Journal of microbiological methods最新文献

{"title":"Recovery of short-chain organic acids (SCOAs) obtained from anaerobic fermentation process","authors":"M. Ghalibaf,&nbsp;N. Pap,&nbsp;M. Vainio,&nbsp;N. Honkala,&nbsp;S. Rasi","doi":"10.1016/j.mimet.2024.107031","DOIUrl":"10.1016/j.mimet.2024.107031","url":null,"abstract":"<div><p>Short-chain organic acids (SCOAs) are the intermediates in the anaerobic fermentation process, and can be used in food, textile, and pharmaceutical industries to produce different end use products. SCOAs can be separated, purified, and concentrated by different processes, such as distillation, extraction or membrane-based systems. SCOAs production adds more profitable possibilities to an acidic fermentation process by integration these marketable acids as highly concentrated mixtures with other refinery processes. The present study investigated two approaches for recovering of SCOAs: i) the production of clarified SCOAs liquid by microfiltration (MF) and then performing their concentration by reverse osmosis (RO) and ii) the recovery and concentration by the so-called integrated neutralization and acidified reaction method. The results of MF showed that some SCOAs were retained in the retentate together with the solids. However, in the following RO treatment, SCOAs could be successfully concentrated with a yield retention of over 90 % from the SCOAs liquid. In the latter method, a color-free SCOAs liquid was obtained with an increase in the total SCOAs concentration from 23 g/L to 146 g/L.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107031"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S016770122400143X/pdfft?md5=2943388e82132b3204ea52ff92316efb&pid=1-s2.0-S016770122400143X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid and visual detection of Mycoplasma genitalium using recombinase polymerase amplification combined with lateral flow strips","authors":"Pufang Ren ,&nbsp;Yingmin Zeng ,&nbsp;Yao Feng ,&nbsp;Honghai Hong,&nbsp;Yong Xia","doi":"10.1016/j.mimet.2024.107030","DOIUrl":"10.1016/j.mimet.2024.107030","url":null,"abstract":"<div><p><em>Mycoplasma genitalium</em> (MG) is an important sexually transmitted pathogen that can cause urethritis in males and pelvic inflammatory disease in females. Due to its complex growth requirements and lengthy incubation times, culturing MG in clinical laboratories is impractical. Here we describe a rapid and visual assay combining recombinase polymerase amplification (RPA) with lateral flow (LF) strips to detect MG (MG-RPA-LF). The limit of detection (LoD) of this method was 33.6 genome equivalents (GE) per reaction, using a dilution series of purified genomic DNA. Clinical performance was evaluated by testing 100 urogenital swabs. Compared to the Simultaneous Amplification and Testing assay, our MG-RPA-LF assay showed a sensitivity of 94 % (95 % CI, 82 %–98 %) and a specificity of 100 % (95 % CI, 91 %–100 %). The overall concordance between the two methods was 97 % (95 % CI, 91 %–99 %) with a κ coefficient of 0.94 (<em>P</em> &lt; 0.001). Without cumbersome and expensive instruments, this method is anticipated to be a promising alternative to diagnose MG infection, especially in resource-poor settings.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107030"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154391","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":"The effect of Tyloxapol on the metabolome of Mycobacterium tuberculosis","authors":"Monique Opperman ,&nbsp;Ray-Dean Pietersen ,&nbsp;Du Toit Loots ,&nbsp;Mari van Reenen ,&nbsp;Derylize Beukes ,&nbsp;Bienyameen Baker ,&nbsp;Ilse du Preez","doi":"10.1016/j.mimet.2024.107028","DOIUrl":"10.1016/j.mimet.2024.107028","url":null,"abstract":"<div><p>The use of detergents when culturing <em>Mycobacterium tuberculosis</em> (<em>M. tuberculosis</em>) are essential to prevent clumping. However, these detergents may influence research outcomes by impacting bacterial morphology and metabolism. This study aimed to assess the metabolome of a <em>M. tuberculosis</em> H37Rv strain cultured with Tyloxapol (H37Rv^Tyloxapol), compared to a control group of H37Rv strain cultured without detergent (H37Rv^Control) to evaluate Tyloxapol's suitability for metabolomic studies. Distinct metabolic alterations were observed in H37Rv^Tyloxapol compared to H37Rv^Control, primarily associated with fatty acid, sugar and pentose phosphate metabolic pathways. These changes are associated with the surface stress exerted by Tyloxapol on the bacteria, prompting an adaptation of <em>M. tuberculosis</em> metabolism to that usually observed in stress environments. Nevertheless, the effect of Tyloxapol is less pronounced than that of a previous investigation using Tween 80, indicating its potential as the more favourable choice for culturing <em>M. tuberculosis</em> for metabolomic analysis, with due consideration to dosage and result interpretation.