&nbsp;Ryoko Masumoto ,&nbsp;Masahiro Hamano ,&nbsp;Masaki Ishimatsu ,&nbsp;Shin-ichiro Suemori ,&nbsp;Takayuki Tsujioka ,&nbsp;Masayo Tamura ,&nbsp;Akira Kitanaka","doi":"10.1016/j.mimet.2025.107380","DOIUrl":"10.1016/j.mimet.2025.107380","url":null,"abstract":"<div><h3>Background</h3><div>The BioFire FilmArray® system is an automated multiplex PCR tool for detecting pathogens in clinical samples. False positives occasionally occur due to cross-reactivity, contamination, or assay specificity issues. This study investigated false-positive fungal results in FilmArray® blood culture identification panel 2 (BCID2) detection system.</div></div><div><h3>Method</h3><div>We collected the continuous cases in which bloodstream infection (BSI) was suspected in our institute for 12 months, from April in 2024 to March in 2025. We routinely used Bactec FX culture system (Beckton Dickinson) with BD BACTEC culture bottles. Alongside, we identified fungus using standard culture method and matrix-assisted laser desorption ionization-time of flight mass spectrometry (biomerieux, VITEK MS PRIME).</div></div><div><h3>Results</h3><div>We evaluated continuous 454 blood culture positive sample. Average blood culture sampling were totally 5357 samples per year (44.3/1000 patients days) of blood cultures during our study period. We collected 28 cases of fungemia among totally recruited 454 samples (6.2 %, 28/454). Accordance of blood culture and FilmArray® were 50.0 % (14 samples). We observed eight false positive samples (1.8 %. 8/454) as fungemia out of total 454 samples, in where one false organism was <em>Candida albicans</em> and seven were <em>Candida tropicalis</em>. In the cases of four false <em>Candida tropicalis</em> samples, the FilmArray® reported the two fungal combination, <em>Candida parapsilosis</em> and <em>Candida tropicalis</em>.</div></div><div><h3>Conclusion</h3><div>Our investigation revealed a substantial incident of false positive of <em>Candida</em>. The study highlights recurrent false positives of <em>Candida tropicalis</em>, often detected alongside <em>Candida parapsilosis</em>. The main cause of the detection of false positive organism in BCID2 including <em>Candida</em> spp. has been reported as contamination or technical errors. We speculated that our observation could be derived from the non-viable DNA fragments (<em>Candida albicans</em>) contained in the blood culture media and cross-reaction of <em>Candida parapsilosis</em> with <em>Candida tropicalis</em>. We should remember these FilmArray® assay limitations linked to non-viable DNA contamination and high reactivity of sensitive PCR analysis. False positive results for <em>Candida</em> spp. in BCID2 assays require careful interpretation with microbiological expertise. Clinical decisions should be guided by the patient's overall context. Further research is necessary to assess the accuracy of fungal BSI. (341/500 words).</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107380"},"PeriodicalIF":1.9,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A strategy to enhance detection of Corynebacterium in pus from human non-puerperal mastitis via pre-culture and extended incubation","authors":"Nan Zheng,&nbsp;Xidong Gu,&nbsp;Jiangting Yu,&nbsp;Jiaying Chen,&nbsp;Tianjian Huang,&nbsp;Yiming Zhou,&nbsp;Bei Yang,&nbsp;Aimei Shi,&nbsp;Zhejiong Wang","doi":"10.1016/j.mimet.2025.107381","DOIUrl":"10.1016/j.mimet.2025.107381","url":null,"abstract":"<div><div>This study aimed to optimize the detection method for <em>Corynebacterium</em> in pus from patients with non-puerperal mastitis (NPM) to enhance diagnostic accuracy and provide guidance for clinical treatment. A total of 216 pus samples from NPM patients were retrospectively included and randomly divided into a control group and an experimental group, with 108 cases in each group. The control group was subjected to the traditional direct plate culture method, while the experimental group was treated with an improved method involving pre-cultivation in blood culture bottles followed by extended incubation for up to 5 days. The results showed that the improved method significantly increased the overall detection rate of <em>Corynebacterium</em> from 36.1 % (39/108) to 60.2 % (65/108), with the difference between the groups being statistically significant (χ² = 12.5, <em>P</em> &lt; 0.001, 95 % CI: 11.0–37.1, Cramér's V = 0.24). These findings indicate that optimizing culture conditions and extending incubation time can effectively enhance the detection sensitivity of <em>Corynebacterium</em> in NPM pus. The proposed method demonstrates good clinical applicability and can provide laboratory support for the etiological diagnosis and subsequent individualized treatment of NPM.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107381"},"PeriodicalIF":1.9,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Restoration of crude oil-contaminated soil using microbes with degradative and plant-growth-promoting abilities","authors":"Mukesh Aakula ,&nbsp;Mayur Mahindra Kedare ,&nbsp;Sanjukta Patra ,&nbsp;Tarun Gangar ,&nbsp;Siddhartha Singha ,&nbsp;Subham Meher ,&nbsp;Lingaraj Sahoo ,&nbsp;Srinivas Rao ,&nbsp;P. Radhakrishnanand","doi":"10.1016/j.mimet.2025.107377","DOIUrl":"10.1016/j.mimet.2025.107377","url":null,"abstract":"<div><div>Microorganisms with traits such as biosurfactant production, hydrocarbonoclastic ability, and PGP activity can be used to restore the soil health of agricultural fields affected by oil pollution. In this study, the ability of a microbial consortium of four microbial strains was assessed to degrade petroleum hydrocarbons and restore the health of oil-contaminated soil. The candidates for bioremediation were selected based on various screening assays (Haemolytic assay, protease activity, siderophore production, ammonia production, and DCPIP assay). The selected candidates for the consortium were: OC4 (<em>Bacillus paralicheniformis KJ-16*</em>), OC9 (<em>Ochrobactrum intermedium</em> NBRC 15820*), <em>Pseudomonas aeruginosa</em> NCIM 5514, and <em>Pseudomonas aeruginosa</em> MTCC 7815. Further, a soil microcosm study was done over 90 days with a focus on plant parameters such as chlorophyll content and concentration of H₂O₂ and MDA in leaf tissue. Finally, the residual hydrocarbons in the soil were assessed by GC–MS and FTIR analysis. The results indicate a reduction in the total chlorophyll content and the accumulation of H₂O₂ and MDA. These results are indicative of oxidative stress in plants. The FT-IR and GC–MS data positively dictate the success of bioremediation via microbial consortium. The consortium of four microbial strains developed in this study have the potential to bioremediate oil-contaminated soil.