Journal of microbiological methods最新文献_第6页

Prospective study on combined use of Sabouraud dextrose agar and blood agar for improved recovery of etiological agents in mycotic and Pythium keratitis 沙乌地葡萄糖琼脂与血琼脂联合应用对真菌性角膜炎和皮癣性角膜炎病原菌恢复的前瞻性研究

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-09-05 DOI: 10.1016/j.mimet.2025.107247

Harsimran Kaur , Mahuya Roy , Imola Jamir , Sukriti Yadav , Amit Gupta , Anup Ghosh , Archana Angrup , Shivaprakash M. Rudramurthy

{"title":"Prospective study on combined use of Sabouraud dextrose agar and blood agar for improved recovery of etiological agents in mycotic and Pythium keratitis","authors":"Harsimran Kaur , Mahuya Roy , Imola Jamir , Sukriti Yadav , Amit Gupta , Anup Ghosh , Archana Angrup , Shivaprakash M. Rudramurthy","doi":"10.1016/j.mimet.2025.107247","DOIUrl":"10.1016/j.mimet.2025.107247","url":null,"abstract":"<div><div>We evaluated the effectiveness of using blood agar (BA) and Sabouraud dextrose agar (SDA) together to isolate fungi and <em>Pythium insidiosum</em> for the diagnosis of fungal and <em>Pythium</em> keratitis respectively. The overall recovery rate was higher in SDA than BA (93.75 % vs 88.28 %; <em>p</em> = 0.595). BA demonstrated lower isolation of dematiaceous fungi (unadjusted <em>p</em> = 0.039: FDR adjusted <em>p</em> = 0.062). 11.71 % and 6.25 % of fungal isolates were not recovered on BA and SDA, respectively. While BA showed faster growth of fungi than SDA (unadjusted <em>p</em> = 0.002; FDR adjusted <em>p</em> = 0.005), both BA and SDA showed rapid recovery of <em>Aspergillus</em> spp. as compared to <em>Fusarium</em> spp. (unadjusted <em>p</em> < 0.001; FDR adjusted <em>p</em> = 0.004). The combined use of both media may enhance detection of certain fungi missed by either medium alone, hence guiding the appropriate patient management.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107247"},"PeriodicalIF":1.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010276","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}

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Evaluation of a nucleic acid preservation protocol for microbiome studies involving samples from the oral cavity 口腔微生物组研究中核酸保存方案的评价。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-09-05 DOI: 10.1016/j.mimet.2025.107248

Tilman E. Klassert , Jenny Fiebig , Cristina Zubiria-Barrera , Ludwig Wurschi , Robert Neubert , Annika Döding , Ulrike Schulze-Späte , Hortense Slevogt

{"title":"Evaluation of a nucleic acid preservation protocol for microbiome studies involving samples from the oral cavity","authors":"Tilman E. Klassert , Jenny Fiebig , Cristina Zubiria-Barrera , Ludwig Wurschi , Robert Neubert , Annika Döding , Ulrike Schulze-Späte , Hortense Slevogt","doi":"10.1016/j.mimet.2025.107248","DOIUrl":"10.1016/j.mimet.2025.107248","url":null,"abstract":"<div><h3>Purpose</h3><div>The accuracy of oral microbiome research depends significantly on specimen sampling protocols, as well as their storage and preservation. Traditional methods, such as freezing, may not only involve logistical hurdles but can also impact the quality of microbial data, leading to difficulties in the comparability between different studies. This study evaluates the effectiveness of the room temperature nucleic acid preservation protocol using DNA/RNA Shield buffer as compared to standard freezing in preserving oral microbial communities over the course of 7 days.</div></div><div><h3>Results</h3><div>Comparative analyses based on 16S rRNA gene sequencing revealed a high overall consistency between the microbiome data retrieved by both preservation strategies. In terms of DNA yield, qPCR analysis showed a significant increase in bacterial DNA recovered from tongue swabs, dental pockets and saliva samples when using DNA/RNA Shield. In the taxonomic analyses, the Shield buffer preserved a higher abundance of <em>Veillonella</em> as compared to freezing. However, the compositional data was highly comparable between both protocols for all other taxonomic groups. While no major differences in microbial diversity were observed between both preservation methods for most samples, saliva samples stored in DNA/RNA Shield exhibited significantly higher diversity. Both preservation methods performed in a highly comparable manner in their ability to retrieve consistent biological readouts, such as site-specificity and health status.</div></div><div><h3>Conclusion</h3><div>Storing oral samples at room temperature in DNA/RNA Shield buffer provides a reliable and efficient alternative to freezing for preserving microbiome samples. Furthermore, it may enhance DNA yield while preserving microbial diversity in the samples.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107248"},"PeriodicalIF":1.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015662","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}

