Microbial Biotechnology最新文献

Combined oxygen and glucose oscillations distinctly change the transcriptional and physiological state of Escherichia coli 氧和葡萄糖的联合振荡明显改变了大肠杆菌的转录和生理状态。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-15 DOI: 10.1111/1751-7915.70051

Jonas Bafna-Rührer, Jean V. Orth, Suresh Sudarsan

{"title":"Combined oxygen and glucose oscillations distinctly change the transcriptional and physiological state of Escherichia coli","authors":"Jonas Bafna-Rührer, Jean V. Orth, Suresh Sudarsan","doi":"10.1111/1751-7915.70051","DOIUrl":"10.1111/1751-7915.70051","url":null,"abstract":"Escherichia coli, a common microbial host for industrial bioproduction, experiences a highly dynamic environment in industrial-scale bioreactors due to significant glucose and oxygen gradients. In this study, we mimic the combined gradients of glucose and oxygen in high-throughput bioreactors to study the transcriptional response of E. coli to industrial-scale conditions. Under oscillating oxygen conditions, E. coli formed less biomass and accumulated the anaerobic by-product acetate. With respect to oxygen-responsive genes, we found that genes of the TCA cycle and of different electron transport chain complexes were differentially expressed. A global analysis of the expression data revealed that oxygen oscillations had caused a transition towards a catabolite-repressed state and upregulation of several stress-related regulatory programs. Interestingly, the transcriptional changes persisted after oxygen limitation stopped. In contrast, the changes we observed due to glucose starvation, such as induction of the stringent response, were primarily transient. Most importantly, we found that effects of combined oxygen and glucose oscillations were distinct from the ones of oxygen and substrate oscillations alone, suggesting an important interplay between the different metabolic regimes in industrial-scale bioreactors.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643564","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

New insights for the development of efficient DNA vaccines 开发高效 DNA 疫苗的新见解。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-15 DOI: 10.1111/1751-7915.70053

Simone Berger, Yanira Zeyn, Ernst Wagner, Matthias Bros

{"title":"New insights for the development of efficient DNA vaccines","authors":"Simone Berger, Yanira Zeyn, Ernst Wagner, Matthias Bros","doi":"10.1111/1751-7915.70053","DOIUrl":"10.1111/1751-7915.70053","url":null,"abstract":"Despite the great potential of DNA vaccines for a broad range of applications, ranging from prevention of infections, over treatment of autoimmune and allergic diseases to cancer immunotherapies, the implementation of such therapies for clinical treatment is far behind the expectations up to now. The main reason is the poor immunogenicity of DNA vaccines in humans. Consequently, the improvement of the performance of DNA vaccines in vivo is required. This mini-review provides an overview of the current state of DNA vaccines and the various strategies to enhance the immunogenic potential of DNA vaccines, including (i) the optimization of the DNA construct itself regarding size, nuclear transfer and transcriptional regulation; (ii) the use of appropriate adjuvants; and (iii) improved delivery, for example, by careful choice of the administration route, physical methods such as electroporation and nanomaterials that may allow cell type-specific targeting. Moreover, combining nanoformulated DNA vaccines with other immunotherapies and prime-boost strategies may help to enhance success of treatment.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637973","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

Bacterial Catabolism of Phthalates With Estrogenic Activity Used as Plasticisers in the Manufacture of Plastic Products 在塑料制品生产中用作增塑剂的具有雌激素活性的邻苯二甲酸盐的细菌分解作用。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-15 DOI: 10.1111/1751-7915.70055

