Microbial Biotechnology最新文献

{"title":"Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation","authors":"Yutong Yin,&nbsp;Chang Liu,&nbsp;Xianglin Ji,&nbsp;Yun Wang,&nbsp;Juthathip Mongkolsapaya,&nbsp;Gavin R. Screaton,&nbsp;Zhanfeng Cui,&nbsp;Wei E. Huang","doi":"10.1111/1751-7915.70109","DOIUrl":"https://doi.org/10.1111/1751-7915.70109","url":null,"abstract":"<p>The COVID-19 pandemic has caused unparalleled impacts on global social dynamics, healthcare systems and economies, highlighting the urgent need for effective interventions to address current challenges and future pandemic preparedness. This study introduces a novel virus neutralisation platform based on SimCells (~1 μm) and mini-SimCells (100–200 nm), which are chromosome-free and non-replicating bacteria from an LPS-free <i>Escherichia coli</i> strain (ClearColi). SimCells and mini-SimCells were engineered to display nanobodies on their surface, specifically targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein – a critical immunogenic fragment essential for viral entry into host cells. It was demonstrated that nanobody-expressing SimCells achieved over 90% blocking efficiency against synthesised RBD from both the original Wuhan and the B.1.351 (Beta) variant using competitive enzyme-linked immunosorbent assay (ELISA) assay. More importantly, live virus neutralisation assays demonstrated that NB6 nanobody-presenting mini-SimCells effectively neutralised the live SARS-CoV-2 Victoria variant with an IC50 of 2.95 × 10⁹ ± 1.40 × 10⁸ mini-SimCells/mL. Similarly, VE nanobody-presenting mini-SimCells effectively neutralised the B.1.351 (Beta) variant of the SARS-CoV-2 virus with an IC50 of 5.68 × 10⁹ ± 9.94 × 10⁸ mini-SimCells/mL. The mini-SimCells successfully protected Vero cells, a cell line derived from the kidney of an African green monkey, from infection by the live virus of SARS-CoV-2 and its variants. These results suggest that SimCell-based neutralisation offers a promising strategy for the prevention and treatment of SARS-CoV-2, and potentially other viral infections.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554454","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":"Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability","authors":"Ruole Chen,&nbsp;Yuhao You,&nbsp;Yanchao Liu,&nbsp;Xin Sun,&nbsp;Tianyue Ma,&nbsp;Xingzhen Lao,&nbsp;Heng Zheng","doi":"10.1111/1751-7915.70121","DOIUrl":"https://doi.org/10.1111/1751-7915.70121","url":null,"abstract":"<p>Antimicrobial peptides (AMPs) face stability and toxicity challenges in clinical use. Stapled modification enhances their stability and effectiveness, but its application in peptide design is rarely reported. This study built ten prediction models for stapled AMPs using deep and machine learning, tested their accuracy with an independent data set and wet lab experiments, and characterised stapled loop structures using structural, sequence and amino acid descriptors. AlphaFold improved stapled peptide structure prediction. The support vector machine model performed best, while two deep learning models achieved the highest accuracy of 1.0 on an external test set. Designed cysteine- and lysine-stapled peptides inhibited various bacteria with low concentrations and showed good serum stability and low haemolytic activity. This study highlights the potential of the deep learning method in peptide modification and design.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554406","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":"Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation","authors":"Yutong Yin,&nbsp;Chang Liu,&nbsp;Xianglin Ji,&nbsp;Yun Wang,&nbsp;Juthathip Mongkolsapaya,&nbsp;Gavin R. Screaton,&nbsp;Zhanfeng Cui,&nbsp;Wei E. Huang","doi":"10.1111/1751-7915.70109","DOIUrl":"https://doi.org/10.1111/1751-7915.70109","url":null,"abstract":"<p>The COVID-19 pandemic has caused unparalleled impacts on global social dynamics, healthcare systems and economies, highlighting the urgent need for effective interventions to address current challenges and future pandemic preparedness. This study introduces a novel virus neutralisation platform based on SimCells (~1 μm) and mini-SimCells (100–200 nm), which are chromosome-free and non-replicating bacteria from an LPS-free <i>Escherichia coli</i> strain (ClearColi). SimCells and mini-SimCells were engineered to display nanobodies on their surface, specifically targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein – a critical immunogenic fragment essential for viral entry into host cells. It was demonstrated that nanobody-expressing SimCells achieved over 90% blocking efficiency against synthesised RBD from both the original Wuhan and the B.1.351 (Beta) variant using competitive enzyme-linked immunosorbent assay (ELISA) assay. More importantly, live virus neutralisation assays demonstrated that NB6 nanobody-presenting mini-SimCells effectively neutralised the live SARS-CoV-2 Victoria variant with an IC50 of 2.95 × 10⁹ ± 1.40 × 10⁸ mini-SimCells/mL. Similarly, VE nanobody-presenting mini-SimCells effectively neutralised the B.1.351 (Beta) variant of the SARS-CoV-2 virus with an IC50 of 5.68 × 10⁹ ± 9.94 × 10⁸ mini-SimCells/mL. The mini-SimCells successfully protected Vero cells, a cell line derived from the kidney of an African green monkey, from infection by the live virus of SARS-CoV-2 and its variants. These results suggest that SimCell-based neutralisation offers a promising strategy for the prevention and treatment of SARS-CoV-2, and potentially other viral infections.