Journal of microbiological methods最新文献_第7页

Single-cell RNA seq reveals heterogeneous survival strategies of Vibrio parahaemolyticus against ampicillin 单细胞RNA测序揭示副溶血性弧菌对氨苄西林的异质生存策略

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-24 DOI: 10.1016/j.mimet.2025.107343

Zhangxi Gong , Yu Zhou , Yongbing Ba , Yao Yang , Yingjie Pan , Yong Zhao , Haiquan Liu

{"title":"Single-cell RNA seq reveals heterogeneous survival strategies of Vibrio parahaemolyticus against ampicillin","authors":"Zhangxi Gong , Yu Zhou , Yongbing Ba , Yao Yang , Yingjie Pan , Yong Zhao , Haiquan Liu","doi":"10.1016/j.mimet.2025.107343","DOIUrl":"10.1016/j.mimet.2025.107343","url":null,"abstract":"<div><div>Bulk RNA-Seq only captures the average gene expression level of bacterial populations and has limitations in analysing functional differences between bacterial subpopulations. Therefore, the study innovatively applied droplet-based single-cell RNA sequencing (scRNA-seq) to resolve ampicillin resistance heterogeneity in <em>Vibrio parahaemolyticus</em> (<em>V. parahaemolyticus</em>). Findings indicate that high levels of drug resistance (MIC = 1000 μg/mL) demonstrate a significant impact on the phenotypes of interest, particularly when subinhibitory concentrations are considered. To further elucidate the phenotypic heterogeneity results, functionally specialized cellular subpopulations was identified by scRNA-seq, such as an oxidative stress defense subpopulation mediated by <em>gorA</em> upregulation, virulence modulation achieved through <em>exsD</em>-mediated repression of the type III secretion system, drug resistance conferred by MATE family efflux pumps, protein homeostasis maintained by Hsp20, metabolic reprogramming driven by NirD/YgiW/YdeI family proteins, and membrane damage repair facilitated by <em>pspA</em> upregulation. The phenotypic heterogeneity analysis results support some of the newly discovered functional annotations of resistant subpopulations, demonstrating the biological basis of bacterial heterogeneity under antibiotic pressure. The discovery of these functional drug-resistant subpopulations provides deeper insight into <em>V. parahaemolyticus</em> resistance and paves the way for developing novel antimicrobial strategies targeting key signaling proteins for population-level coordination.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107343"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616465","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

Development of gene manipulation methods for Enterococcus cecorum 盲肠球菌基因操作方法的研究进展。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-14 DOI: 10.1016/j.mimet.2025.107331

Daisuke Takamatsu , Mariko Okamoto , Takashi Mada , Ayako Watanabe-Yanai , Koume Matsubara , Masatoshi Okura

引用次数: 0

A qPCR assay for the detection and quantification of Pseudomonas syringae pv. syringae in susceptible tissues of sweet cherry 丁香假单胞菌的qPCR检测与定量。甜樱桃易感组织中的丁香。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-12-02 DOI: 10.1016/j.mimet.2025.107351

Yerko Lovera , Juan San Martin , Braulio Ruiz , Richard M. Bastías , Macarena Gerding , Juan Hirzel , Ernesto Moya-Elizondo

引用次数: 0

The relationship between Enterolert and ddPCR concentrations of enterococci in summer samples from beaches in Coronado, California 加州科罗纳多海滩夏季样品中肠球菌Enterolert和ddPCR浓度的关系

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-26 DOI: 10.1016/j.mimet.2025.107346