Rinita Dhar, Suman Basu, Mousumi Bhattacharyya, Debarun Acharya, Tapan K. Dutta

{"title":"Bacterial Catabolism of Phthalates With Estrogenic Activity Used as Plasticisers in the Manufacture of Plastic Products","authors":"Rinita Dhar, Suman Basu, Mousumi Bhattacharyya, Debarun Acharya, Tapan K. Dutta","doi":"10.1111/1751-7915.70055","DOIUrl":"10.1111/1751-7915.70055","url":null,"abstract":"Phthalic acid esters (PAEs), the pervasive and ubiquitous endocrine-disrupting chemicals of environmental concern, generated annually on a million-ton scale, are primarily employed as plasticisers in the production of a variety of plastic products and as additives in a large number of commercial supplies. The increased awareness of various adverse effects on the ecosystem and human health including reproductive and developmental disorders has led to a striking increase in research interest aimed at managing these man-made oestrogenic chemicals. In these circumstances, microbial metabolism appeared as the major realistic process to neutralise the toxic burdens of PAEs in an ecologically accepted manner. Among a wide variety of microbial species capable of degrading/transforming PAEs reported so far, bacteria-mediated degradation has been studied most extensively. The main purpose of this review is to provide current knowledge of metabolic imprints of microbial degradation/transformation of PAEs, a co-contaminant of plastic pollution. In addition, this communication illustrates the recent advancement of the structure–functional aspects of the key metabolic enzyme phthalate hydrolase, their inducible regulation of gene expression and evolutionary relatedness, besides prioritising future research needs to facilitate the development of new insights into the bioremediation of PAE in the environment.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643563","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

Design, potential and limitations of conjugation-based antibacterial strategies 基于共轭的抗菌策略的设计、潜力和局限性。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-15 DOI: 10.1111/1751-7915.70050

Elisabeth Derollez, Christian Lesterlin, Sarah Bigot

引用次数: 0

Microbial biosensors for diagnostics, surveillance and epidemiology: Today's achievements and tomorrow's prospects 用于诊断、监测和流行病学的微生物生物传感器：今天的成就和明天的前景。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-15 DOI: 10.1111/1751-7915.70047

Julien Capin, Emile Chabert, Ana Zuñiga, Jerome Bonnet

引用次数: 0

Phage biocontrol success of bacterial wilt depends on synergistic interactions with resident rhizosphere microbiota 噬菌体生物防治细菌枯萎病的成功取决于与根瘤菌群的协同作用。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-13 DOI: 10.1111/1751-7915.70049

Sara Franco Ortega, Bryden Fields, Daniel Narino Rojas, Lauri Mikonranta, Matthew Holmes, Andrea L. Harper, Ville-Petri Friman

{"title":"Phage biocontrol success of bacterial wilt depends on synergistic interactions with resident rhizosphere microbiota","authors":"Sara Franco Ortega, Bryden Fields, Daniel Narino Rojas, Lauri Mikonranta, Matthew Holmes, Andrea L. Harper, Ville-Petri Friman","doi":"10.1111/1751-7915.70049","DOIUrl":"10.1111/1751-7915.70049","url":null,"abstract":"Phages can successfully be used in vitro and in planta to biocontrol the phytopathogenic Ralstonia solanacearum bacterium—the causal agent of bacterial wilt disease. However, phage biocontrol outcomes are still variable, and it is unclear what causes this. In this study, we assessed the efficiency of four phages in controlled in vitro and in planta experiments in all one- and two-phage combinations. We found that using phages in combination did not improve the phage biocontrol efficiency relative to single phage treatments, while certain phages and their combinations were more effective than the others. High intra-treatment variability in phage efficiency was observed across all phage treatments, which was associated with clear shifts in microbiome composition, a reduction in R. solanacearum and an increase in phage densities. We further identified the bacterial taxa that were associated with these ‘shifted’ microbiomes and conducted additional plant growth experiments, demonstrating that some of the enriched bacterial species could protect plants from R. solanacearum infections—a pattern which was also observed using partial least squares path modelling (PLS-PM). Together, these results suggest that phages could open niche space for beneficial bacteria by reducing pathogen densities and that variability in phage biocontrol outcomes is rhizosphere microbiome-dependent, which can introduce between-replicate variation, even in controlled greenhouse conditions.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613277","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

De novo biosynthesis and nicotinamide biotransformation of nicotinamide mononucleotide by engineered yeast cells 工程酵母细胞对烟酰胺单核苷酸的新生物合成和烟酰胺生物转化。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-09 DOI: 10.1111/1751-7915.70048