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554622","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":"Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data","authors":"Marco A. Campos-Magaña,&nbsp;Vitor A. P. Martins dos Santos,&nbsp;Luis Garcia-Morales","doi":"10.1111/1751-7915.70104","DOIUrl":"https://doi.org/10.1111/1751-7915.70104","url":null,"abstract":"<p>Natural products comprise a wide diversity of compounds with a range of biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access a small portion of these compounds due to various technical difficulties. We have herein developed a novel and efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The pipeline uses a combination of long-read sequencing, antiSMASH for BGC identification and Transformation-associated recombination (TAR) for cloning the BGCs. We hypothesized that a genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate the detection of large BGCs at a relatively fast and low-cost DNA sequencing. Despite the relative low accuracy and sequence mistakes due to high GC content and sequence repetitions frequently found in BGC containing bacteria, we demonstrate that ONT long-read sequencing and antiSMASH are effective for identifying novel BGCs and enabling TAR cloning to isolate the BGC in a desired vector. We applied this pipeline on a previously non-sequenced myxobacteria <i>Aetherobacter fasciculatus</i> SBSr002. Our approach enabled us to clone a previously unknown BGC into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533399","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":"The Spread of the Mosquito-Transmitted West Nile Virus in North America and Europe","authors":"Harald Brüssow,&nbsp;Jordi Figuerola","doi":"10.1111/1751-7915.70120","DOIUrl":"https://doi.org/10.1111/1751-7915.70120","url":null,"abstract":"<p>West Nile virus (WNV) disease, a mosquito-transmitted Flavivirus infection, represents a substantial public health research interest. This virus was unknown in the Western hemisphere until it was introduced in 1999 into an immunologically naïve population. WNV caused an epizootic and epidemic in New York City. The infection then swept over North America, causing mass mortality in birds and cumulatively 60,000 human cases, half of whom were hospitalised, mostly with neurological symptoms. The virus closely resembled a goose virus isolated in Israel in 1998. Mosquitoes of the genus <i>Culex</i> were identified as the insect viral vectors. WNV can infect more than 300 bird species, but in the US, the American robin <i>(Turdus migratorius</i>) represented the ecologically most important bird viral reservoir. Mosquito-to-mosquito viral transmission might amplify the viral spread, and iatrogenic WNV transmission was also observed, leading to the screening of blood products. Compared with African WNV isolates, the New York WNV isolate NY99 showed a mutation in the nonstructural protein NS3 that increased its virulence in birds and was also observed in WNV outbreaks from Romania in 1996 and from Russia in 1999. During its spread across the US, NY99 acquired a mutation in the envelope gene E that favoured viral infection in the insect vector. Europe reported 1200 annual WNV cases in 2024, with a focus in Mediterranean countries, but a northward spread of the infection to Germany and The Netherlands was also noted. Global warming is likely to affect the geographical distribution of vector-borne infections such that people living in temperate climate areas might be increasingly exposed to these infections. Therefore, research on temperature effects on WNV transmission by <i>Culex</i> mosquitoes has become a recent focus of research. Pertinent climate aspects of WNV infections are retraced in the present review.