Matthew E. Verbyla , Rosanna Lacarra

{"title":"The relationship between Enterolert and ddPCR concentrations of enterococci in summer samples from beaches in Coronado, California","authors":"Matthew E. Verbyla , Rosanna Lacarra","doi":"10.1016/j.mimet.2025.107346","DOIUrl":"10.1016/j.mimet.2025.107346","url":null,"abstract":"<div><div>Enterococci, widely used as a fecal indicator in coastal recreational waters, can be quantified using different methods, including the culture-based Enterolert method and the newer, more rapid droplet digital polymerase chain reaction (ddPCR) method. Previous studies on the correlation between culture-based and PCR-based methods have shown mixed results. To address this knowledge gap, data from a study conducted at three beaches in the city of Coronado, California during the summer of 2023 were analyzed to compare ddPCR-based concentrations of <em>Enterococcus</em> with Enterolert-based concentrations of enterococci in samples collected daily for approximately two months. The concentrations using both methods were consistent with the lognormal distribution. A linear regression between ddPCR and Enterolert concentrations was statistically significant with an R<sup>2</sup> value of 0.41, but the slope was significantly lower than slopes reported in previous studies. The index of agreement between the two methods was 0.25, but it increased to 0.47 when the ddPCR concentrations were scaled to Enterolert equivalents using the regression. When comparing beach action values based on Enterolert and ddPCR, the false positive rate associated with the use of ddPCR was 56.3 %. Overall, the results of this study showed a discordance between the Enterolert and ddPCR methods at Coronado beaches during the summer of 2023, indicating that the relationship may be influenced by spatial and temporal factors.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107346"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145634628","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

Improving the identification of pneumonia pathogens by using the real-time polymerase chain reaction (qPCR) alongside culture methods 利用实时聚合酶链反应（qPCR）和培养方法提高肺炎病原体的鉴定。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-28 DOI: 10.1016/j.mimet.2025.107349

Nurul Izzaty Najwa Zahari , Jia Ying Wong , Siti Asma’ Hassan , Rafidah Hanim Shueb , Rohimah Mohamud , Chan Yean Yean

{"title":"Improving the identification of pneumonia pathogens by using the real-time polymerase chain reaction (qPCR) alongside culture methods","authors":"Nurul Izzaty Najwa Zahari , Jia Ying Wong , Siti Asma’ Hassan , Rafidah Hanim Shueb , Rohimah Mohamud , Chan Yean Yean","doi":"10.1016/j.mimet.2025.107349","DOIUrl":"10.1016/j.mimet.2025.107349","url":null,"abstract":"<div><div><em>Streptococcus pneumoniae</em>, <em>Haemophilus influenzae</em>, and <em>Klebsiella pneumoniae</em> are among colonizers of the upper respiratory tract flora that can cause pneumonia upon invading the lungs. Molecular techniques have increasingly become the preferred diagnostic approach for detecting respiratory pathogens. However, sputum culture remains the standard diagnostic method for identifying respiratory pathogens in many underdeveloped and developing countries. In this cross-sectional perspective study, 94 sputum specimens were evaluated using both culture and an in-house multiplex qPCR assay. The multiplex qPCR demonstrated greater sensitivity, detecting pathogens in 79 specimens (84.04 %), compared with 32 specimens (31.37 %) identified by culture. The qPCR assay detected <em>K. pneumoniae</em> in 54 of 94 sputum samples, making it the most predominant bacterium, followed by <em>S. pneumoniae</em> (26/94), and <em>H. influenzae</em> (20/94). In contrast, culture detected <em>S. pneumoniae</em>, <em>K. pneumoniae</em>, and <em>H. influenzae</em> in 1, 14, and 3 cases, respectively. These findings support the integration of qPCR into the diagnostic routine alongside culture methods for respiratory samples, as the inclusion of qPCR methods enhances diagnostic sensitivity and accuracy, which are critical for effective patient management and treatment planning.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107349"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145634647","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

Bioconversion of naringin to naringenin by a characterized Naringinase from aspergillus Niger HO32: Toward the valorization of citrus flavonoids 来自黑曲霉HO32的柚皮酶将柚皮苷生物转化为柚皮素：柑橘类黄酮的增殖研究。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-22 DOI: 10.1016/j.mimet.2025.107342

