Journal of Industrial Microbiology & Biotechnology最新文献

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Correction to: Vegan grade medium component screening and concentration optimization for the fermentation of the probiotic strain Lactobacillus paracasei IMC 502® using Design of Experiments. 更正:使用实验设计法筛选和优化用于益生菌株准乳杆菌 IMC 502® 发酵的素食级培养基成分和浓度。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae043
{"title":"Correction to: Vegan grade medium component screening and concentration optimization for the fermentation of the probiotic strain Lactobacillus paracasei IMC 502® using Design of Experiments.","authors":"","doi":"10.1093/jimb/kuae043","DOIUrl":"10.1093/jimb/kuae043","url":null,"abstract":"","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"51 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11578288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Development of platensimycin, platencin, and platensilin overproducers by biosynthetic pathway engineering and fermentation medium optimization. 通过生物合成途径工程和发酵培养基优化,开发普拉滕霉素、普拉滕辛和普拉滕辛过度生产者。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae003
Lucas L Fluegel, Ming-Rong Deng, Ping Su, Edward Kalkreuter, Dong Yang, Jeffrey D Rudolf, Liao-Bin Dong, Ben Shen
{"title":"Development of platensimycin, platencin, and platensilin overproducers by biosynthetic pathway engineering and fermentation medium optimization.","authors":"Lucas L Fluegel, Ming-Rong Deng, Ping Su, Edward Kalkreuter, Dong Yang, Jeffrey D Rudolf, Liao-Bin Dong, Ben Shen","doi":"10.1093/jimb/kuae003","DOIUrl":"10.1093/jimb/kuae003","url":null,"abstract":"<p><p>The platensimycin (PTM), platencin (PTN), and platensilin (PTL) family of natural products continues to inspire the discovery of new chemistry, enzymology, and medicine. Engineered production of this emerging family of natural products, however, remains laborious due to the lack of practical systems to manipulate their biosynthesis in the native-producing Streptomyces platensis species. Here we report solving this technology gap by implementing a CRISPR-Cas9 system in S. platensis CB00739 to develop an expedient method to manipulate the PTM, PTN, and PTL biosynthetic machinery in vivo. We showcase the utility of this technology by constructing designer recombinant strains S. platensis SB12051, SB12052, and SB12053, which, upon fermentation in the optimized PTM-MS medium, produced PTM, PTN, and PTL with the highest titers at 836 mg L-1, 791 mg L-1, and 40 mg L-1, respectively. Comparative analysis of these resultant recombinant strains also revealed distinct chemistries, catalyzed by PtmT1 and PtmT3, two diterpene synthases that nature has evolved for PTM, PTN, and PTL biosynthesis. The ΔptmR1/ΔptmT1/ΔptmT3 triple mutant strain S. platensis SB12054 could be envisaged as a platform strain to engineer diterpenoid biosynthesis by introducing varying ent-copalyl diphosphate-acting diterpene synthases, taking advantage of its clean metabolite background, ability to support diterpene biosynthesis in high titers, and the promiscuous tailoring biosynthetic machinery.</p><p><strong>One-sentence summary: </strong>Implementation of a CRISPR-Cas9 system in Streptomyces platensis CB00739 enabled the construction of a suite of designer recombinant strains for the overproduction of platensimycin, platencin, and platensilin, discovery of new diterpene synthase chemistries, and development of platform strains for future diterpenoid biosynthesis engineering.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10847714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Transcriptional and translational flux optimization at the key regulatory node for enhanced production of naringenin using acetate in engineered Escherichia coli. 在关键调控节点优化转录和翻译通量,以提高工程大肠杆菌利用醋酸生产柚皮苷的能力。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae006
Dong H Kim, Hyun G Hwang, Dae-Yeol Ye, Gyoo Y Jung