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107028"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154393","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":"Physical radiation induced the yield of triterpenoids in hypha of Inonotus obliquus to increase","authors":"Yan Wang ,&nbsp;Xin Liu ,&nbsp;Lirui Sun ,&nbsp;Boxin Dou ,&nbsp;Jiaying Xin ,&nbsp;Na Zhang ,&nbsp;Lanwei Zhang","doi":"10.1016/j.mimet.2024.107025","DOIUrl":"10.1016/j.mimet.2024.107025","url":null,"abstract":"<div><p>HSD-IO01, a new pure strain of <em>I. obliquus</em>, was isolated and purified from the sclerotium of <em>I. obliquus</em> of Daxing'an Mountains. Physical radiation-assisted liquid fermentation technology was explored to increase the triterpenoids yield of HSD-IO01. In the 100 mL optimized liquid fermentation system, the hypha dry weight of HSD-IO01 was 1.7734 g, and the triterpenoids yield was 43.43 mg. Yields of triterpenoids increased after induction with ultrasound, microwave, or UV light, respectively. Among them, ultrasonic treatment had the most remarkable induction effect. The yield of triterpenoids would be increased to 68.35 mg (57.38 %) when the HSD-IO01 was treated by 100 W ultrasonic for 45 min. Establishing ultrasonic-assisted liquid fermentation technology could further promote the detailed development and comprehensive utilization of <em>I. obliquus</em> resources.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107025"},"PeriodicalIF":1.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108283","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 “Visualisation of Mycobacterium avium subsp. paratuberculosis in cultured cells, infected sheep and human tissue sections using fluorescent in situ hybridization (FISH)” [Journal of Microbiological Methods 224 (2024) 107001]","authors":"Neil Rayment ,&nbsp;Glenn Rhodes ,&nbsp;Barry Hudspith ,&nbsp;Valerie Hughes ,&nbsp;Francesca Chianini ,&nbsp;Gaurav Agrawal ,&nbsp;Tim J. Bull ,&nbsp;Roger Pickup ,&nbsp;Jeremy Sanderson","doi":"10.1016/j.mimet.2024.107024","DOIUrl":"10.1016/j.mimet.2024.107024","url":null,"abstract":"","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107024"},"PeriodicalIF":1.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224001362/pdfft?md5=5666f32d0def5b16e3f9ae5e390ae78a&pid=1-s2.0-S0167701224001362-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protocols to enable fluorescence microscopy of microbial interactions on living maize silks (style tissue)","authors":"Michelle E.H. Thompson,&nbsp;Manish N. Raizada","doi":"10.1016/j.mimet.2024.107027","DOIUrl":"10.1016/j.mimet.2024.107027","url":null,"abstract":"<div><p>There is interest in studying microbes that colonize maize silks (style tissue, critical for reproduction) including the fungal pathogen <em>Fusarium graminearum</em> (<em>Fg</em>) and its interactions with the microbiome and biocontrol agents. <em>In planta</em> imaging of these interactions on living silks using confocal fluorescence microscopy would provide key insights. However, newly discovered microbes have unknown effects on human health, and there are regulatory requirements to prevent the release of fluorescently tagged microbes into the environment. Therefore, the microbe infection, colonization, and interaction stages on silks prior to microscopy must be contained. At the same time, silk viability must be maintained and experiments conducted that are biologically relevant (e.g. silks should remain attached to the cob), yet the silk tissue must be accessible to the researcher (i.e. not within husk leaves) and allow for multiple replicates. Here we present methods that meet these five contrasting criteria. We tested these methods using <em>Fg</em> and four silk-derived bacterial endophytes. The endophytes were previously known to have anti-<em>Fg</em> activity in vitro, but <em>in planta</em> observations were lacking. In Method 1, a portion of the tip of a cob was dissected, and silks remained attached to the cob in a Petri dish. The cob was placed on a water agar disc to maintain hydration. DsRed-tagged bacteria and GFP-tagged <em>Fg</em> were inoculated onto the silks and incubated, allowing the two microbes to grow towards one another before staining with propidium iodide for confocal microscopy. A variation of the protocol was presented in Method 2, where detached silk segments were placed directly on water agar where they were inoculated with bacteria and <em>Fg</em> to promote dense colonization, and to allow for many replicates and interventions such as silk wounding. The bacterial endophytes were successfully observed colonizing <em>Fg</em> hyphae, silk trichomes, and entering silks via cut ends and wounds. These protocols can be used to study other silk-associated microbes including several globally important fungal pathogens that enter maize grain through silks.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107027"},"PeriodicalIF":1.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224001398/pdfft?md5=ceb70988dd3da6a0a097114fe12f9c40&pid=1-s2.0-S0167701224001398-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142098211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment and methodological evaluation of a rapid detection method for Cryptococcus neoformans and Cryptococcus gattii species complexes based on CRISPR-Cas12a technology","authors":"Runde Liu ,&nbsp;Yuqing Xing ,&nbsp;Jilu Shen","doi":"10.1016/j.mimet.2024.107026","DOIUrl":"10.1016/j.mimet.2024.107026","url":null,"abstract":"<div><h3>Purpose</h3><p>The opportunistic pathogens causing Cryptococcal meningitis are <em>Cryptococcus neoformans</em> and <em>Cryptococcus gattii</em> species complexes<em>.</em> At present, clinical detection methods for this condition include culture, ink staining, and cryptococcal antigen detection. In addition, enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and real-time quantitative PCR (qPCR) can be applied for the detection of <em>Cryptococcus</em>. Nevertheless, these methods cannot achieve point-of-care detection (POCT); thus, there is a pressing need to establish a fast, sensitive, and effective detection method.