Zhaochen Wu, Junting Zhang, Jianjun Hao, Pengfei Liu, Xili Liu
{"title":"Understanding Efflux-Mediated Multidrug Resistance in Botrytis cinerea for Improved Management of Fungicide Resistance","authors":"Zhaochen Wu, Junting Zhang, Jianjun Hao, Pengfei Liu, Xili Liu","doi":"10.1111/1751-7915.70074","DOIUrl":"https://doi.org/10.1111/1751-7915.70074","url":null,"abstract":"<p><i>Botrytis cinerea</i> is a major fungal pathogen infecting over 1400 plant species. It poses a significant threat to agriculture due to multiple fungicide resistance and multidrug resistance, involves resistance to fungicides with different modes of action. Multiple fungicide resistance is mostly due to an accumulation of point mutations in target genes over time, and MDR is result from efflux (e-MDR) and metabolism (m-MDR). This review introduces the occurrence of e-MDR of <i>B. cinerea</i>, the key mechanisms, origins and management strategies of e-MDR in fields. New materials such as nanomaterials become a strategy to overcoming MDR via inhibition of ABC transporter. A deeper understanding of efflux-mediated MDR will provide a support for the MDR management of <i>B. cinerea</i> and the efficient utilization of fungicides.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698880","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}
Zhaochen Wu, Junting Zhang, Jianjun Hao, Pengfei Liu, Xili Liu
{"title":"Understanding Efflux-Mediated Multidrug Resistance in Botrytis cinerea for Improved Management of Fungicide Resistance","authors":"Zhaochen Wu, Junting Zhang, Jianjun Hao, Pengfei Liu, Xili Liu","doi":"10.1111/1751-7915.70074","DOIUrl":"https://doi.org/10.1111/1751-7915.70074","url":null,"abstract":"<p><i>Botrytis cinerea</i> is a major fungal pathogen infecting over 1400 plant species. It poses a significant threat to agriculture due to multiple fungicide resistance and multidrug resistance, involves resistance to fungicides with different modes of action. Multiple fungicide resistance is mostly due to an accumulation of point mutations in target genes over time, and MDR is result from efflux (e-MDR) and metabolism (m-MDR). This review introduces the occurrence of e-MDR of <i>B. cinerea</i>, the key mechanisms, origins and management strategies of e-MDR in fields. New materials such as nanomaterials become a strategy to overcoming MDR via inhibition of ABC transporter. A deeper understanding of efflux-mediated MDR will provide a support for the MDR management of <i>B. cinerea</i> and the efficient utilization of fungicides.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698835","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}
George B. Cheng, Erik Bongcam-Rudloff, Anna Schnürer
{"title":"Metagenomic Exploration Uncovers Several Novel ‘Candidatus’ Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes","authors":"George B. Cheng, Erik Bongcam-Rudloff, Anna Schnürer","doi":"10.1111/1751-7915.70133","DOIUrl":"https://doi.org/10.1111/1751-7915.70133","url":null,"abstract":"<p>Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7–1.0 g/L; TAN 3.6–4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl-CoA pathway (Wood–Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, ‘<i>Candidatus</i> Thermodarwinisyntropha acetovorans’, ‘<i>Candidatus</i> Thermosyntrophaceticus schinkii’, ‘<i>Candidatus</i> Thermotepidanaerobacter aceticum’, and a potential lipid-degrader ‘<i>Candidatus</i> Thermosyntrophomonas ammoiaca’.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689943","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}
George B. Cheng, Erik Bongcam-Rudloff, Anna Schnürer
{"title":"Metagenomic Exploration Uncovers Several Novel ‘Candidatus’ Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes","authors":"George B. Cheng, Erik Bongcam-Rudloff, Anna Schnürer","doi":"10.1111/1751-7915.70133","DOIUrl":"https://doi.org/10.1111/1751-7915.70133","url":null,"abstract":"<p>Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7–1.0 g/L; TAN 3.6–4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl-CoA pathway (Wood–Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, ‘<i>Candidatus</i> Thermodarwinisyntropha acetovorans’, ‘<i>Candidatus</i> Thermosyntrophaceticus schinkii’, ‘<i>Candidatus</i> Thermotepidanaerobacter aceticum’, and a potential lipid-degrader ‘<i>Candidatus</i> Thermosyntrophomonas ammoiaca’.