{"title":"Transcriptional and translational flux optimization at the key regulatory node for enhanced production of naringenin using acetate in engineered Escherichia coli.","authors":"Dong H Kim, Hyun G Hwang, Dae-Yeol Ye, Gyoo Y Jung","doi":"10.1093/jimb/kuae006","DOIUrl":"10.1093/jimb/kuae006","url":null,"abstract":"<p><p>As a key molecular scaffold for various flavonoids, naringenin is a value-added chemical with broad pharmaceutical applicability. For efficient production of naringenin from acetate, it is crucial to precisely regulate the carbon flux of the oxaloacetate-phosphoenolpyruvate (OAA-PEP) regulatory node through appropriate pckA expression control, as excessive overexpression of pckA can cause extensive loss of OAA and metabolic imbalance. However, considering the critical impact of pckA on naringenin biosynthesis, the conventional strategy of transcriptional regulation of gene expression is limited in its ability to cover the large and balanced solution space. To overcome this hurdle, in this study, pckA expression was fine-tuned at both the transcriptional and translational levels in a combinatorial expression library for the precise exploration of optimal naringenin production from acetate. Additionally, we identified the effects of regulating pckA expression by validating the correlation between phosphoenolpyruvate kinase (PCK) activity and naringenin production. As a result, the flux-optimized strain exhibited a 49.8-fold increase compared with the unoptimized strain, producing 122.12 mg/L of naringenin. Collectively, this study demonstrated the significance of transcriptional and translational flux rebalancing at the key regulatory node, proposing a pivotal metabolic engineering strategy for the biosynthesis of various flavonoids derived from naringenin using acetate.</p><p><strong>One-sentence summary: </strong>In this study, transcriptional and translational regulation of pckA expression at the crucial regulatory node was conducted to optimize naringenin biosynthesis using acetate in E. coli.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion. 嗜热菌中的糖运输:木质纤维素解构与生物转化的桥梁
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae020
Hansen Tjo, Jonathan M Conway
{"title":"Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion.","authors":"Hansen Tjo, Jonathan M Conway","doi":"10.1093/jimb/kuae020","DOIUrl":"10.1093/jimb/kuae020","url":null,"abstract":"<p><p>Biomass degrading thermophiles play an indispensable role in building lignocellulose-based supply chains. They operate at high temperatures to improve process efficiencies and minimize mesophilic contamination, can overcome lignocellulose recalcitrance through their native carbohydrate-active enzyme (CAZyme) inventory, and can utilize a wide range of sugar substrates. However, sugar transport in thermophiles is poorly understood and investigated, as compared to enzymatic lignocellulose deconstruction and metabolic conversion of sugars to value-added chemicals. Here, we review the general modes of sugar transport in thermophilic bacteria and archaea, covering the structural, molecular, and biophysical basis of their high-affinity sugar uptake. We also discuss recent genetic studies on sugar transporter function. With this understanding of sugar transport, we discuss strategies for how sugar transport can be engineered in thermophiles, with the potential to enhance the conversion of lignocellulosic biomass into renewable products.</p><p><strong>One-sentence summary: </strong>Sugar transport is the understudied link between extracellular biomass deconstruction and intracellular sugar metabolism in thermophilic lignocellulose bioprocessing.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Determining the accuracy and suitability of common analytical techniques for sophorolipid biosurfactants. 确定槐脂类生物表面活性剂常用分析技术的准确性和适用性。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae021
Benjamin Ingham, Rehana Sung, Phil Kay, Katherine Hollywood, Phavit Wongsirichot, Alistair Veitch, James Winterburn