</p></div><div><h3>Methods</h3><p>Recombinase polymerase amplification (RPA) and clustered regularly spaced short palindromic repeat (CRISPR) techniques are effective tools for achieving rapid POCT. In this study, RPA was combined with CRISPR-Cas12a to establish a fast, sensitive, and specific detection method for cryptococcal meningitis.</p></div><div><h3>Results</h3><p>This study included RPA-Cas12a fluorescence detection and RPA-Cas12a immunochromatographic detection, which can be performed within 50 min. Moreover, the detection limit was as low as 10² copies/μL. Interestingly, the developed method demonstrated satisfactory specificity and no cross-reactivity with other fungi and bacteria. 36 clinical samples were tested, and the consistency between the test results and those obtained using the commonly used clinical culture method was 100 %.</p></div><div><h3>Conclusion</h3><p>In this study, a rapid detection method for <em>Cryptococcus neoformans</em> and <em>Cryptococcus gattii</em> species complexes was developed based on CRISPR-Cas12a technology, characterized by its high sensitivity and specificity, ease of use, and cost-effectiveness, making it suitable for on-site detection.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107026"},"PeriodicalIF":1.7,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055825","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":"Image cropping for malaria parasite detection on heterogeneous data","authors":"Ibrahim Mouazamou Laoualy Chaharou ,&nbsp;Ismail Lawani ,&nbsp;Theophile Dagba ,&nbsp;Jules Degila ,&nbsp;Habiboulaye Amadou Boubacar","doi":"10.1016/j.mimet.2024.107022","DOIUrl":"10.1016/j.mimet.2024.107022","url":null,"abstract":"<div><p>Malaria is a deadly disease of significant concern for the international community. It is an infectious disease caused by a <em>Plasmodium</em> spp. parasite and transmitted by the bite of an infected female <em>Anopheles</em> mosquito. The parasite multiplies in the liver and then destroys the person's red blood cells until it reaches the severe stage, leading to death. The most used tools for diagnosing this disease are the microscope and the rapid diagnostic test (RDT), which have limitations preventing control of the disease. Computer vision technologies present alternatives by providing the means for early detection of this disease before it reaches the severe stage, facilitating treatment and saving patients. In this article, we suggest deep learning methods for earlier and more accurate detection of malaria parasites with high generalization capabilities using microscopic images of blood smears from many heterogeneous patients. These techniques are based on an image preprocessing method that mitigates some of the challenges associated with the variety of red cell characteristics due to patient diversity and other artifacts present in the data.</p><p>For the study, we collected 65,970 microscopic images from 876 different patients to form a dataset of 33,007 images with a variety that enables us to create models with a high level of generalization. Three types of convolutional neural networks were used, namely Convolutional Neural Network (CNN), DenseNet, and LeNet-5, and the highest classification accuracy on the test data was 97.50% found with the DenseNet model.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107022"},"PeriodicalIF":1.7,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036051","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":"Mass production of Isaria fumosorosea pfu5 for community approach management of rugose spiraling whitefly in oil palm","authors":"A.R.N.S. Subbanna,&nbsp;P. Kalidas","doi":"10.1016/j.mimet.2024.107023","DOIUrl":"10.1016/j.mimet.2024.107023","url":null,"abstract":"<div><p>The management of an alien Rugose spiraling whitefly (RSW) on oil palm using a native entomopathogenic fungus, <em>Isaria fumosorosea</em> pfu5 necessitated community approach for pest management. Moreover, coverage of huge leaf biomass warrants massive multiplication of biocontrol agent. In this communication, a two-step strategy, first including pure culture production and the second including ready-to-use culture production of the biocontrol agent is disclosed. The production costs and success of this technology in RSW management of oil palm are also discussed.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107023"},"PeriodicalIF":1.7,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004480","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 the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients","authors":"Danfeng Zhang ,&nbsp;Ali Yang ,&nbsp;Kai Sheng ,&nbsp;Shuyu Fang ,&nbsp;Liang Zhou","doi":"10.1016/j.mimet.2024.107021","DOIUrl":"10.1016/j.mimet.2024.107021","url":null,"abstract":"<div><h3>Objective</h3><p>To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection.</p></div><div><h3>Methods</h3><p>We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics.</p></div><div><h3>Results</h3><p>The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107021"},"PeriodicalIF":1.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224001337/pdfft?md5=76785589bd399a508377d26423988ea4&pid=1-s2.0-S0167701224001337-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}