Journal of microbiological methods最新文献

{"title":"Classifying fungi biodiversity using hybrid transformer models","authors":"Madhurie Kumar Seth,&nbsp;K. Srinivas,&nbsp;A. Charan Kumari","doi":"10.1016/j.mimet.2025.107155","DOIUrl":"10.1016/j.mimet.2025.107155","url":null,"abstract":"<div><div>Fungi are essential members of ecosystems, playing key roles in nutrient cycling, agriculture, and medicine. Their classification into proper species helps us to understand their biodiversity, allowing us to leverage their ecological and practical benefits. A new hybrid deep learning-based technique has been proposed, merging the Vision Transformer and Swin Transformer models with transfer learning frameworks like MobileNetV2, DenseNet121, and EfficientNetB0 for Fungi multiclass classification. This study utilized a publicly available dataset containing 9115 images of five fungal species from UC Irvine Machine Learning Repository. To address significant class imbalance, several data augmentation techniques were employed. The results showed that the Swin Transformer combined with DenseNet121 achieved the highest classification accuracy of 96.96 % for training, 95.97 % for validation, and 95.57 % for testing, while other models like ViT-DenseNet121 and Swin-MobileNetV2 also delivered competitive results. Using confusion matrices and benchmark classification metrics, and paired statistical testing, the analysis highlights the models' ability to generalize effectively and minimize misclassifications. To further ensure the robustness of the findings, a five-fold cross-validation was performed across all hybrid models. Additionally, explainable AI techniques, specifically Grad-CAM visualizations, were employed to interpret the model's focus areas, confirming attention to biologically significant structures. This research demonstrates a balance between modeling local features and capturing global context. Indeed, these hybrid models prove to be scalable and efficient for complex biological datasets. This interdisciplinary study bridges ecology and advanced technology by applying deep learning to enhance fungal classification. This study aims to improve the management and understanding of fungal biodiversity for the promotion of conservational and sustainable practices for the betterment of our ecosystem. The findings have significant applications, including sustainable agriculture through early detection of fungal plant pathogens, improved medical diagnostics for fungal infections, and biodiversity conservation through precise species monitoring.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107155"},"PeriodicalIF":1.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216116","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":"Bibliometric review and perspectives on the biological activity of polyoxometalates against resistant bacterial strains","authors":"Júlio C. Silva ,&nbsp;Heryka R.A. Costa ,&nbsp;Katiely F. Sousa ,&nbsp;Olivia C.M. Moura ,&nbsp;Amanda M.T. Moreira ,&nbsp;Talysson F. Moura ,&nbsp;Matheus S. Brito ,&nbsp;Thayanne L.S. Januário ,&nbsp;Cícera D.M.O. Tintino ,&nbsp;Francisco N. Pereira Júnior ,&nbsp;Thiago M.B.F. Oliveira","doi":"10.1016/j.mimet.2025.107157","DOIUrl":"10.1016/j.mimet.2025.107157","url":null,"abstract":"<div><div>Research into alternative compounds for the treatment of bacterial infections has intensified in recent years due to the emergence of resistant bacterial strains and the obsolescence of traditional antibiotics. Polyoxometalates (POMs) are metal‑oxygen clusters of high-valent early transition metals that show promising biological activity against multidrug-resistant bacteria, with molybdenum-, tungsten-, and vanadium-containing POMs standing out. While the synthesis and physicochemical characterization of POMs has been studied and gradually understood in recent decades, the scientific community lacks more detailed information about their activity and biological action mechanism, demanding more scientific efforts for this purpose. This bibliometric review seeks to reduce part of this asymmetry by addressing the latest evidence on the antibacterial activity of POMs against different strains. To this end, scientific articles were searched in the SCOPUS and Web of Science databases between 1996 and 2023, using the descriptors “bacteria”, “polyoxometalates”, and “antibiotic activity”, resulting in over 1200 direct and indirect correlations. By focusing the research on case studies, around 60 scientific reports were selected and used in this review. Although the antibacterial activity of POMs is not recent, there has been an increase in speculation about this characteristic over the last decade, especially identified in <em>Escherichia coli</em> and <em>Staphylococcus aureus</em> strains. The different strategies studied to improve dose-response results, as well as the challenges and perspectives in this issue are also within the scope of this review, supporting further research in this area.