Journal of microbiological methods最新文献

{"title":"Application of integrated in vitro fecal cultivation and 16S rRNA gene sequencing for optimizing beneficial gut microbiota combinations","authors":"Emmanuel Hitayezu ,&nbsp;Intan Rizki Mauliasari ,&nbsp;Seonmi Yu ,&nbsp;Sung Hyun Moon ,&nbsp;Bo-Ram Cho ,&nbsp;Yoon-Han Kang ,&nbsp;Sang Kyun Lim ,&nbsp;Kwang Hyun Cha","doi":"10.1016/j.mimet.2025.107269","DOIUrl":"10.1016/j.mimet.2025.107269","url":null,"abstract":"<div><div>Obesity is a global health concern closely linked to changes in gut microbiota and other metabolic disorders. In this study, we used 16S rRNA gene amplicon sequencing to analyze the gut microbiota composition of normal and obese fecal samples. We further investigated the influence of a beneficial gut microbiota combination, consisting of <em>Phocaeicola vulgatus</em> KBL981, <em>Roseburia intestinalis</em> KBL982, and <em>Akkermansia muciniphila</em> KBL983, strains considered beneficial for obesity management, using <em>in vitro</em> feces cultivation. Results showed a significant difference between the microbiota composition of normal and obesity fecal samples, with the obesity group displaying lower diversity and higher levels of pathogenic <em>Shigella boydii</em> and inflammation-related <em>Bacteroides fragilis</em>. The ideal beneficial gut microbiota mixture (1:1:100) significantly enhanced microbial diversity, balanced the short-chain fatty acid ratio, promoted the growth of beneficial bacteria, and inhibited the growth of harmful obesity-related species. However, oversupplementation of beneficial microbiota reduced the microbial diversity and disrupted the microbial ecosystem. The current study demonstrates that a combined beneficial gut microbiota treatment can help manage obesity-related dysbiosis.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107269"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091897","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":"Prediction of carbon and nitrogen source preferences in microbial metabolism using protein sequence data","authors":"Zhenfeng Wang,&nbsp;Shuzhen Li,&nbsp;Haixia Pan,&nbsp;Yunlong Li,&nbsp;Xue Wang,&nbsp;Hao Zhou,&nbsp;Jiajia Shan","doi":"10.1016/j.mimet.2025.107266","DOIUrl":"10.1016/j.mimet.2025.107266","url":null,"abstract":"<div><div>Microbial precision cultivation technology holds significant application value in the field of environmental pollutant remediation. Precise quantification of microbial carbon and nitrogen requirements is critical for optimizing culture conditions and enhancing microbial growth and productivity. This study aims to explore the intrinsic relationship between microbial protein sequences and their specific nutritional requirements (e.g., the types of carbon and nitrogen sources as well as the optimal carbon-to‑nitrogen (<em>C/N</em>) ratio) using deep learning algorithms. A total of 432 microbial species and 61 culture media formulations were collected from authoritative databases, including Ensembl Bacteria, DSMZ, and NCBI Protein. For data analysis, microbial protein sequences were converted into high-dimensional numerical feature matrices using the Position-Specific Scoring Matrix (PSSM) and Pseudo Position-Specific Scoring Matrix (PsePSSM), followed by dimensionality reduction. Multiple machine learning algorithms were employed to construct predictive models for microbial <em>C/N</em> source utilization. Among the classification tasks, <em>C/N</em> ratio prediction performed best, with an accuracy of 99.60 %, followed by carbon source prediction with an accuracy of 82.76 % and nitrogen source prediction with an accuracy of 70.05 %, suggesting a strong correlation between microbial <em>C/N</em> requirements and their associated protein sequences. Furthermore, model interpretability was enhanced using the SHapley Additive exPlanations (SHAP) framework to analyze feature contributions. The primary contribution of this study lies in proposing an integrated framework that combines protein function annotation with sequence-based feature extraction for predicting microbial nutritional requirements, thereby offering new insights for optimizing microbial culture conditions.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107266"},"PeriodicalIF":1.