{"title":"Determining the accuracy and suitability of common analytical techniques for sophorolipid biosurfactants.","authors":"Benjamin Ingham, Rehana Sung, Phil Kay, Katherine Hollywood, Phavit Wongsirichot, Alistair Veitch, James Winterburn","doi":"10.1093/jimb/kuae021","DOIUrl":"10.1093/jimb/kuae021","url":null,"abstract":"<p><p>To determine the performance of a sophorolipid biosurfactant production process, it is important to have accurate and specific analytical techniques in place. Among the most popular are the anthrone assay, gravimetric quantification (hexane:ethyl acetate extraction), and high-performance liquid chromatography (HPLC). The choice of analytical tool varies depending on cost, availability, and ease of use; however, these techniques have never been compared directly against one another. In this work, 75 fermentation broths with varying product/substrate concentrations were comprehensively tested with the 3 techniques and compared. HPLC-ultraviolet detection (198 nm) was capable of quantifying C18:1 subterminal hydroxyl diacetylated lactonic sophorolipid down to a lower limit of 0.3 g/L with low variability (<3.21%). Gravimetric quantification of the broths following liquid:liquid extraction with hexane and ethyl acetate showed some linearity (R2 = .658) when compared to HPLC but could not quantify lower than 11.06 g/L, even when no sophorolipids were detected in the sample, highlighting the non-specificity of the method to co-extract non-sophorolipid components in the final gravimetric measure. The anthrone assay showed no linearity (R2 = .129) and was found to cross-react with media components (rapeseed oil, corn steep liquor, glucose), leading to consistent overestimation of sophorolipid concentration. The appearance of poor biomass separation during sample preparation with centrifugation was noted and resolved with a novel sample preparation method with pure ethanol. Extensive analysis and comparisons of the most common sophorolipid quantification techniques are explored and the limitations/advantages are highlighted. The findings provide a guide for scientists to make an informed decision on the suitable quantification tool that meets their needs, exploring all aspects of the analysis process from harvest, sample preparation, and analysis.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Enhancing the erythritol production of Yarrowia lipolytica by high-throughput screening based on highly sensitive artificial sensor and anchor protein cwp2. 基于高灵敏度人工传感器和锚蛋白 cwp2 的高通量筛选,提高脂肪溶解亚罗威氏菌的赤藓糖醇产量。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae045
Quan Cui, Hui Liu, Chuanzhuang Guo, Jianbin Wang, Yuehan Liu, Yaqi Zhao, Ruiming Wang, Piwu Li, Ting Wang, Junqing Wang, Nan Li
{"title":"Enhancing the erythritol production of Yarrowia lipolytica by high-throughput screening based on highly sensitive artificial sensor and anchor protein cwp2.","authors":"Quan Cui, Hui Liu, Chuanzhuang Guo, Jianbin Wang, Yuehan Liu, Yaqi Zhao, Ruiming Wang, Piwu Li, Ting Wang, Junqing Wang, Nan Li","doi":"10.1093/jimb/kuae045","DOIUrl":"10.1093/jimb/kuae045","url":null,"abstract":"<p><p>Yarrowia lipolytica is widely used for the industrial production of the natural sweetener erythritol. Despite improvements in fermentation process control and metabolic pathway regulation, bottlenecks still exist in terms of yield and screening technology. Therefore, we constructed an artificial sensor system for effective erythritol detection, established a single-cell droplet-based high-throughput screening system based on fluorescence-activated cell sorting, and obtained Y. lipolytica with improved erythritol production through mutagenesis and high-throughput screening. We used a droplet generator to co-cultivate Y. lipolytica 5-14 with Escherichia coli and used the E. coli fluorescent signal to detect the concentration of erythritol synthesized by Y. lipolytica 5-14 for high-throughput screening. Strains were subjected to UV mutagenesis for 120 s. Under optimized fermentation conditions using Y. lipolytica mutants in 96-well plates, the screening efficiency reached 16.7%. Yarrowia lipolytica 5-14-E6 showed a 21% increase in erythritol to 109.84 g/L. After fermentation at 30°C in a 100-m3 fermenter for 75 hr, the mutant Y. lipolytica 5-14-E6 erythritol yield reached 178 g/L.</p><p><strong>One-sentence summary: </strong>In this study, we constructed an artificial sensor system for effective erythritol detection, established a single-cell droplet-based high-throughput screening system based on fluorescence-activated cell sorting, and induced and screened mutant strains of Yarrowia lipolytica with improved erythritol production through mutagenesis and high-throughput screening.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. 采用自上而下和自下而上的微生物组工程方法,利用废弃生物质进行生物制造。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae025