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Multiplex polymerase chain reaction and testing of complex food matrices: A preliminary study on E. coli and Salmonella spp 多重聚合酶链反应与复杂食品基质的检测：大肠杆菌和沙门氏菌的初步研究。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-09-05 DOI: 10.1016/j.mimet.2025.107251

Stéphanie Watier-Grillot , Christian Sauvageot , Evelyne Thiébaut , Vincent Pommier de Santi , Aurélie Chesnay

{"title":"Multiplex polymerase chain reaction and testing of complex food matrices: A preliminary study on E. coli and Salmonella spp","authors":"Stéphanie Watier-Grillot , Christian Sauvageot , Evelyne Thiébaut , Vincent Pommier de Santi , Aurélie Chesnay","doi":"10.1016/j.mimet.2025.107251","DOIUrl":"10.1016/j.mimet.2025.107251","url":null,"abstract":"<div><div>Foodborne diseases are caused by various pathogens and generally present with similar symptoms, mainly digestive disorders. Adopting a syndromic approach is therefore important when investigating foodborne disease outbreaks. This involves using multiplex PCR-based methods to test stool and food samples. In this study, the BioFire® FilmArray® Gastrointestinal Panel (BF-GIP) was evaluated as an alternative food microbiology method, in compliance with the ISO 16140-2 standard. We tested 205 naturally and artificially-contaminated mixed salad samples for <em>Escherichia</em> (<em>E.</em>) <em>coli</em> and <em>Salmonella</em> spp., comparing the results with BF-GIP and culture-based reference methods. For <em>Salmonella</em> spp., BF-GIP sensitivity was 100 % and the rate of false positives was 2.4 %, suggesting a good specificity. For <em>E. coli,</em> BF-GIP sensitivity was 92.9 %, with no significant difference from the reference method sensitivity. Shortcomings were highlighted for the accurate identification of <em>E. coli</em> strains artificially inoculated in food samples, with error percentages of 14 % and 9 % for the inclusivity and exclusivity studies respectively. BF-GIP is a suitable alternative method for the screening of <em>Salmonella</em> spp. and <em>E. coli</em> in complex food matrices, notably when investigating foodborne disease outbreaks. However, due to a lack of specificity, the determination of the <em>E. coli</em> strain(s) needs to be confirmed by a reference method.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107251"},"PeriodicalIF":1.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015631","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}

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Emulating visual evaluations in the microscopic agglutination test with deep learning 用深度学习模拟显微凝集测试中的视觉评价。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-09-05 DOI: 10.1016/j.mimet.2025.107249

Risa Nakano , Yuji Oyamada , Ryo Ozuru , Satoshi Miyahara , Michinobu Yoshimura , Kenji Hiromatsu

{"title":"Emulating visual evaluations in the microscopic agglutination test with deep learning","authors":"Risa Nakano , Yuji Oyamada , Ryo Ozuru , Satoshi Miyahara , Michinobu Yoshimura , Kenji Hiromatsu","doi":"10.1016/j.mimet.2025.107249","DOIUrl":"10.1016/j.mimet.2025.107249","url":null,"abstract":"<div><div>The Microscopic Agglutination Test (MAT) is widely recognized as the gold standard for diagnosing zoonosis leptospirosis. However, the MAT relies on subjective evaluations by human experts, which can lead to inconsistencies and inter-observer variability. In this study, we aimed to emulate expert assessments using deep learning and convert them into reproducible numerical outputs to achieve greater objectivity. By leveraging a pre-trained DenseNet121, the network benefits from better initialization, facilitating more effective training. We validated our approach using an in-house dataset, and the experimental results demonstrate that the proposed network achieved accurate agglutination rate estimates. In addition, we employed UMAP, a dimensionality reduction technique, to visualize the learned feature representations, revealing that the network captured image features indicative of <em>Leptospira</em> abundance. Overall, our findings suggest that deep learning can consistently estimate agglutination rates in a manner that approximates expert evaluations and that enhancing interpretability provides visual cues that could aid in understanding the behavior of deep learning models, potentially facilitating future clinical integration.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107249"},"PeriodicalIF":1.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015613","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}

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Efficacy of different “boiling” methods for bacterial DNA extraction 不同“煮沸”方法提取细菌DNA的效果。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-30 DOI: 10.1016/j.mimet.2025.107245