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107157"},"PeriodicalIF":1.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216115","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":"Dispersin-based modification of bacterial community composition in domestic washing machines","authors":"Susanne Jacksch ,&nbsp;Mirko Weide ,&nbsp;Markus Egert","doi":"10.1016/j.mimet.2025.107154","DOIUrl":"10.1016/j.mimet.2025.107154","url":null,"abstract":"<div><div>EPS-attached soil targeting dispersin represent a new, sustainable approach to improve laundry and washing machine hygiene at low temperatures. We present initial data that dispersin, formulated into a liquid laundry detergent, can influence the bacterial community composition in sump samples of domestic washing machines, thereby supporting washing machine hygiene.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107154"},"PeriodicalIF":1.7,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144194567","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":"Corrigendum to “Investigation of cagA, dupA and babA genes among clinical Helicobacter pylori isolates collected from patients suffering from H. pylori gastric disease using real-time PCR” [Journal of Microbiological Methods volume 235 (2025) 107143]","authors":"Zahra Naderi ,&nbsp;Reza Mirnejad ,&nbsp;Mansour Bayat","doi":"10.1016/j.mimet.2025.107150","DOIUrl":"10.1016/j.mimet.2025.107150","url":null,"abstract":"","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107150"},"PeriodicalIF":1.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144159681","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":"Evaluation of Rapid antimicrobial susceptibility testing (RAST) by disk diffusion on early subculture growth from positive blood culture bottles","authors":"Nidhi Tejan ,&nbsp;Radhika Chaudhary ,&nbsp;Chinmoy Sahu ,&nbsp;Sangram Singh Patel ,&nbsp;Atul Garg ,&nbsp;Gerlin Varghese ,&nbsp;Akshay Kumar Arya","doi":"10.1016/j.mimet.2025.107153","DOIUrl":"10.1016/j.mimet.2025.107153","url":null,"abstract":"<div><div>Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for management of patients with sepsis. Standard turnaround time (TAT) to isolate and perform AST is around 48–96 h. This study was planned to evaluate the performance of rapid antimicrobial susceptibility testing (RAST) on early subculture (s/c) growth of positive blood culture bottle (PBCB) and compare this with standard 24 h (h) growth. Gram stain along with s/c was done for positive blood culture bottle (PBCB) in three sets of plates that were incubated at 37⁰C for 4,8 and 24 h. Each plate was examined for growth after 4, 8 and 24 h and AST was performed from each plate and was read after 4, 8 and 24 h for each plate. Out of 161 isolates, 84.4 % (136/161) isolates were gram-negative bacilli (GNB) and15.5 % (25/161) were identified as gram-positive cocci (GPC). Our study results showed that interpretable RAST results for <em>Escherichia coli,Klebsiella pneumoniae,Acinetobacter</em> species, <em>Serratia marcescens</em> and <em>Enterobacter</em> species could be achieved for 4 h s/c growth whose AST is read at 4 h. For <em>Pseudomonas aeruginosa</em>, <em>Burkholderia cepacia complex</em> and <em>Stenotrophomonas maltophilia</em> interpretable RAST results could be achieved for 8 h s/c growth whose AST is read at 4 h. For <em>Staphylococcus</em> species, <em>Enterococcus</em> species, <em>Ochrobactrum, Achromobacter</em> and <em>Ralstonia</em> species interpretable RAST results could be achieved for 24 h s/c growth whose AST is read at 4 h. RAST testing from the early s/c growth can be performed to decrease the TAT of AST results.