Yasaman Ahmadi, Yejiong Yu, Zhanfeng Cui, Wei E. Huang, Monique I. Andersson
{"title":"Clinical Validation of Loop-Mediated Isothermal Amplification Assays for the Rapid Detection of Neisseria gonorrhoeae and Chlamydia trachomatis","authors":"Yasaman Ahmadi, Yejiong Yu, Zhanfeng Cui, Wei E. Huang, Monique I. Andersson","doi":"10.1111/1751-7915.70214","DOIUrl":"https://doi.org/10.1111/1751-7915.70214","url":null,"abstract":"<p><i>Neisseria gonorrhoeae</i> (GC) and <i>Chlamydia trachomatis</i> (CT) are the predominant causes of bacterial sexually transmitted diseases. While nucleic acid amplification testing (NAATs), primarily polymerase chain reaction (PCR), is regarded as the gold standard for identifying these two pathogens, it usually takes a prolonged turnaround time and requires sophisticated equipment with considerable expense. In this study, we developed novel loop-mediated isothermal amplification (LAMP) assays for rapid detection (< 30 min) of GC and CT in clinical urine and swab specimens. We analysed 208 clinical samples with three different pre-treatment techniques including heating inactivation, centrifugation, and DNA extraction. LAMP results were compared with clinical results from the FDA-approved BD ProbeTec ET assay. After heating inactivation, LAMP detected merely 41% and 65% of BD-identified GC- and CT-positive samples, respectively. Introducing centrifugation as an affordable and rapid pre-treatment step increased detection rates to 81% and 91% for GC and CT, respectively. DNA extraction further enhanced the detection rates to 96% and 95% for GC- and CT-LAMP, respectively. All these LAMP assays exhibited clinical specificity of ≥ 98%, underscoring the specificity of the chosen target genes (the <i>porA</i> pesudogene for GC and the <i>ftsK</i> gene for CT). Discrepant samples were verified by real-time PCR; results were consistent with our LAMP findings. The overall LAMP performance met the WHO criteria for sensitivity and specificity for GC/CT point-of-care testing.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144914865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prioritising Microbiology in Secondary Education Addresses Emerging Scientific-Social-Educational Challenges and Competency Needs","authors":"Lara Amorim, Conceição Santos, Kenneth Timmis","doi":"10.1111/1751-7915.70224","DOIUrl":"https://doi.org/10.1111/1751-7915.70224","url":null,"abstract":"<p>This paper explores the potential of microbiology education at the secondary school level as a catalyst for enhancing both science, technology, engineering and mathematics (STEM) literacy and essential 21st-century competencies. As an inherently interdisciplinary field, microbiology offers an effective platform to develop scientific and technological knowledge while cultivating broader competencies, such as emotional intelligence, creativity and critical thinking, as outlined by UNESCO (UNESCO, 2016). Scientific, societal and educational (SSE) challenges for the next decade are interlinked, and many of these trans-dimensional issues require a solid foundation in biology and microbiology. Thus, research and education must evolve in step with these trends. Despite growing advocacy for microbiology in high school curricula, a significant gap remains in understanding how its teaching aligns with these broader developmental goals. This disconnection is particularly evident in Europe, where STEM engagement among youth remains low. As an experimental and accessible science, microbiology offers unique pedagogical strategies that address not only the cognitive dimensions of STEM but also the skills and attitudes needed for a complex, digital and interdependent world. By integrating microbiology into secondary education, teachers can bridge the gap between scientific literacy and future readiness, empowering students to build a generation capable of shaping a sustainable and innovative future. In this discourse, we describe examples of topics and strategies that could be implemented at the secondary education level, as well as at other educational levels, including university.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144914977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jair J. Pineda-Pineda, Jesús Muñoz-Rojas, Yolanda E. Morales-García, Esperanza Trenado-Sánchez, José M. Sigarreta
{"title":"Quantification and Determination of Compatible Bacterial Consortia","authors":"Jair J. Pineda-Pineda, Jesús Muñoz-Rojas, Yolanda E. Morales-García, Esperanza Trenado-Sánchez, José M. Sigarreta","doi":"10.1111/1751-7915.70198","DOIUrl":"https://doi.org/10.1111/1751-7915.70198","url":null,"abstract":"<p>The sustainable use of terrestrial ecosystems is crucial to ensure food security for future generations, and the formulation of plant growth–promoting bacterial consortia has proven useful not only in sustainable agriculture but also in applications such as phytopathogen biocontrol, bioremediation of contaminated soils and waters, biofertilization, organic waste degradation, and the production of industrially relevant enzymes. In this work, we developed a mathematical model to quantify and identify antagonism-free consortia based on double-agar-layer assays with 20 and 33 bacterial strains from independent studies. Simultaneously, we implemented a graph-based geometric model to analyse their topological properties and defined an index to quantify feasible consortia. The proposed methods were experimentally validated, identifying 36,851 and 376,126 subsets of compatible strains, for 20 and 33 strains, respectively. These subsets have the potential to promote plant growth and other biotechnological functions, thus providing a scalable tool for the management of agricultural resources, environmental restoration, and the design of sustainable biotechnological practices.