Microbial Biotechnology最新文献_第5页

A novel DNA damage detection method based on a distinct DNA damage response system 基于独特 DNA 损伤反应系统的新型 DNA 损伤检测方法

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-17 DOI: 10.1111/1751-7915.70008

Shitong Zhong, Shuang Song, Linjia Wang, Yufeng Liu, Hong Xu, Liangyan Wang, Huizhi Lu, Yuejin Hua

{"title":"A novel DNA damage detection method based on a distinct DNA damage response system","authors":"Shitong Zhong, Shuang Song, Linjia Wang, Yufeng Liu, Hong Xu, Liangyan Wang, Huizhi Lu, Yuejin Hua","doi":"10.1111/1751-7915.70008","DOIUrl":"https://doi.org/10.1111/1751-7915.70008","url":null,"abstract":"DNA damage occurs when cells encounter exogenous and endogenous stresses such as long periods of desiccation, ionizing radiation and genotoxic chemicals. Efforts have been made to detect DNA damage in vivo and in vitro to characterize or quantify the damage level. It is well accepted that single-stranded DNA (ssDNA) is one of the important byproducts of DNA damage to trigger the downstream regulation. A recent study has revealed that PprI efficiently recognizes ssDNA and cleaves DdrO at a specific site on the cleavage site region (CSR) loop in the presence of ssDNA, which enables the radiation resistance of Deinococcus. Leveraging this property, we developed a quantitative DNA damage detection method in vitro based on fluorescence resonance energy transfer (FRET). DdrO protein was fused with eYFP and eCFP on the N-terminal and C-terminal respectively, between which the FRET efficiency serves as an indicator of cleavage efficiency as well as the concentration of ssDNA. The standard curve between the concentration of ssDNA and the FRET efficiency was constructed, and application examples were tested, validating the effectiveness of this method.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142244527","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}

引用次数: 0

Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi 用于增强丝状真菌异源表达的基于 AMA1 的新一代质粒

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-14 DOI: 10.1111/1751-7915.70010

Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi

{"title":"Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi","authors":"Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi","doi":"10.1111/1751-7915.70010","DOIUrl":"https://doi.org/10.1111/1751-7915.70010","url":null,"abstract":"Episomal AMA1-based plasmids are increasingly used for expressing biosynthetic pathways and CRISPR/Cas systems in filamentous fungi cell factories due to their high transformation efficiency and multicopy nature. However, the gene expression from AMA1 plasmids has been observed to be highly heterogeneous in growing mycelia. To overcome this limitation, here we developed next-generation AMA1-based plasmids that ensure homogeneous and strong expression. We achieved this by evaluating various degradation tags fused to the auxotrophic marker gene on the AMA1 plasmid, which introduces a more stringent selection pressure throughout multicellular fungal growth. With these improved plasmids, we observed in Aspergillus nidulans a 5-fold increase in the expression of a fluorescent reporter, a doubling in the efficiency of a CRISPRa system for genome mining, and a up to a 10-fold increase in the production of heterologous natural product metabolites. This strategy has the potential to be applied to diverse filamentous fungi.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233122","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}

引用次数: 0

Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi 用于增强丝状真菌异源表达的基于 AMA1 的新一代质粒

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-14 DOI: 10.1111/1751-7915.70010

Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi

{"title":"Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi","authors":"Indra Roux, Clara Woodcraft, Nicolau Sbaraini, Amy Pepper, Emily Wong, Joe Bracegirdle, Yit-Heng Chooi","doi":"10.1111/1751-7915.70010","DOIUrl":"https://doi.org/10.1111/1751-7915.70010","url":null,"abstract":"Episomal AMA1-based plasmids are increasingly used for expressing biosynthetic pathways and CRISPR/Cas systems in filamentous fungi cell factories due to their high transformation efficiency and multicopy nature. However, the gene expression from AMA1 plasmids has been observed to be highly heterogeneous in growing mycelia. To overcome this limitation, here we developed next-generation AMA1-based plasmids that ensure homogeneous and strong expression. We achieved this by evaluating various degradation tags fused to the auxotrophic marker gene on the AMA1 plasmid, which introduces a more stringent selection pressure throughout multicellular fungal growth. With these improved plasmids, we observed in Aspergillus nidulans a 5-fold increase in the expression of a fluorescent reporter, a doubling in the efficiency of a CRISPRa system for genome mining, and a up to a 10-fold increase in the production of heterologous natural product metabolites. This strategy has the potential to be applied to diverse filamentous fungi.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233209","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}