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107377"},"PeriodicalIF":1.9,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145827972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative review of vector insertion techniques in Saccharomyces cerevisiae","authors":"Ritika Gopalakrishnan ,&nbsp;Kamala Kannan ,&nbsp;Ragul Gunasekaran ,&nbsp;Priya Ramachandran ,&nbsp;Dhanraj Ganapathy ,&nbsp;Sivaperumal Pitchiah","doi":"10.1016/j.mimet.2025.107378","DOIUrl":"10.1016/j.mimet.2025.107378","url":null,"abstract":"<div><div><em>Saccharomyces cerevisiae</em>, a model organism in genetics and molecular biology has been extensively engineered using various vector insertion techniques. This review compares and contrasts three prominent techniques: <em>In vivo</em> homologous recombination (HR), Cre-<em>lox</em> recombination and CRISPR/Cas9. <em>In vivo</em> HR leverages the organism's innate DNA repair machinery for easy vector integration and targeted genome modifications. Cre-<em>lox</em> recombination offers high specificity and efficiency at <em>loxP</em> sites, making it ideal for targeted gene excision or integration. CRISPR/Cas9 has revolutionized genome engineering with its precision and ability to target multiple loci simultaneously. Each technique has its strengths and limitations, including site dependency, off-target effects, and strain-specific variability. This review provides a comprehensive overview of these vector insertion techniques, highlighting their applications, advantages, and limitations in <em>S. cerevisiae</em> genome engineering and synthetic biology.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107378"},"PeriodicalIF":1.9,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145819757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental and computational approaches to adaptive viral evolution: Linking molecular variation to phenotypic outcomes","authors":"Yanfeng Huang ,&nbsp;Zhiying Ou ,&nbsp;Xi Xue ,&nbsp;Huiling Zhou ,&nbsp;Kangpeng Xiao","doi":"10.1016/j.mimet.2025.107379","DOIUrl":"10.1016/j.mimet.2025.107379","url":null,"abstract":"<div><div>Viruses pose a persistent global health threat due to their high mutation rates and rapid evolutionary capacity, which drive zoonotic spillover, vaccine escape, and drug resistance. Even single amino acid substitutions might impact viral invasion, receptor binding, immune evasion, or transmissibility, as illustrated by recent influenza, SARS-CoV-2 and other emerging viruses' outbreaks. Understanding these processes requires linking molecular variation to phenotypic consequences. This review summarizes five experimental and computational technologies—pseudovirus systems, minigenome assays, display systems, deep mutational scanning (DMS), and in silico modeling—that together form an iterative framework for studying viral adaptation. A representative integration of DMS with reverse genetics has validated computationally predicted escape mutations and revealed trade-offs between binding and replication that conventional assays could not capture. We discuss each approach's strengths and limitations, highlighting how their coordinated use supports mechanism-based evaluation and data-driven design of vaccines and antiviral strategies.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107379"},"PeriodicalIF":1.9,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145810361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of a representative sampling protocol for studying grape berry microbiota at the plot scale","authors":"Gabriela Pinto Miguel ,&nbsp;Olivier Rué ,&nbsp;Martine Pradal ,&nbsp;Evelyne Aguera ,&nbsp;Cécile Neuvéglise","doi":"10.1016/j.mimet.2025.107376","DOIUrl":"10.1016/j.mimet.2025.107376","url":null,"abstract":"<div><div>In viticulture, a comprehensive understanding of the grape microbiota is crucial, as it influences various aspects of the winemaking process, from vine health and grape development to fermentation dynamics and the final sensory profile of the wine. Monitoring these communities helps optimize vineyard practices and ensure product authenticity. Metagenetics is a fast culture-independent approach that allows identification of the microorganisms present in grape berries' microbiota at the genus or species level. In this context, it is crucial to assess the quality of sampling methods in terms of their representativeness of the diversity of microbial communities on grape berries at the plot level. In this study, the microbiota of the variety Artaban was examined. This variety is resistant to powdery mildew and tolerant to downy mildew. Two sampling methods for studying microbiota were investigated by forming two groups: one that pooled the microbiota of 10 vines, and another that studied the microbiota of each vine separately.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107376"},"PeriodicalIF":1.9,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145799491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}