Isabella R. Loberiza , Fletcher E. Falk , Timothy J. Green , Andrew H. Loudon

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Systematic review of co-culture methods for studying vaginal biofilm formation in bacterial vaginosis 研究细菌性阴道病阴道生物膜形成的共培养方法的系统综述。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-29 DOI: 10.1016/j.mimet.2025.107243

Bárbara Pontarollo Dal Santos , Alexandre Gnoatto , Sahra Madalena Heiden , Vivian Heimbecker , Newton Sergio de Carvalho , Camila Marconi

{"title":"Systematic review of co-culture methods for studying vaginal biofilm formation in bacterial vaginosis","authors":"Bárbara Pontarollo Dal Santos , Alexandre Gnoatto , Sahra Madalena Heiden , Vivian Heimbecker , Newton Sergio de Carvalho , Camila Marconi","doi":"10.1016/j.mimet.2025.107243","DOIUrl":"10.1016/j.mimet.2025.107243","url":null,"abstract":"<div><h3>Background</h3><div>Bacterial vaginosis (BV) is characterized by depletion of <em>Lactobacillus</em> spp. and increased abundance of facultative and strict anaerobic species. <em>Gardnerella</em> spp. initiates biofilm formation associated with BV pathogenesis. Vaginal biofilms act as virulence factors and reduce the effectiveness of antibiotic treatment for BV.</div></div><div><h3>Objectives</h3><div>To systematically review the most commonly used methodologies for studying bacterial biofilms in bacterial vaginosis (BV), and to discuss how standardization can improve future studies.</div></div><div><h3>Methods</h3><div>A search was conducted in PubMed, Virtual Health Library (VHL), and Embase databases for articles addressing BV biofilms in vaginal dysbiosis, resulting in 66 included studies. Non-original studies, those involving bacteria unrelated to the vaginal environment, fungal species, and studies whose methods did not include bacterial biofilm models were excluded. The risk of bias in the selected articles was assessed using the RobDEMAT tool for in vitro studies and the RoB2 tool for in vivo studies.</div></div><div><h3>Results</h3><div>The most commonly used method for biofilm experiments was the co-culture of <em>Gardnerella vaginalis</em> and <em>Lactobacillus</em> spp. Molecular-based studies consistently demonstrate the polymicrobial nature of vaginal biofilms, reinforcing the importance of utilizing co-culture assays with multiple bacterial species related to BV.</div></div><div><h3>Conclusions</h3><div>Standardizing bacterial co-culture models will allow that data from future studies to be reproducible and comparable. This will optimize time and resources in the search for novel treatments for BV, including testing for prebiotic and probiotic candidates.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107243"},"PeriodicalIF":1.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957585","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}

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Comparing and optimizing protein extraction methods with different lysis buffers for the analyses of human fecal microbiome via metaproteomics approach 比较和优化不同裂解缓冲液提取蛋白质的方法，用宏蛋白质组学法分析人粪便微生物组。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-29 DOI: 10.1016/j.mimet.2025.107244

Shuaixin Gao , Li Chen , Huan Zhang , Amrik Singh Khalsa , Michael T. Bailey , Brett R. Loman , Colleen K. Spees , Jiangjiang Zhu

{"title":"Comparing and optimizing protein extraction methods with different lysis buffers for the analyses of human fecal microbiome via metaproteomics approach","authors":"Shuaixin Gao , Li Chen , Huan Zhang , Amrik Singh Khalsa , Michael T. Bailey , Brett R. Loman , Colleen K. Spees , Jiangjiang Zhu","doi":"10.1016/j.mimet.2025.107244","DOIUrl":"10.1016/j.mimet.2025.107244","url":null,"abstract":"<div><div>Metaproteomic analysis offers critical insights into gut microbiome function; however, efficient microbial protein extraction from fecal samples remains challenging due to the complexity of different types of bacterial cell walls in the microbiome. In this study, we systematically compared three representative detergent-based lysis buffers (sodium dodecyl sulfate_urea, dodecyl β-D-maltoside_urea, sodium dodecyl sulfate_ dodecyl β-D-maltoside_urea) for metaproteomics sample preparation. After multiple levels of analyses, we identified SDS_DDM_urea as the most efficient option for extracting diverse microbial proteins, peptides, and identifying microbial species. Applying this optimized method to samples from a community based dietary intervention study (Summer Harvest Adventure), we found minimal group-level microbial diversity shifts during this type of intervention, but substantial individual-specific variations reflected by metaproteomics results. Functional analyses also revealed microbial protein changes, especially proteins related to metabolic adaptations, including enhanced carbohydrate metabolism, amino acid biosynthesis, vitamin transport, and increased expression of membrane-associated proteins. Our results highlighted the personalized microbiome response to dietary interventions and underscored the importance of selecting appropriate protein extraction methods to accurately capture microbiome functional dynamics in microbiome analyses via metaproteomics.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107244"},"PeriodicalIF":1.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957668","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}