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prioritising Microbiology in Secondary Education Addresses Emerging Scientific-Social-Educational Challenges and Competency Needs","authors":"Lara Amorim, Conceição Santos, Kenneth Timmis","doi":"10.1111/1751-7915.70224","DOIUrl":"https://doi.org/10.1111/1751-7915.70224","url":null,"abstract":"<p>This paper explores the potential of microbiology education at the secondary school level as a catalyst for enhancing both science, technology, engineering and mathematics (STEM) literacy and essential 21st-century competencies. As an inherently interdisciplinary field, microbiology offers an effective platform to develop scientific and technological knowledge while cultivating broader competencies, such as emotional intelligence, creativity and critical thinking, as outlined by UNESCO (UNESCO, 2016). Scientific, societal and educational (SSE) challenges for the next decade are interlinked, and many of these trans-dimensional issues require a solid foundation in biology and microbiology. Thus, research and education must evolve in step with these trends. Despite growing advocacy for microbiology in high school curricula, a significant gap remains in understanding how its teaching aligns with these broader developmental goals. This disconnection is particularly evident in Europe, where STEM engagement among youth remains low. As an experimental and accessible science, microbiology offers unique pedagogical strategies that address not only the cognitive dimensions of STEM but also the skills and attitudes needed for a complex, digital and interdependent world. By integrating microbiology into secondary education, teachers can bridge the gap between scientific literacy and future readiness, empowering students to build a generation capable of shaping a sustainable and innovative future. In this discourse, we describe examples of topics and strategies that could be implemented at the secondary education level, as well as at other educational levels, including university.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jair J. Pineda-Pineda, Jesús Muñoz-Rojas, Yolanda E. Morales-García, Esperanza Trenado-Sánchez, José M. Sigarreta
{"title":"Quantification and Determination of Compatible Bacterial Consortia","authors":"Jair J. Pineda-Pineda, Jesús Muñoz-Rojas, Yolanda E. Morales-García, Esperanza Trenado-Sánchez, José M. Sigarreta","doi":"10.1111/1751-7915.70198","DOIUrl":"https://doi.org/10.1111/1751-7915.70198","url":null,"abstract":"<p>The sustainable use of terrestrial ecosystems is crucial to ensure food security for future generations, and the formulation of plant growth–promoting bacterial consortia has proven useful not only in sustainable agriculture but also in applications such as phytopathogen biocontrol, bioremediation of contaminated soils and waters, biofertilization, organic waste degradation, and the production of industrially relevant enzymes. In this work, we developed a mathematical model to quantify and identify antagonism-free consortia based on double-agar-layer assays with 20 and 33 bacterial strains from independent studies. Simultaneously, we implemented a graph-based geometric model to analyse their topological properties and defined an index to quantify feasible consortia. The proposed methods were experimentally validated, identifying 36,851 and 376,126 subsets of compatible strains, for 20 and 33 strains, respectively. These subsets have the potential to promote plant growth and other biotechnological functions, thus providing a scalable tool for the management of agricultural resources, environmental restoration, and the design of sustainable biotechnological practices.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144914863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasaman Ahmadi, Yejiong Yu, Zhanfeng Cui, Wei E. Huang, Monique I. Andersson
{"title":"Clinical Validation of Loop-Mediated Isothermal Amplification Assays for the Rapid Detection of Neisseria gonorrhoeae and Chlamydia trachomatis","authors":"Yasaman Ahmadi, Yejiong Yu, Zhanfeng Cui, Wei E. Huang, Monique I. Andersson","doi":"10.1111/1751-7915.70214","DOIUrl":"https://doi.org/10.1111/1751-7915.70214","url":null,"abstract":"<p><i>Neisseria gonorrhoeae</i> (GC) and <i>Chlamydia trachomatis</i> (CT) are the predominant causes of bacterial sexually transmitted diseases. While nucleic acid amplification testing (NAATs), primarily polymerase chain reaction (PCR), is regarded as the gold standard for identifying these two pathogens, it usually takes a prolonged turnaround time and requires sophisticated equipment with considerable expense. In this study, we developed novel loop-mediated isothermal amplification (LAMP) assays for rapid detection (< 30 min) of GC and CT in clinical urine and swab specimens. We analysed 208 clinical samples with three different pre-treatment techniques including heating inactivation, centrifugation, and DNA extraction. LAMP results were compared with clinical results from the FDA-approved BD ProbeTec ET assay. After heating inactivation, LAMP detected merely 41% and 65% of BD-identified GC- and CT-positive samples, respectively. Introducing centrifugation as an affordable and rapid pre-treatment step increased detection rates to 81% and 91% for GC and CT, respectively. DNA extraction further enhanced the detection rates to 96% and 95% for GC- and CT-LAMP, respectively. All these LAMP assays exhibited clinical specificity of ≥ 98%, underscoring the specificity of the chosen target genes (the <i>porA</i> pesudogene for GC and the <i>ftsK</i> gene for CT). Discrepant samples were verified by real-time PCR; results were consistent with our LAMP findings. The overall LAMP performance met the WHO criteria for sensitivity and specificity for GC/CT point-of-care testing.