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086172","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 ‘Development and validation of a multi-target TaqMan qPCR method for detection of Borrelia burgdorferi sensu lato’ [Journal of Microbiological Methods 222 (2024) 106941]","authors":"Sébastien Masséglia ,&nbsp;Magalie René-Martellet ,&nbsp;Maxime Rates ,&nbsp;Cecilia Hizo-Teufel ,&nbsp;Volker Fingerle ,&nbsp;Gabriele Margos ,&nbsp;Xavier Bailly","doi":"10.1016/j.mimet.2025.107253","DOIUrl":"10.1016/j.mimet.2025.107253","url":null,"abstract":"","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107253"},"PeriodicalIF":1.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080809","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":"Rapid detection of Staphylococcus pseudintermedius and Staphylococcus coagulans by combining fast VPCR with nucleic acid lateral flow immunoassay (NALFIA)","authors":"Ananda Chitra Murugesan,&nbsp;Kaviya Karthikeyan,&nbsp;Nivedita Jeyaraja,&nbsp;Pavithraa Damodaran,&nbsp;Karthik Raj Bodepogu Nandagopal,&nbsp;Anju Anil,&nbsp;Tirumurugaan Krishnaswamy Gopalan","doi":"10.1016/j.mimet.2025.107254","DOIUrl":"10.1016/j.mimet.2025.107254","url":null,"abstract":"<div><div>In dogs, pyoderma is primarily caused by coagulase-positive <em>Staphylococcus pseudintermedius</em> (SP)<em>, S. coagulans</em> (SC) and <em>S. aureus</em> (SA). Standard culture and biochemical methods for identifying these organisms are laborious, and potential misidentification is a possibility. Molecular methods, like PCR, are a viable alternative for early and accurate diagnosis of these organisms. In this study, we collected 83 swab samples from pyoderma cases of dogs and compared the sensitivity and specificity of the fast VPCR in conventional agarose gel electrophoresis with Nucleic Acid Lateral Flow Immunoassay (NALFIA) in detecting SP and SC. Bacterial DNA was extracted by a simple and quick NaOH lysis method. Primers targeting the <em>rodA</em> gene of SC and the <em>spsK</em> gene of SP were used in PCR, and labelled primers of the same genes were used in NALFIA. The limit of detection of SP and SC in VPCR with gel electrophoresis was 10² CFU/ml and 10⁴ CFU/ml for NALFIA. Though VPCR with gel electrophoresis was found to be more sensitive than NALFIA, it required specialized equipment like agarose gel electrophoretic apparatus with power pack and gel documentation system and carcinogenic ethidium bromide dye for detection of the bands in agarose gel. The VPCR, combined with NALFIA, offers sensitive and reliable detection of these bacteria in 45 min, even to the naked eye. The simplicity, portability, and cost-effectiveness of the NALFIA make them particularly suitable for resource-limited settings and point-of-care testing.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107254"},"PeriodicalIF":1.9,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075464","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":"Rapid detection of Fructilactobacillus sanfranciscensis in sourdough by lateral flow immunochromatographic assay","authors":"Kyoka Aiki ,&nbsp;Tatsuya Tominaga","doi":"10.1016/j.mimet.2025.107256","DOIUrl":"10.1016/j.mimet.2025.107256","url":null,"abstract":"<div><div>When maintaining sourdough by backslopping, there is a risk that the desired lactic acid bacteria (LAB) strain may be replaced by another. To rapidly monitor the proliferative status of the desired LAB, we developed a lateral flow immunochromatographic assay (LFIA) targeting <em>Fructilactobacillus sanfranciscensis</em>. We investigated the detection sensitivity of LFIA for 13 strains of <em>F. sanfranciscensis</em>. The limit of detection was 5–6 Log (cells/test). No positive result was obtained when the newly developed LFIA was applied against 51 strains other than <em>F. sanfranciscensis</em>, suggesting that it can specifically detect <em>F. sanfranciscensis</em>. To verify the practicality of LFIA, sourdough supplemented with <em>F. sanfranciscensis</em> and <em>Saccharomyces cerevisiae</em> as starters was passaged for 10 days at three different temperatures (23 °C, 30 °C, and 37 °C) with daily backslopping. The condition of these sourdoughs was monitored by pH measurements, yeast and LAB count surveys, amplicon analysis, and LFIA, and the methods were compared for their effectiveness as a management tool. Compared to the 23 °C-incubated samples, fewer <em>F. sanfranciscensis</em> cells were seen in the 30 °C-incubated samples, and the major LAB was replaced by putative <em>Pediococcus acidilactici</em> in the 37 °C-incubated samples. LFIA was successful in detecting both of these sourdough abnormalities. Lateral flow immunochromatographic assay could detect <em>F. sanfranciscensis</em> within 30 min, including the pretreatment step. The newly developed LFIA is expected to be a useful tool for artisan bakeries that want to provide customers with consistent quality sourdough bread every day.