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533401","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":"Actinobacteria Warfare Against the Plant Pathogen Sclerotinia sclerotiorum: 2,4,6-Trimethylpyridine Identified as a Bacterial Derived Volatile With Antifungal Activity","authors":"Katharina Belt,&nbsp;Gavin R. Flematti,&nbsp;Björn Bohman,&nbsp;Heng Chooi,&nbsp;Margaret M. Roper,&nbsp;Lachlan Dow,&nbsp;Andrew W. Truman,&nbsp;Barrie Wilkinson,&nbsp;Karam B. Singh,&nbsp;Louise F. Thatcher","doi":"10.1111/1751-7915.70082","DOIUrl":"https://doi.org/10.1111/1751-7915.70082","url":null,"abstract":"<p>Bacteria and fungi produce a wide range of specialised metabolites, including volatile organic compounds (VOCs) that can act as signals or act directly to inhibit niche-competing microbes. Despite their ecological importance, most VOCs involved as signalling compounds remain uncharacterised. We have previously screened a collection of Actinobacteria strains sourced from Western Australia for their ability in vitro to suppress the growth of plant fungal pathogens. Here we explored the potential of four of the most active strains to produce antifungal metabolites by growing the strains on a range of nutrient-containing media. A casein-based (CYPS) culture medium was found to induce the production of antifungal compounds with high activity against <i>Sclerotinia sclerotiorum</i>, a major necrotrophic fungal pathogen of crops such as canola. We further observed that VOCs were produced that influenced pH and affected the bacterium-fungus interaction. The presence of <i>Sclerotinia</i> induced further VOC production in the Actinobacteria. Solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC–MS) analysis identified 2,4,6-trimethylpyridine, a compound not identified previously from Actinobacteria, which showed antifungal activity against different isolates of <i>S. sclerotiorum</i> and increased the pH of the medium. Overall, this study showed that Actinobacteria or their volatile products have the potential to be used in the protection of crops against <i>S. sclerotiorum</i>.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554588","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":"The Spread of the Mosquito-Transmitted West Nile Virus in North America and Europe","authors":"Harald Brüssow,&nbsp;Jordi Figuerola","doi":"10.1111/1751-7915.70120","DOIUrl":"https://doi.org/10.1111/1751-7915.70120","url":null,"abstract":"<p>West Nile virus (WNV) disease, a mosquito-transmitted Flavivirus infection, represents a substantial public health research interest. This virus was unknown in the Western hemisphere until it was introduced in 1999 into an immunologically naïve population. WNV caused an epizootic and epidemic in New York City. The infection then swept over North America, causing mass mortality in birds and cumulatively 60,000 human cases, half of whom were hospitalised, mostly with neurological symptoms. The virus closely resembled a goose virus isolated in Israel in 1998. Mosquitoes of the genus <i>Culex</i> were identified as the insect viral vectors. WNV can infect more than 300 bird species, but in the US, the American robin <i>(Turdus migratorius</i>) represented the ecologically most important bird viral reservoir. Mosquito-to-mosquito viral transmission might amplify the viral spread, and iatrogenic WNV transmission was also observed, leading to the screening of blood products. Compared with African WNV isolates, the New York WNV isolate NY99 showed a mutation in the nonstructural protein NS3 that increased its virulence in birds and was also observed in WNV outbreaks from Romania in 1996 and from Russia in 1999. During its spread across the US, NY99 acquired a mutation in the envelope gene E that favoured viral infection in the insect vector. Europe reported 1200 annual WNV cases in 2024, with a focus in Mediterranean countries, but a northward spread of the infection to Germany and The Netherlands was also noted. Global warming is likely to affect the geographical distribution of vector-borne infections such that people living in temperate climate areas might be increasingly exposed to these infections. Therefore, research on temperature effects on WNV transmission by <i>Culex</i> mosquitoes has become a recent focus of research. Pertinent climate aspects of WNV infections are retraced in the present review.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533398","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":"Citizen Science to Raise Antimicrobial Resistance Awareness in the Community: The MicroMundo Project in Spain and Portugal","authors":"Jessica Gil-Serna,&nbsp;Patricia Antunes,&nbsp;Susana Campoy,&nbsp;Ángeles Cid,&nbsp;Antonio Cobo-Molinos,&nbsp;Paulo Durão,&nbsp;Carmen Fajardo,&nbsp;Belén Fouz,&nbsp;Ana R. Freitas,&nbsp;Filipa Grosso,&nbsp;Piet W. J. de Groot,&nbsp;Trinidad de Miguel,&nbsp;Bruno González Zorn,&nbsp;Belén Hinojosa,&nbsp;Maria João Leão,&nbsp;Montserrat Llagostera,&nbsp;Rosa de Llanos,&nbsp;Ainhoa Lucía,&nbsp;Sergi Maicas,&nbsp;Irma Marín,&nbsp;Magdalena Martínez-Cañamero,&nbsp;Carla Miranda,&nbsp;José Manuel Molina-Guijarro,&nbsp;Diego A. Moreno,&nbsp;María de los Llanos Palop,&nbsp;María José Pérez-Álvarez,&nbsp;Pedro M. Pereira,&nbsp;María Teresa Pérez-Gracia,&nbsp;Sandra Quinteira,&nbsp;Carmen Rioboo,&nbsp;Beatriz Robredo,&nbsp;José María Rodríguez-Calleja,&nbsp;Rafael R. de la Haba,&nbsp;Sandra Sánchez,&nbsp;Manuel Sánchez Angulo,&nbsp;Cristina Sánchez-Porro,&nbsp;Félix J. Sangari,&nbsp;Beatriz Santos,&nbsp;Eduarda Silveira,&nbsp;Begonya Vicedo,&nbsp;Víctor J. Cid,&nbsp;all members of