Nour Eddine Bentouhami , Sarra Yousfi , Meryem Idrissi Yahyaoui , Sara Moumnassi , Fatima Brahmi , Reda Bellaouchi , Houssam Abouloifa , Nabil Ghabbour , Ennouamane Saalaoui , Bassem Jaouadi , Abdelkarim Abousalham , Adem Gharsallaoui , Nour Eddine Chihib , Loubna Firdaous , Abdeslam Asehraou

{"title":"Bioconversion of naringin to naringenin by a characterized Naringinase from aspergillus Niger HO32: Toward the valorization of citrus flavonoids","authors":"Nour Eddine Bentouhami , Sarra Yousfi , Meryem Idrissi Yahyaoui , Sara Moumnassi , Fatima Brahmi , Reda Bellaouchi , Houssam Abouloifa , Nabil Ghabbour , Ennouamane Saalaoui , Bassem Jaouadi , Abdelkarim Abousalham , Adem Gharsallaoui , Nour Eddine Chihib , Loubna Firdaous , Abdeslam Asehraou","doi":"10.1016/j.mimet.2025.107342","DOIUrl":"10.1016/j.mimet.2025.107342","url":null,"abstract":"<div><div>In this study, we investigated the production and characterization of a naringinase by <em>Aspergillus niger</em> HO32, after which the enzyme was precipitated by fractionation using 80% ammonium sulfate and dialyzed at 4 °C overnight. The obtained results showed that its optimum pH and temperature are 5.5 and 55 °C, respectively, and it was stable at a pH range between 3 and 7 and at temperatures of 40, 50, and 60 °C. Naringinase is also capable of hydrolyzing the glycosides naringin, hesperidin, and others. HPLC-MS analysis, demonstrating the bioconversion of naringin to naringenin with a simultaneous increase of naringenin content. The <em>K</em><sub><em>m</em></sub>, <em>V</em><sub><em>max</em></sub>, and <em>k</em><sub><em>cat</em></sub> parameters using naringin substrate were 2 mM, 1428.6 U/mg, and 340.14 min<sup>−1</sup>, respectively. The results obtained suggest that our naringinase has revealed an immense potential for application in the food sciences and industrial biotechnology fields, mainly for the bio-debittering of orange juices, and for the biotransformation of various foods.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107342"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145596604","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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Cost-effective immobilization of Chaetomium erraticum dextranase on c-MWCNT 在c-MWCNT上固定化羊绒毛菌葡聚糖酶的成本效益研究

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-11-27 DOI: 10.1016/j.mimet.2025.107348

Barzan Ismael Ghafour, Yakup Aslan

引用次数: 0

Application of a two-level factorial design to investigate the effects of pH, temperature, nitrate concentration, and photoperiod on novel extracellular lipase activity of Nodosilinea sp. LGS3 应用双水平因子设计研究pH、温度、硝酸盐浓度和光周期对Nodosilinea sp. LGS3新型胞外脂肪酶活性的影响

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-12-04 DOI: 10.1016/j.mimet.2025.107354