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 9","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing the Potential of mRNA Vaccines Against Infectious Diseases","authors":"Nouran Rezk, Siobhán McClean","doi":"10.1111/1751-7915.70212","DOIUrl":"https://doi.org/10.1111/1751-7915.70212","url":null,"abstract":"<p>mRNA vaccines have emerged as promising alternatives to conventional vaccines because of their flexible design, high immunogenicity, favourable safety profile, efficacy and potential for rapid clinical development. The accelerated development of mRNA vaccines during the COVID-19 pandemic has revolutionised the field of vaccinology, highlighting their potential for combating emerging infectious diseases. The mRNA platforms can induce robust humoral as well as CD4+ and CD8+ T-cell-mediated immunity, offering broader protection than subunit protein vaccines. Consequently, they have been extensively studied against a wide range of viral, bacterial and parasitic infections, although the development of mRNA vaccines against bacterial and parasitic infections has lagged behind those targeting viruses. This review highlights recent studies on mRNA vaccine development and applications against a wide range of infectious diseases including non-COVID viral infections, bacterial pathogens such as Mycobacteria or <i>Pseudomonas aeruginosa</i> and parasitic infections, including malaria. Moreover, it discusses key optimisation strategies and highlights candidates that have progressed to clinical trials, and the current challenges in enhancing immunogenicity and improving delivery systems.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 8","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144894159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing the Potential of mRNA Vaccines Against Infectious Diseases","authors":"Nouran Rezk, Siobhán McClean","doi":"10.1111/1751-7915.70212","DOIUrl":"https://doi.org/10.1111/1751-7915.70212","url":null,"abstract":"<p>mRNA vaccines have emerged as promising alternatives to conventional vaccines because of their flexible design, high immunogenicity, favourable safety profile, efficacy and potential for rapid clinical development. The accelerated development of mRNA vaccines during the COVID-19 pandemic has revolutionised the field of vaccinology, highlighting their potential for combating emerging infectious diseases. The mRNA platforms can induce robust humoral as well as CD4+ and CD8+ T-cell-mediated immunity, offering broader protection than subunit protein vaccines. Consequently, they have been extensively studied against a wide range of viral, bacterial and parasitic infections, although the development of mRNA vaccines against bacterial and parasitic infections has lagged behind those targeting viruses. This review highlights recent studies on mRNA vaccine development and applications against a wide range of infectious diseases including non-COVID viral infections, bacterial pathogens such as Mycobacteria or <i>Pseudomonas aeruginosa</i> and parasitic infections, including malaria. Moreover, it discusses key optimisation strategies and highlights candidates that have progressed to clinical trials, and the current challenges in enhancing immunogenicity and improving delivery systems.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 8","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144894346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unlocking the Synthetic Potential of Yarrowia lipolytica: Innovating Gene Expression Tools","authors":"Xiaoqin Liu, Qingsheng Qi","doi":"10.1111/1751-7915.70185","DOIUrl":"https://doi.org/10.1111/1751-7915.70185","url":null,"abstract":"<p><i>Yarrowia lipolytica</i>, with its robust lipid metabolism capabilities, efficient secretion system and generally recognised as safe (GRAS) status, has become a highly promising microbial chassis in synthetic biology. However, compared with model microorganisms such as <i>Saccharomyces cerevisiae</i>, the underdevelopment of gene expression tools in <i>Y. lipolytica</i> has become a critical bottleneck, limiting its industrial application. Currently, its core tools face two critical challenges: promoters with limited dynamic regulatory capacity, leading to metabolic flux imbalance; and gene editing systems plagued by low efficiency and poor multiplex compatibility. This opinion article focuses on these two pivotal directions to dissect their technical bottlenecks and propose innovative solutions: constructing dynamic transcriptional regulatory modules through machine learning guided design and synthetic biology approaches and developing orthogonal CRISPR systems and multiplex editing platforms.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 8","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144891568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unlocking the Synthetic Potential of Yarrowia lipolytica: Innovating Gene Expression Tools","authors":"Xiaoqin Liu, Qingsheng Qi","doi":"10.1111/1751-7915.70185","DOIUrl":"https://doi.org/10.1111/1751-7915.70185","url":null,"abstract":"<p><i>Yarrowia lipolytica</i>, with its robust lipid metabolism capabilities, efficient secretion system and generally recognised as safe (GRAS) status, has become a highly promising microbial chassis in synthetic biology. However, compared with model microorganisms such as <i>Saccharomyces cerevisiae</i>, the underdevelopment of gene expression tools in <i>Y. lipolytica</i> has become a critical bottleneck, limiting its industrial application. Currently, its core tools face two critical challenges: promoters with limited dynamic regulatory capacity, leading to metabolic flux imbalance; and gene editing systems plagued by low efficiency and poor multiplex compatibility. This opinion article focuses on these two pivotal directions to dissect their technical bottlenecks and propose innovative solutions: constructing dynamic transcriptional regulatory modules through machine learning guided design and synthetic biology approaches and developing orthogonal CRISPR systems and multiplex editing platforms.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 8","pages":""},"PeriodicalIF":5.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144891601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}