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689719","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":"Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440","authors":"Blas Blázquez, Juan Nogales","doi":"10.1111/1751-7915.70132","DOIUrl":"https://doi.org/10.1111/1751-7915.70132","url":null,"abstract":"<p>Beyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug-and-play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for <i>Pseudomonas putida</i>), a framework to optimise genetic circuit performance by means of (i) chromosome-location-based differential gene expression and (ii) subsequent fitness improvement through evolutionary engineering if needed. Using gene expression strength and cell-to-cell variation, we characterised 10 <i>P. putida</i> chromosomal loci (ppLPS) to show that genome context rather than distance to ORI is the main factor driving differential expression performance. We further contextualised ppLPS gene expression against well-known chromosomal integration sites and plasmids displaying different copy numbers. GENIO supports comprehensive exploration of the gene expression space across <i>P. putida</i>'s genome while unlocking performance optimization of complex heterologous metabolic pathways through evolutionary engineering. To demonstrate the usability of GENIO, we restored <i>P. putida</i>'s aromatic hydrocarbon metabolism by (de)constructing the toluene/<i>m</i>-xylene catabolic pathway coded in the pWW0 plasmid. We also showed that engineering complex phenotypes requires accurate contextualisation of the synthetic pathways involved, a process that benefits from biological robustness.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689942","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":"Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440","authors":"Blas Blázquez, Juan Nogales","doi":"10.1111/1751-7915.70132","DOIUrl":"https://doi.org/10.1111/1751-7915.70132","url":null,"abstract":"<p>Beyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug-and-play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for <i>Pseudomonas putida</i>), a framework to optimise genetic circuit performance by means of (i) chromosome-location-based differential gene expression and (ii) subsequent fitness improvement through evolutionary engineering if needed. Using gene expression strength and cell-to-cell variation, we characterised 10 <i>P. putida</i> chromosomal loci (ppLPS) to show that genome context rather than distance to ORI is the main factor driving differential expression performance. We further contextualised ppLPS gene expression against well-known chromosomal integration sites and plasmids displaying different copy numbers. GENIO supports comprehensive exploration of the gene expression space across <i>P. putida</i>'s genome while unlocking performance optimization of complex heterologous metabolic pathways through evolutionary engineering. To demonstrate the usability of GENIO, we restored <i>P. putida</i>'s aromatic hydrocarbon metabolism by (de)constructing the toluene/<i>m</i>-xylene catabolic pathway coded in the pWW0 plasmid. We also showed that engineering complex phenotypes requires accurate contextualisation of the synthetic pathways involved, a process that benefits from biological robustness.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689857","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}
Kailin Shao, Xiaobin Yu, Yan Zhao, Ying Zhang, Xiaobo Liu
{"title":"Semirational Design of SenC to Enhance Organic Selenium Biosynthesis","authors":"Kailin Shao, Xiaobin Yu, Yan Zhao, Ying Zhang, Xiaobo Liu","doi":"10.1111/1751-7915.70130","DOIUrl":"10.1111/1751-7915.70130","url":null,"abstract":"<p>Organic selenium, a bioavailable form of the essential trace element selenium, holds significant potential for improving human health through dietary supplements and functional foods. However, low bioconversion efficiency has primarily limited the biosynthesis of organic selenium compounds. Here, we focused on enhancing the biosynthesis of organic selenium by optimising the expression and activity of two key enzymes, SenB and SenC, involved in the conversion process. We compared several expression systems, including fusion expression and dual-promoter approaches, and optimised reaction conditions such as temperature, pH and incubation time. Our results showed that mutations of SenC more than doubled enzyme activity, resulting in a corresponding rise in the intermediate SeP. Notably, the fusion expression of SenB and SenC exhibited the highest conversion rate of organic selenium, achieving over 95% under optimal conditions. Our findings provide a basis for organic selenium production through microbial biotechnology.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676709","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}
Zeynep Efsun Duman-Özdamar, Mattijs K. Julsing, Vitor A. P. Martins dos Santos, Jeroen Hugenholtz, Maria Suarez-Diez