S. Sangeetha, Lali Growther

{"title":"Application of a two-level factorial design to investigate the effects of pH, temperature, nitrate concentration, and photoperiod on novel extracellular lipase activity of Nodosilinea sp. LGS3","authors":"S. Sangeetha, Lali Growther","doi":"10.1016/j.mimet.2025.107354","DOIUrl":"10.1016/j.mimet.2025.107354","url":null,"abstract":"<div><div>The production of extracellular lipases from cyanobacteria offers a sustainable alternative to conventional enzyme sources for industrial and environmental applications. This study reports, for the first time, the production of a novel extracellular lipase from the cyanobacterium <em>Nodosilinea</em> sp. LGS3. The effects of pH, temperature, nitrate concentration, and photoperiod on lipase activity were systematically evaluated using a two-level factorial experimental design. Sixteen treatment combinations were examined, and quantitative measurements of biomass, nitrate consumption, extracellular protein, and lipase activity were recorded over a 288-h cultivation period. The highest biomass yield (12.2 ± 0.07 g L<sup>−1</sup>) was obtained under T5 conditions (pH 6, 25 °C, 0.5 g NaNO₃ L<sup>−1</sup>, 16 h photoperiod at 192 h). ANOVA revealed that pH and NaNO₃ concentration had highly significant effects on biomass production (<em>p</em> < 0.05). Meanwhile, the highest extracellular lipase activity (15.36 ± 0.12 U mL<sup>−1</sup>) and protein production (0.193 ± 0.06 g L<sup>−1</sup>) were recorded under T6 conditions (pH 6, 23 °C, 16 h photoperiod, and 0.5 g NaNO₃ L<sup>−1</sup> at 240 h). ANOVA indicated that the interaction between pH and nitrate concentration significantly influenced extracellular protein production (<em>p</em> < 0.05), while the interaction between pH and photoperiod was the most influential factor affecting extracellular lipase activity (<em>p</em> < 0.05). Overall, the findings underscore the potential of cyanobacteria as valuable sources of novel biocatalysts for diverse biotechnological applications.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107354"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681881","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

Fourier-transform infrared spectroscopy reliably differentiates Klebsiella pneumoniae outbreak isolates 傅里叶变换红外光谱可靠地鉴别肺炎克雷伯菌爆发分离物

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-12-04 DOI: 10.1016/j.mimet.2025.107355

Miriam Cordovana , Markus Kostrzewa , Jürgen A. Bohnert , Elias Eger , Nils-Olaf Hübner , Karsten Becker , Katharina Schaufler , Stefan E. Heiden , Evgeny A. Idelevich

{"title":"Fourier-transform infrared spectroscopy reliably differentiates Klebsiella pneumoniae outbreak isolates","authors":"Miriam Cordovana , Markus Kostrzewa , Jürgen A. Bohnert , Elias Eger , Nils-Olaf Hübner , Karsten Becker , Katharina Schaufler , Stefan E. Heiden , Evgeny A. Idelevich","doi":"10.1016/j.mimet.2025.107355","DOIUrl":"10.1016/j.mimet.2025.107355","url":null,"abstract":"<div><div>International, multidrug-resistant (MDR) high-risk clonal <em>Klebsiella pneumoniae</em> lineages are a frequent cause of outbreaks, posing a serious public health threat. Tracking, understanding and containing such outbreaks remain a challenge for infection control. In this study, we evaluated Fourier-transform infrared (FTIR) spectroscopy – a method previously shown to enable bacterial typing at various intraspecies levels – as a tool to type 53 MDR <em>K. pneumoniae</em> isolates that had been geno- and phenotypically characterized and collected during an outbreak in North-Eastern Germany in 2019. Infrared (IR) spectra were acquired from dried spots of bacterial suspensions in ethanol solution, with three independent cultures of each isolate. FTIR spectroscopy exploratory data analysis, performed by Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA), revealed six distinct clusters. These showed perfect concordance with K locus typing (Adjusted Rand index [AR]: 100 %), very high concordance with sequence type (ST) (AR: 99.1 %), and high but lower concordance with the O locus (AR: 90.6 %). All MDR outbreak isolates clustered tightly together, indicating strong spectral similarity and confirming their clonal relatedness. These findings demonstrate that FTIR spectroscopy could serve as a rapid, first-line screening tool to support early detection of cross-transmission events involving clonally related <em>K. pneumoniae</em> strains.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107355"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681882","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

A streamlined protocol for high-quality RNA extraction from bread dough 从面包面团中提取高质量RNA的简化方案

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-01-01 Epub Date: 2025-12-04 DOI: 10.1016/j.mimet.2025.107352

Akira Nishimura , Shigeyuki Ota , Shota Isogai , Hiroshi Takagi

引用次数: 0