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Thin Layer Chromatography Bioautography Scanning Electron Microscopy (TLCBA SEM) method for antimicrobial fraction testing 薄层色谱生物自扫描电镜（TLCBA SEM）检测抗菌成分的方法

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-27 DOI: 10.1016/j.mimet.2025.107242

Anna du Toit , Chaitali Dekiwadia , Lisa Cornell , Diane Purcell , Anusuya Willis , Rajaraman Eri , Danilla Grando , Charmaine Lloyd

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Detection of phosphatidylserine exposure on Mycoplasma hyorhinis by flow cytometry 流式细胞术检测乙肝支原体的磷脂酰丝氨酸暴露

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-27 DOI: 10.1016/j.mimet.2025.107241

Mengyuan Li , Qingqing Guo , Lichun Mo , Ting Zheng

{"title":"Detection of phosphatidylserine exposure on Mycoplasma hyorhinis by flow cytometry","authors":"Mengyuan Li , Qingqing Guo , Lichun Mo , Ting Zheng","doi":"10.1016/j.mimet.2025.107241","DOIUrl":"10.1016/j.mimet.2025.107241","url":null,"abstract":"<div><div><em>Mycoplasma</em> often contaminates eukaryotic cell cultures. Determining <em>Mycoplasma</em> cell viability is important when evaluating the cellular response to drug treatment. One method to test cell viability is using a membrane-impermeant nucleic acid dye that is generally excluded from viable cells. When cell death occurs, the plasma membrane phosphatidylserine (PS) is translocated from the inner side to the outer layer. This exposed PS has a high affinity for a Ca<sup>2+</sup>-dependent phospholipid-binding protein, Annexin V. In the present study we evaluated the potential application of Annexin V and propidium iodide (PI) in determining the cellular viability of <em>Mycoplasma hyorhinis</em> parasitized in host cell-culture supernatants. After <em>Mycoplasma</em> cells were treated with anti-<em>Mycoplasma</em> antibiotics, flow cytometry analysis was performed at a single-cell level and the untreated samples were included as negative controls. Subsequently, a robust association between PS exposure (Annexin V-positive) and drug dilution factor was observed. These data showed that Annexin V was an optimal probe for studying the physiological state of <em>Mycoplasma</em> in the early stages of death, characterized by disruption of phospholipid asymmetry.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107241"},"PeriodicalIF":1.9,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144912917","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}

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Application of online spectroscopic techniques for detection of Bacillus spores in cultivations with complex medium 在线光谱技术在复杂培养基培养芽孢杆菌孢子检测中的应用

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2025-08-26 DOI: 10.1016/j.mimet.2025.107239

Jennifer Goldmanns , Monique Schulze , Theresa Scholand , Tobias May , Evangeline Priya Haas , Matthias Boy , Andrea Herold , Jochen Büchs

{"title":"Application of online spectroscopic techniques for detection of Bacillus spores in cultivations with complex medium","authors":"Jennifer Goldmanns , Monique Schulze , Theresa Scholand , Tobias May , Evangeline Priya Haas , Matthias Boy , Andrea Herold , Jochen Büchs","doi":"10.1016/j.mimet.2025.107239","DOIUrl":"10.1016/j.mimet.2025.107239","url":null,"abstract":"<div><div><em>Bacillus</em> spores are important in a range of biotechnological applications. Real-time spore detection methods are advantageous for effectively characterizing and optimizing the spore production processes. In this study, a qualitative high-throughput method for online monitoring of <em>Bacillus</em> spore formation using spectroscopic techniques is presented. An increase in specific fluorescence at an excitation wavelength of 390 nm and an emission wavelength of 460 nm was observed during the cultivation of the spore-forming <em>Bacillus subtilis</em> PY79 strain in a BioLector device, which correlated with the release of spores from the mother cells in a complex medium. Therefore, spore release can be monitored in high-throughput experiments by real-time measurement of this fluorescence wavelength combination. Additionally, the applicability of this method to <em>Bacillus</em> strains other than <em>B. subtilis</em> highlights its broad relevance in industrial processes. This method has the potential to detect spores more reliably and efficiently than conventional methods such as plating techniques. Finally, quenching experiments with iron ions indicated that a siderophore causes the characteristic fluorescence signal, demonstrating the usefulness of this method also in research areas focused on siderophores.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107239"},"PeriodicalIF":1.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144932558","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}

引用次数: 0