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107153"},"PeriodicalIF":1.7,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146992","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":"Development of a gold nanoparticle-based colorimetric assay for rapid detection of total bacterial count and coliform bacteria using the molecular hybridization approach","authors":"Juan Du ,&nbsp;Ziqi Huang ,&nbsp;Zongshuang Li ,&nbsp;Limin Wang ,&nbsp;Quanfeng Zhang ,&nbsp;Yurui Dai ,&nbsp;Yanhong Bai","doi":"10.1016/j.mimet.2025.107151","DOIUrl":"10.1016/j.mimet.2025.107151","url":null,"abstract":"<div><div>Total bacterial counts (TBC) and coliforms bacteria have been used as the index of microbial quality and fecal contamination for foods, the detection of them is involved in microbiological criteria of most countries to guarantee food safety. In this study, a gold nanoparticle (AuNPs) based colorimetric assay for rapid detection of TBC and coliform bacteria was developed by using the molecular hybridization approach. Thiol modified primers SH-27F and SH-<em>lacZ</em>F were designed and conjugated with AuNPs, which was acted as both hybridization probe and signal probe, and salt induced aggregation of AuNPs was indicator of the hybridization and detection. <em>Escherichia coli</em> was studied as model strain in this study. The result showed that under the optimal conditions, the limit of detection for TBC and coliforms bacteria were 10² CFU/mL and 10¹ CFU/mL by visual detection, and 10¹ CFU/mL by UV–vis spectrum analysis, a smart phone application named ColorPicker was used for the quantitative analysis of the colorimetric assay. The colour signal had good linear relationship of <em>E. coli</em> concentration in the range of 10¹–10⁴ CFU/mL. The detection is rapid, simple and sensitive, without the needing of culture enrichment and precious equipment, has good application potential for the on-site detection of TBC and coliforms bacteria. In addition, the proposed strategy provides a direction for the design of highly sensitive colorimetric signal probes for other pathogenic microorganisms.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107151"},"PeriodicalIF":1.7,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139550","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 rapid, reliable, and cost-effective method for monitoring Mycoplasma spp. growth in real-time using Resazurin fluorescence","authors":"Sahar Zare,&nbsp;Amir H. Noormohammadi,&nbsp;Marc S. Marenda","doi":"10.1016/j.mimet.2025.107152","DOIUrl":"10.1016/j.mimet.2025.107152","url":null,"abstract":"<div><div><em>Mycoplasmas</em> are small, slow-growing bacteria that do not produce visible turbidity in broth. Monitoring the growth of these fastidious organisms requires the manual sampling of cultures over several days, followed by cumbersome enumeration methods with long incubation periods or complex assays unable to differentiate live and dead cells. Here, a simple, automated assay was developed to measure <em>Mycoplasma</em> growth by quantifying the reduction of resazurin, a non-toxic dye, into a fluorescent product by live organisms. <em>Mycoplasma</em> species were cultivated in broth containing 2.5 mg/L resazurin. Fluorescence (520 nm excitation, 555 nm emission) was recorded every 5 min for 24 h using a qPCR thermocycler set at 37 °C, to capture the logarithmic and plateau phases. Growth curves and generation times obtained from fluorescence readings were highly similar to those calculated from the Most Probable Number (MPN) titres analysis of broth cultures sampled every 2 h over the same timeframe. Additionally, the resazurin assay could rapidly differentiate temperature-sensitive mutants from wild-type strains, by comparing their maximal growth rates in permissive (33 °C) and non-permissive (39 °C) conditions. While the MPN titration protocol required tedious liquid handling and weeks-long incubation to produce interpretable data, the resazurin assay delivered results in less than 24 h. Unlike the MPN method, which relies on pH changes, the resazurin assay could be used with non-acidifying <em>Mycoplasmas</em>. In conclusion, resazurin-based fluorescence monitoring provides a practical and accurate solution to quantify <em>Mycoplasma</em> growth, with strong potential for diagnostic and research applications.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107152"},"PeriodicalIF":1.