Xuejiao Lyu, Mujaheed Nuhu, Pieter Candry, Jenna Wolfanger, Michael Betenbaugh, Alexis Saldivar, Cristal Zuniga, Ying Wang, Shilva Shrestha
{"title":"Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass.","authors":"Xuejiao Lyu, Mujaheed Nuhu, Pieter Candry, Jenna Wolfanger, Michael Betenbaugh, Alexis Saldivar, Cristal Zuniga, Ying Wang, Shilva Shrestha","doi":"10.1093/jimb/kuae025","DOIUrl":"10.1093/jimb/kuae025","url":null,"abstract":"<p><p>Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted.</p><p><strong>One-sentence summary: </strong>This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Improving the alcohol respiratory chain and energy metabolism by enhancing PQQ synthesis in Acetobacter pasteurianus. 通过提高巴氏醋酸杆菌中 PQQ 的合成,改善酒精呼吸链和能量代谢。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae036
Wenqing Zhang, Chen Feng, Chunxue Zhang, Jia Song, Li Li, Menglei Xia, Wei Ding, Yu Zheng, Min Wang
{"title":"Improving the alcohol respiratory chain and energy metabolism by enhancing PQQ synthesis in Acetobacter pasteurianus.","authors":"Wenqing Zhang, Chen Feng, Chunxue Zhang, Jia Song, Li Li, Menglei Xia, Wei Ding, Yu Zheng, Min Wang","doi":"10.1093/jimb/kuae036","DOIUrl":"10.1093/jimb/kuae036","url":null,"abstract":"<p><p>Pyrroloquinoline quinone (PQQ) is one of the important coenzymes in living organisms. In acetic acid bacteria (AAB), it plays a crucial role in the alcohol respiratory chain, as a coenzyme of alcohol dehydrogenase (ADH). In this work, the PQQ biosynthetic genes were overexpressed in Acetobacter pasteurianus CGMCC 3089 to improve the fermentation performance. The result shows that the intracellular and extracellular PQQ contents in the recombinant strain A. pasteurianus (pBBR1-p264-pqq) were 152.53% and 141.08% higher than those of the control A. pasteurianus (pBBR1-p264), respectively. The catalytic activity of ADH and aldehyde dehydrogenase increased by 52.92% and 67.04%, respectively. The results indicated that the energy charge and intracellular ATP were also improved in the recombinant strain. The acetic acid fermentation was carried out using a 5 L self-aspirating fermenter, and the acetic acid production rate of the recombinant strain was 23.20% higher compared with the control. Furthermore, the relationship between the PQQ and acetic acid tolerance of cells was analyzed. The biomass of recombinant strain was 180.2%, 44.3%, and 38.6% higher than those of control under 2%, 3%, and 4% acetic acid stress, respectively. After being treated with 6% acetic acid for 40 min, the survival rate of the recombinant strain was increased by 76.20% compared with the control. Those results demonstrated that overexpression of PQQ biosynthetic genes increased the content of PQQ, therefore improving the acetic acid fermentation and the cell tolerance against acetic acid by improving the alcohol respiratory chain and energy metabolism.</p><p><strong>One sentence summary: </strong>The increase in PQQ content enhances the activity of the alcohol respiratory chain of Acetobacter pasteurianus, and the increase in energy charge enhances the tolerance of cells against acetic acid, therefore, improving the efficiency of acetic acid fermentation.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142348234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Use of qPCR to monitor 2,4-dinitroanisole degrading bacteria in water and soil slurry cultures. 使用 qPCR 监测水和土壤泥浆培养物中的 2,4-二硝基苯甲醚降解细菌。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae047
Lisa A Waidner, Carrie E Daniel, Sarah E Kovar, Jim C Spain