引用次数: 0

A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi 基于荧光素酶的新型报告工具，用于监测丝状真菌中碳代谢抑制的动态变化

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-13 DOI: 10.1111/1751-7915.70012

Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz

{"title":"A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi","authors":"Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz","doi":"10.1111/1751-7915.70012","DOIUrl":"https://doi.org/10.1111/1751-7915.70012","url":null,"abstract":"Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in Neurospora crassa, Aspergillus niger and Aspergillus nidulans over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231039","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}

引用次数: 0

A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi 基于荧光素酶的新型报告工具，用于监测丝状真菌中碳代谢抑制的动态变化

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-13 DOI: 10.1111/1751-7915.70012

Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz

{"title":"A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi","authors":"Marcel Rüllke, Franziska Meyer, Kevin Schmitz, Hannes Blase, Elisabeth Tamayo, J. Philipp Benz","doi":"10.1111/1751-7915.70012","DOIUrl":"https://doi.org/10.1111/1751-7915.70012","url":null,"abstract":"Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in Neurospora crassa, Aspergillus niger and Aspergillus nidulans over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231040","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}

引用次数: 0

Entrapment of antimicrobial compounds in a metal matrix for crop protection 金属基质中的抗菌化合物用于作物保护

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-13 DOI: 10.1111/1751-7915.70005

Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka

{"title":"Entrapment of antimicrobial compounds in a metal matrix for crop protection","authors":"Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka","doi":"10.1111/1751-7915.70005","DOIUrl":"https://doi.org/10.1111/1751-7915.70005","url":null,"abstract":"Agricultural yields are often limited by damage caused by pathogenic microorganisms, including plant-pathogenic bacteria. The chemical control options to cope with bacterial diseases in agriculture are limited, predominantly relying on copper-based products. These compounds, however, possess limited efficacy. Therefore, there is an urgent need to develop novel technologies to manage bacterial plant diseases and reduce food loss. In this study, a new antimicrobial agent was developed using a doping method that entraps small bioactive organic molecules inside copper as the metal matrix. The food preservative agent lauroyl arginate ethyl ester (ethyl lauroyl arginate; LAE) was chosen as the doped organic compound. The new composites were termed LAE@[Cu]. Bactericidal assays against Acidovorax citrulli, a severe plant pathogen, revealed that LAE and copper in the composites possess a synergistic interaction as compared with each component individually. LAE@[Cu] composites were further characterised in terms of chemical properties and in planta assays demonstrated their potential for further development as crop protection agents.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231038","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}

引用次数: 0

Entrapment of antimicrobial compounds in a metal matrix for crop protection 金属基质中的抗菌化合物用于作物保护

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-13 DOI: 10.1111/1751-7915.70005

Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka

{"title":"Entrapment of antimicrobial compounds in a metal matrix for crop protection","authors":"Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka","doi":"10.1111/1751-7915.70005","DOIUrl":"https://doi.org/10.1111/1751-7915.70005","url":null,"abstract":"Agricultural yields are often limited by damage caused by pathogenic microorganisms, including plant-pathogenic bacteria. The chemical control options to cope with bacterial diseases in agriculture are limited, predominantly relying on copper-based products. These compounds, however, possess limited efficacy. Therefore, there is an urgent need to develop novel technologies to manage bacterial plant diseases and reduce food loss. In this study, a new antimicrobial agent was developed using a doping method that entraps small bioactive organic molecules inside copper as the metal matrix. The food preservative agent lauroyl arginate ethyl ester (ethyl lauroyl arginate; LAE) was chosen as the doped organic compound. The new composites were termed LAE@[Cu]. Bactericidal assays against Acidovorax citrulli, a severe plant pathogen, revealed that LAE and copper in the composites possess a synergistic interaction as compared with each component individually. LAE@[Cu] composites were further characterised in terms of chemical properties and in planta assays demonstrated their potential for further development as crop protection agents.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231041","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}

引用次数: 0

Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes 从海洋卤虫（Haloarchaea Haloferax marinum）中提取的细菌黄素：LPS 处理的 C2C12 肌细胞中的成分鉴定、抗氧化活性和抗萎缩作用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-12 DOI: 10.1111/1751-7915.70009

Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo

{"title":"Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes","authors":"Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo","doi":"10.1111/1751-7915.70009","DOIUrl":"https://doi.org/10.1111/1751-7915.70009","url":null,"abstract":"Carotenoids are natural pigments utilized as colourants and antioxidants across food, pharmaceutical and cosmetic industries. They exist in carbon chain lengths of C30, C40, C45 and C50, with C40 variants being the most common. Bacterioruberin (BR) and its derivatives are part of the less common C50 carotenoid group, synthesized primarily by halophilic archaea. This study analysed the compositional characteristics of BR extract (BRE) isolated from ‘Haloferax marinum’ MBLA0078, a halophilic archaeon isolated from seawater near Yeoungheungdo Island in the Republic of Korea, and investigated its antioxidant activity and protective effect on lipopolysaccharide (LPS)-induced C2C12 myotube atrophy. The main components of BRE included all-trans-BR, monoanhydrobacterioruberin, 2-isopentenyl-3,4-dehydrorhodopin and all-trans-bisanhydrobacterioruberin. BRE exhibited higher antioxidant activity and DNA nicking protection activity than other well-known C40 carotenoids, such as β-carotene, lycopene and astaxanthin. In C2C12 myotubes, LPS treatment led to a reduction in myotube diameter and number, as well as the hypertranscription of the muscle-specific ubiquitin ligase MAFbx and MuRF1. BRE mitigated these changes by activating the Akt/mTOR pathway. Furthermore, BRE abolished the elevated cellular reactive oxygen species levels and the inflammation response induced by LPS. This study demonstrated that ‘Hfx. marinum’ is an excellent source of natural microbial C50 carotenoids with strong antioxidant capacity and may offer potential protective effects against muscle atrophy.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174196","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}

引用次数: 0

Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes 从海洋卤虫（Haloarchaea Haloferax marinum）中提取的细菌黄素：LPS 处理的 C2C12 肌细胞中的成分鉴定、抗氧化活性和抗萎缩作用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-12 DOI: 10.1111/1751-7915.70009

Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo

{"title":"Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes","authors":"Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo","doi":"10.1111/1751-7915.70009","DOIUrl":"https://doi.org/10.1111/1751-7915.70009","url":null,"abstract":"Carotenoids are natural pigments utilized as colourants and antioxidants across food, pharmaceutical and cosmetic industries. They exist in carbon chain lengths of C30, C40, C45 and C50, with C40 variants being the most common. Bacterioruberin (BR) and its derivatives are part of the less common C50 carotenoid group, synthesized primarily by halophilic archaea. This study analysed the compositional characteristics of BR extract (BRE) isolated from ‘Haloferax marinum’ MBLA0078, a halophilic archaeon isolated from seawater near Yeoungheungdo Island in the Republic of Korea, and investigated its antioxidant activity and protective effect on lipopolysaccharide (LPS)-induced C2C12 myotube atrophy. The main components of BRE included all-trans-BR, monoanhydrobacterioruberin, 2-isopentenyl-3,4-dehydrorhodopin and all-trans-bisanhydrobacterioruberin. BRE exhibited higher antioxidant activity and DNA nicking protection activity than other well-known C40 carotenoids, such as β-carotene, lycopene and astaxanthin. In C2C12 myotubes, LPS treatment led to a reduction in myotube diameter and number, as well as the hypertranscription of the muscle-specific ubiquitin ligase MAFbx and MuRF1. BRE mitigated these changes by activating the Akt/mTOR pathway. Furthermore, BRE abolished the elevated cellular reactive oxygen species levels and the inflammation response induced by LPS. This study demonstrated that ‘Hfx. marinum’ is an excellent source of natural microbial C50 carotenoids with strong antioxidant capacity and may offer potential protective effects against muscle atrophy.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174195","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}

引用次数: 0

Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media 在固体和液体培养基中利用 MALDI-TOF MS 进行脓肿分枝杆菌亚种鉴定的机器学习贡献

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-10 DOI: 10.1111/1751-7915.14545

Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry

{"title":"Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media","authors":"Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry","doi":"10.1111/1751-7915.14545","DOIUrl":"https://doi.org/10.1111/1751-7915.14545","url":null,"abstract":"Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170091","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}

引用次数: 0