MicroMundo Teams in Spain and Portugal","doi":"10.1111/1751-7915.70123","DOIUrl":"10.1111/1751-7915.70123","url":null,"abstract":"<p>Antimicrobial resistance (AMR) poses a global threat to human, animal and environmental health. Among the multidisciplinary tasks aimed at collectively tackling the AMR crisis, surveillance, research and education stand as major priorities. Based on a crowdsourcing research strategy, the MicroMundo project, a partner of the Tiny Earth initiative in Spain and Portugal, has been developed and consolidated with success in the academic environment. The objectives are focused on promoting research and, especially, on bringing knowledge of One Health and microbiology concepts, as well as AMR awareness to the community. Following a service-learning approach, MicroMundo integrates university and secondary/high school students in a citizen science-based research project to collectively isolate microorganisms with the potential to produce new antibiotics from soil environments. Over the last 7 years, 32 MicroMundo hubs operating across 31 different Portuguese and Spanish universities have recruited thousands of teenagers in this quest. Here we review the outcome of this unprecedented effort from a scientific and an educational perspective.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539727","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":"Actinobacteria Warfare Against the Plant Pathogen Sclerotinia sclerotiorum: 2,4,6-Trimethylpyridine Identified as a Bacterial Derived Volatile With Antifungal Activity","authors":"Katharina Belt,&nbsp;Gavin R. Flematti,&nbsp;Björn Bohman,&nbsp;Heng Chooi,&nbsp;Margaret M. Roper,&nbsp;Lachlan Dow,&nbsp;Andrew W. Truman,&nbsp;Barrie Wilkinson,&nbsp;Karam B. Singh,&nbsp;Louise F. Thatcher","doi":"10.1111/1751-7915.70082","DOIUrl":"https://doi.org/10.1111/1751-7915.70082","url":null,"abstract":"<p>Bacteria and fungi produce a wide range of specialised metabolites, including volatile organic compounds (VOCs) that can act as signals or act directly to inhibit niche-competing microbes. Despite their ecological importance, most VOCs involved as signalling compounds remain uncharacterised. We have previously screened a collection of Actinobacteria strains sourced from Western Australia for their ability in vitro to suppress the growth of plant fungal pathogens. Here we explored the potential of four of the most active strains to produce antifungal metabolites by growing the strains on a range of nutrient-containing media. A casein-based (CYPS) culture medium was found to induce the production of antifungal compounds with high activity against <i>Sclerotinia sclerotiorum</i>, a major necrotrophic fungal pathogen of crops such as canola. We further observed that VOCs were produced that influenced pH and affected the bacterium-fungus interaction. The presence of <i>Sclerotinia</i> induced further VOC production in the Actinobacteria. Solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC–MS) analysis identified 2,4,6-trimethylpyridine, a compound not identified previously from Actinobacteria, which showed antifungal activity against different isolates of <i>S. sclerotiorum</i> and increased the pH of the medium. Overall, this study showed that Actinobacteria or their volatile products have the potential to be used in the protection of crops against <i>S. sclerotiorum</i>.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554764","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":"Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data","authors":"Marco A. Campos-Magaña,&nbsp;Vitor A. P. Martins dos Santos,&nbsp;Luis Garcia-Morales","doi":"10.1111/1751-7915.70104","DOIUrl":"https://doi.org/10.1111/1751-7915.70104","url":null,"abstract":"<p>Natural products comprise a wide diversity of compounds with a range of biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access a small portion of these compounds due to various technical difficulties. We have herein developed a novel and efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The pipeline uses a combination of long-read sequencing, antiSMASH for BGC identification and Transformation-associated recombination (TAR) for cloning the BGCs. We hypothesized that a genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate the detection of large BGCs at a relatively fast and low-cost DNA sequencing. Despite the relative low accuracy and sequence mistakes due to high GC content and sequence repetitions frequently found in BGC containing bacteria, we demonstrate that ONT long-read sequencing and antiSMASH are effective for identifying novel BGCs and enabling TAR cloning to isolate the BGC in a desired vector. We applied this pipeline on a previously non-sequenced myxobacteria <i>Aetherobacter fasciculatus</i> SBSr002. Our approach enabled us to clone a previously unknown BGC into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533397","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}