{"title":"Model-Driven Engineering of Yarrowia lipolytica for Improved Microbial Oil Production","authors":"Zeynep Efsun Duman-Özdamar, Mattijs K. Julsing, Vitor A. P. Martins dos Santos, Jeroen Hugenholtz, Maria Suarez-Diez","doi":"10.1111/1751-7915.70089","DOIUrl":"10.1111/1751-7915.70089","url":null,"abstract":"<p>Extensive usage of plant-based oils, especially palm oil, has led to environmental and social issues, such as deforestation and loss of biodiversity, thus sustainable alternatives are required. Microbial oils, especially from <i>Yarrowia lipolytica</i>, offer a promising solution because of their similar composition to palm oil, low carbon footprint and ability to utilise low-cost substrates. In this study, we employed the Design-Build-Test-Learn (DBTL) approach to enhance lipid production in <i>Y. lipolytica</i>. We systematically evaluated predictions from the genome-scale metabolic model to identify and overcome bottlenecks in lipid biosynthesis. We tested the effect of predicted medium supplements (glutamate, leucine, methionine and threonine) and genetic intervention targets, including the overexpression of ATP-citrate lyase (<i>ACL</i>), acetyl-CoA carboxylase (<i>ACC</i>), threonine synthase (<i>TS</i>), diacylglycerol acyltransferase(<i>DGA1</i>), the deletion of citrate exporter gene (<i>CEX1</i>) and disruption of β-oxidation pathway (<i>MFE1</i>). This work revealed the critical roles of <i>ACC</i>, <i>ACL</i>, <i>TS</i> and <i>DGA1</i> and the interaction of these genes with elevated intracellular citrate availability in lipid biosynthesis. Combining <i>TS</i> and <i>DGA1</i> overexpression in the <i>Δmfe_Δcex</i> background achieved a remarkable 200% increase in lipid content (56% w/w) and a 230% increase in lipid yield on glycerol. These findings underscore the potential of <i>Y. lipolytica</i> as an efficient microbial cell factory for fatty acid production. Our study advances the understanding of lipid metabolism in <i>Y. lipolytica</i> and demonstrates a viable approach for developing sustainable and economically feasible alternatives to palm oil.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668615","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}
Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee
{"title":"Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications","authors":"Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee","doi":"10.1111/1751-7915.70131","DOIUrl":"https://doi.org/10.1111/1751-7915.70131","url":null,"abstract":"<p>The combination of artificial intelligence (AI) with microbial technology marks the start of a major transformation, improving applications throughout biotechnology, especially in healthcare. With the capability of AI to process vast amounts of biological big data, advanced microbial technology allows for a comprehensive understanding of complex biological systems, advancing disease diagnosis, treatment and the development of microbial therapeutics. This mini review explores the impact of AI-integrated microbial technologies in healthcare, highlighting advancements in microbial biomarker-based diagnosis, the development of microbial therapeutics and the microbial production of therapeutic compounds. This exploration promises significant improvements in the design and implementation of health-related solutions, steering a new era in biotechnological applications.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638707","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}
Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee
{"title":"Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications","authors":"Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee","doi":"10.1111/1751-7915.70131","DOIUrl":"https://doi.org/10.1111/1751-7915.70131","url":null,"abstract":"<p>The combination of artificial intelligence (AI) with microbial technology marks the start of a major transformation, improving applications throughout biotechnology, especially in healthcare. With the capability of AI to process vast amounts of biological big data, advanced microbial technology allows for a comprehensive understanding of complex biological systems, advancing disease diagnosis, treatment and the development of microbial therapeutics. This mini review explores the impact of AI-integrated microbial technologies in healthcare, highlighting advancements in microbial biomarker-based diagnosis, the development of microbial therapeutics and the microbial production of therapeutic compounds. This exploration promises significant improvements in the design and implementation of health-related solutions, steering a new era in biotechnological applications.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638705","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}