{"title":"Use of qPCR to monitor 2,4-dinitroanisole degrading bacteria in water and soil slurry cultures.","authors":"Lisa A Waidner, Carrie E Daniel, Sarah E Kovar, Jim C Spain","doi":"10.1093/jimb/kuae047","DOIUrl":"10.1093/jimb/kuae047","url":null,"abstract":"<p><p>Prediction and process monitoring during natural attenuation, bioremediation, and biotreatment require effective strategies for detection and enumeration of the responsible bacteria. The use of 2,4-dinitroanisole (DNAN) as a component of insensitive munitions leads to environmental contamination of firing ranges and manufacturing waste streams. Nocardioides sp. strain JS1661 degrades DNAN under aerobic conditions via a pathway involving an unusual DNAN demethylase. We used the deeply branched sequences of DNAN degradation functional genes as a target for development of a molecular method for detection of the bacteria. A qPCR assay was designed for the junction between dnhA and dnhB, the adjacent genes encoding DNAN demethylase. The assay allowed reproducible enumeration of JS1661 during growth in liquid media and soil slurries. Results were consistent with biodegradation of DNAN, accumulation of products, and classical biomass estimates, including most probable number and OD600. The results provide a sensitive and specific molecular method for prediction of degradation potential and process evaluation during degradation of DNAN.</p><p><strong>One-sentence summary: </strong>A unique target sequence in functional genes enables the design of a simple and specific qPCR assay for enumeration of aerobic 2,4-dinitroanisole-degrading bacteria in soil and water.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Development of automated metabolite control using mid-infrared probe for bioprocesses and vaccine manufacturing. 利用中红外探头开发用于生物工艺和疫苗生产的自动代谢物控制。
IF 3.2 4区 生物学
Journal of Industrial Microbiology & Biotechnology Pub Date : 2024-01-09 DOI: 10.1093/jimb/kuae019
Jennifer Reid, Manjit Haer, Airong Chen, Calvin Adams, Yu Chen Lin, Jim Cronin, Zhou Yu, Marina Kirkitadze, Tao Yuan
{"title":"Development of automated metabolite control using mid-infrared probe for bioprocesses and vaccine manufacturing.","authors":"Jennifer Reid, Manjit Haer, Airong Chen, Calvin Adams, Yu Chen Lin, Jim Cronin, Zhou Yu, Marina Kirkitadze, Tao Yuan","doi":"10.1093/jimb/kuae019","DOIUrl":"10.1093/jimb/kuae019","url":null,"abstract":"<p><p>Automation of metabolite control in fermenters is fundamental to develop vaccine manufacturing processes more quickly and robustly. We created an end-to-end process analytical technology and quality by design-focused process by replacing manual control of metabolites during the development of fed-batch bioprocesses with a system that is highly adaptable and automation-enabled. Mid-infrared spectroscopy with an attenuated total reflectance probe in-line, and simple linear regression using the Beer-Lambert Law, were developed to quantitate key metabolites (glucose and glutamate) from spectral data that measured complex media during fermentation. This data was digitally connected to a process information management system, to enable continuous control of feed pumps with proportional-integral-derivative controllers that maintained nutrient levels throughout fed-batch stirred-tank fermenter processes. Continuous metabolite data from mid-infrared spectra of cultures in stirred-tank reactors enabled feedback loops and control of the feed pumps in pharmaceutical development laboratories. This improved process control of nutrient levels by 20-fold and the drug substance yield by an order of magnitude. Furthermore, the method is adaptable to other systems and enables soft sensing, such as the consumption rate of metabolites. The ability to develop quantitative metabolite templates quickly and simply for changing bioprocesses was instrumental for project acceleration and heightened process control and automation.</p><p><strong>One-sentence summary: </strong>Intelligent digital control systems using continuous in-line metabolite data enabled end-to-end automation of fed-batch processes in stirred-tank reactors.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11187416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
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