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107256"},"PeriodicalIF":1.9,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075440","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":"Comparison of several methods for preserving ETEC-S3 bacteriophage and its application to food","authors":"Natassja Zandria Pranata ,&nbsp;Diana Elizabeth Waturangi","doi":"10.1016/j.mimet.2025.107257","DOIUrl":"10.1016/j.mimet.2025.107257","url":null,"abstract":"<div><div>Food contamination caused by pathogenic bacteria is commonly controlled using chemical preservatives and physical preservation, which may negatively impact food quality. Bacteriophages are viruses that specifically infect bacteria, it can be used as an alternative antimicrobial agents. For further applications, phage need to be preserved. Phages show varying sensitivities to different preservation conditions, hence it is important to develop reliable long-term phage preservation methods. The ETEC-S3 phage, isolated from soil from previous study, showed lytic activity against <em>Enterotoxigenic Escherichia coli</em> (ETEC) as its original host. However, its preservation methods had not been investigated. This study investigates the effects of lyophilization and low-temperature storage, using trehalose, sucrose, or glycerol as stabilizing agents, on the titer stability of ETEC-S3, and evaluates their application in reducing ETEC populations in various food matrices. Low-temperature storage at −80 °C with sucrose or glycerol, and lyophilization with sucrose, effectively maintained ETEC-S3 stability, with titer reductions of 0.04, 0.08, and 0.26 log units, respectively, after 24 weeks. Lower temperatures performed more effective in preserving phage titers compare to higher temperatures. Stabilizers provided protection, which helped maintain phage viability throughout storage. Furthermore, lyophilized ETEC-S3 with the sucrose addition still performed high lytic activity after being applied to artificially contaminated various food samples. We found that food samples which high moisture content allowed easier phage diffusion, which resulted in higher bacterial reductions. The highest bacterial reductions were observed in tofu at 28 °C (99.86 %), followed by pasteurized milk at the same temperature (94.37 %). These findings indicate the potential preservation condition of ETEC-S3 as a natural food preservative.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107257"},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064950","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 and immunological insights into recombinant/subunit vaccines against avian coccidiosis","authors":"Shagufta Iqbal ,&nbsp;Syed Tanveer ,&nbsp;Idrees Mehraj Allaie ,&nbsp;Yasmeena Jan ,&nbsp;Shahana Tramboo ,&nbsp;Nazima Maqbool","doi":"10.1016/j.mimet.2025.107255","DOIUrl":"10.1016/j.mimet.2025.107255","url":null,"abstract":"<div><div>Coccidiosis is considered as one of the most debilitating diseases responsible for immense economic losses in commercial poultry production. Despite the development of ample number of anticoccidial drugs and vaccines, this disease still remains a major constraint for the poultry production due to emergence of anticoccidial drug resistance and associated limitations with the vaccine administration. Alternative strategies are prerequisite to lessen the effects of coccidiosis on poultry industry. The use of immunomodulators and recent improvements in the generation of recombinant vaccines appear as potential control strategies. To manage the disease, poultry scientists nowadays are interested in enhancing host immunity and promising method of coccidiosis control seems to be the development of alternative vaccination tactics, such as recombinant immunization with the proper adjuvants. Immunomodulation might offer a strong mechanism to improve the host's resistance to disease, and it appears achievable to lessen the financial burden caused by coccidiosis. This review explores and highlights the potential of recombinant/subunit vaccines, along with immunomodulators and adjuvants, as promising alternatives for the effective control of coccidiosis in poultry.