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123859","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":"Application of a rapid and sensitive RPA-CRISPR/Cas12a assay for BCSP31-based Brucella detection","authors":"Xiaoyu Deng ,&nbsp;Wenhong Wang ,&nbsp;Yifang Tao ,&nbsp;Liangjia Yao ,&nbsp;Yiguo Li ,&nbsp;Xiao Huang ,&nbsp;Jinke He","doi":"10.1016/j.mimet.2025.107148","DOIUrl":"10.1016/j.mimet.2025.107148","url":null,"abstract":"<div><div>Brucellosis, a zoonotic disease caused by <em>Brucella</em> species, poses significant health risks to humans and animals. Due to the limitations of current diagnostic methods, such as serological testing and PCR, in terms of sensitivity, specificity, and speed, this study explores the potential of integrating recombinase polymerase amplification (RPA) with the CRISPR-Cas12a system for <em>Brucella</em> detection. This combination leverages the strengths of both technologies for rapid, sensitive, and specific molecular diagnostics. RPA primers and CRISPR RNA (crRNA) targeting the <em>Brucella</em>-specific conserved sequence <em>BCSP31</em> were designed, followed by optimization of the RPA-CRISPR/Cas12a system. Its performance was evaluated using genomic DNA from <em>Brucella</em> and non-<em>Brucella</em> species. The system's capabilities were assessed on clinical blood samples, demonstrating high sensitivity (detection limit of 10 copies per reaction and 16.6 attomoles for <em>Brucella</em> DNA) and excellent specificity. Testing on clinical samples showed strong agreement with qPCR results and an improvement over the RBT.</div><div>The RPA-CRISPR/Cas12a platform represents a rapid, ultra-sensitive, and accurate method for <em>Brucella</em> detection and holds promise as a valuable tool for brucellosis control.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107148"},"PeriodicalIF":1.7,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068921","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":"Development of a high-throughput method for processing sponge-stick samples to detect viable Bacillus anthracis spores","authors":"Vanessa L. Brisson ,&nbsp;Staci R. Kane ,&nbsp;Sanjiv R. Shah","doi":"10.1016/j.mimet.2025.107149","DOIUrl":"10.1016/j.mimet.2025.107149","url":null,"abstract":"<div><div>Since the national validation of the sponge-stick based method for detection of <em>Bacillus anthracis</em> spores in environmental samples, there have not been focused efforts to address the low throughput nature of the method, which processes only one sample at one time. Sample processing remains a serious bottleneck for rapidly analyzing large numbers of samples expected from a biological warfare attack. Therefore, we developed a high-throughput method to simultaneously process multiple sponge-stick samples to be better prepared for rapid response and recovery after wide area anthrax incidents. In this method, sponges are placed in 50 mL tubes containing 25 mL extraction buffer and shaken to release spores, after which the suspension is recovered for analysis. We determined that an additional extraction step, conducted in the same tubes with 10 mL buffer, further increased spore recovery from sponge-stick by approximately 10 %. We determined that orbital shaking and multi-tube vortexing were both more effective than reciprocating shaking for recovering spores. We conducted simultaneous processing of up to 12 sponge-stick samples and demonstrated comparable spore recovery efficiencies to the traditional low-throughput stomacher-based method (approximately 60 % recovery at 10²-spore level and 75 % recovery at 10⁴-spore level for both methods in three replicate experiments, <em>P</em> &gt; 0.05 for two-tailed <em>t</em>-tests for each experiment and spore level). We also demonstrated that our high-throughput method could be integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis and could detect levels as low as 40 spores per sponge even when challenged by a PCR particulate contaminant.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107149"},"PeriodicalIF":1.7,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078514","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":"Beyond cold chain: A cost-effective ambient temperature storage and transportation of viable bacteria","authors":"Pratibha Mambatta Shankaranarayanan,&nbsp;Saranya Kanukollu,&nbsp;Bhavya Bharti,&nbsp;Avinash Shankar,&nbsp;Sneha Palpandi,&nbsp;Anand Babu Vangala,&nbsp;Elango E. Murugaian,&nbsp;Rajanikanth Vangala","doi":"10.1016/j.mimet.2025.107147","DOIUrl":"10.1016/j.mimet.2025.107147","url":null,"abstract":"<div><div>Freeze-drying and cryopreservation are the most common methods for microbial preservation. instaPRESERVE MicrobeSafe (IP-MIS), an innovative alternative for maintaining high bacterial viability and recovery at room temperature for up to 56 days. This study validates IP-MIS as an effective and reliable solution for short-term storage without the need for cold chain.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"235 ","pages":"Article 107147"},"PeriodicalIF":1.7,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143970254","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}