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107255"},"PeriodicalIF":1.9,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048179","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":"Adapting a 96-well liquid culture assay to a colonial growth confirmation assay utilizing a 3D printed guide-frame system for a 96-well replicator","authors":"Micah A. Lewis ,&nbsp;Eric S. Adams ,&nbsp;Elizabeth A. McMillan","doi":"10.1016/j.mimet.2025.107246","DOIUrl":"10.1016/j.mimet.2025.107246","url":null,"abstract":"<div><div>Some bacteria are not suited to assays requiring visual growth in broth; it may be useful to transfer cells from these assays to solid media to confirm growth. Here, we present a novel guide-frame system for accurate transfer of a 96-well assay to solid agar using a replicator.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107246"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040516","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":"Protoplasting of Aspergillus niger using Trichoderma harzianum culture medium after growth on cell walls of the target fungus","authors":"Juan Pablo Morán Torres,&nbsp;Han A.B. Wösten,&nbsp;Luis G. Lugones","doi":"10.1016/j.mimet.2025.107252","DOIUrl":"10.1016/j.mimet.2025.107252","url":null,"abstract":"<div><div>Protoplast yield from <em>Aspergillus niger</em> can be low when using commercial lytic enzymes from <em>Trichoderma harzianum</em>. This study shows that the culture medium of <em>T. harzianum</em> after growth on <em>A. niger</em> cell walls is much more effective in protoplasting than commercial lysing enzymes.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107252"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040519","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":"In vivo Fusarium virulence and efficacy of voriconazole in a Galleria mellonella model of invasive fusariosis","authors":"Claire Cottrel ,&nbsp;Pierre Vermeulen ,&nbsp;Anne-Lyse Babin ,&nbsp;Jean-Pol Frippiat ,&nbsp;Marie Machouart ,&nbsp;Guillaume Gauchotte ,&nbsp;Anne Debourgogne","doi":"10.1016/j.mimet.2025.107250","DOIUrl":"10.1016/j.mimet.2025.107250","url":null,"abstract":"<div><div><em>Fusarium</em> species are transkingdom pathogens involved in invasive fungal infections in immunocompromised patients. Despite high minimum inhibitory concentrations (MICs), voriconazole (VRZ) is the antifungal recommended as a first-line treatment for this infection.</div><div>The objective of this study was to use larvae of the invertebrate <em>Galleria mellonella</em> to describe invasive <em>Fusarium</em> infection, evaluate the virulence profiles of a set of strains and determine the response of <em>Fusarium</em> to antifungal treatment.</div><div>After characterization of the fungal infection in <em>G. mellonella</em> threw histological analysis, fungal burden by qPCR and hemocyte counts, larval survival was evaluated after injection of <em>Fusarium solani</em> species complex (<em>FSSC</em>) conidia, with or without therapeutic VRZ injection.</div><div>In the described model, an increase in fungal burden was observed in relation to the inoculum size and duration of infection, which was associated with an increase in hemocyte counts. Histopathological examination revealed the invasive nature of the filamentous fungus, along with a nodulation process at the highest inoculum concentrations. Mortality and consequently virulence varied according to the strains under investigation. However, a subgroup analysis by VRZ MIC and strain origin revealed slightly increased mortality for the strains most susceptible to VRZ, as well as for the strains of clinical origin in infected larvae. In this model, VRZ presented <em>in vivo</em> activity and post-infection treatment decreased larval mortality.</div><div>The originality of this study lies in the integrated use of the invertebrate model <em>G. mellonella</em>, which is not employed solely for survival analysis, but comprehensively as an <em>in vivo</em> model of invasive fungal infection, with infection monitoring performed through multiple technical approaches.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"237 ","pages":"Article 107250"},"PeriodicalIF":1.9,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145023418","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}