Yanna Ren, Bei Han, Shijie Wang, Xingbin Wang, Qi Liu, Menghao Cai

{"title":"De novo biosynthesis and nicotinamide biotransformation of nicotinamide mononucleotide by engineered yeast cells","authors":"Yanna Ren, Bei Han, Shijie Wang, Xingbin Wang, Qi Liu, Menghao Cai","doi":"10.1111/1751-7915.70048","DOIUrl":"10.1111/1751-7915.70048","url":null,"abstract":"β-Nicotinamide mononucleotide (NMN) is a precursor of NAD+ in mammals. Research on NAD+ has demonstrated its crucial role against aging and disease. Here two technical paths were established for the efficient synthesis of NMN in the yeast Pichia pastoris, enabling the production of NMN from the low-cost nicotinamide (NAM) or basic carbon sources. The yeast host was systematically modified to adapt to the biosynthesis and accumulation of NMN. To improve the semi-biosynthesis of NMN from NAM, nicotinamide phosphoribosyltransferases were expressed intracellular to evaluate their catalytic activities. The accumulation of extracellular NMN was further increased by the co-expression of an NMN transporter. Fine-tuning of gene expression level produced 72.1 mg/L NMN from NAM in flasks. To achieve de novo biosynthesis NMN, a heterologous biosynthetic pathway was reassembled in yeast cells. Fine-tuning of pathway nodes by the modification of gene expression level and enhancement of precursor generation allowed efficient NMN synthesis from glucose (36.9 mg/L) or ethanol (57.8 mg/L) in flask. Lastly, cultivations in a bioreactor in fed-batch mode achieved an NMN titre of 1004.6 mg/L at 165 h from 2 g NAM and 868 g glucose and 980.4 mg/L at 91 h from 160 g glucose and 557 g ethanol respectively. This study provides a foundation for future optimization of NMN biosynthesis by engineered yeast cell factories.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613274","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

Enhanced biosynthesis of poly(3-hydroxybutyrate) in engineered strains of Pseudomonas putida via increased malonyl-CoA availability 通过增加丙二酰-CoA 的供应量，提高假单胞菌工程菌株中聚（3-羟基丁酸）的生物合成能力。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-06 DOI: 10.1111/1751-7915.70044

Giusi Favoino, Nicolas Krink, Tobias Schwanemann, Nick Wierckx, Pablo I. Nikel

{"title":"Enhanced biosynthesis of poly(3-hydroxybutyrate) in engineered strains of Pseudomonas putida via increased malonyl-CoA availability","authors":"Giusi Favoino, Nicolas Krink, Tobias Schwanemann, Nick Wierckx, Pablo I. Nikel","doi":"10.1111/1751-7915.70044","DOIUrl":"10.1111/1751-7915.70044","url":null,"abstract":"Malonyl-coenzyme A (CoA) is a key precursor for the biosynthesis of multiple value-added compounds by microbial cell factories, including polyketides, carboxylic acids, biofuels, and polyhydroxyalkanoates. Owing to its role as a metabolic hub, malonyl-CoA availability is limited by competition in several essential metabolic pathways. To address this limitation, we modified a genome-reduced Pseudomonas putida strain to increase acetyl-CoA carboxylation while limiting malonyl-CoA utilization. Genes involved in sugar catabolism and its regulation, the tricarboxylic acid (TCA) cycle, and fatty acid biosynthesis were knocked-out in specific combinations towards increasing the malonyl-CoA pool. An enzyme-coupled biosensor, based on the rppA gene, was employed to monitor malonyl-CoA levels in vivo. RppA is a type III polyketide synthase that converts malonyl-CoA into flaviolin, a red-colored polyketide. We isolated strains displaying enhanced malonyl-CoA availability via a colorimetric screening method based on the RppA-dependent red pigmentation; direct flaviolin quantification identified four engineered strains had a significant increase in malonyl-CoA levels. We further modified these strains by adding a non-canonical pathway that uses malonyl-CoA as precursor for poly(3-hydroxybutyrate) biosynthesis. These manipulations led to increased polymer accumulation in the fully engineered strains, validating our general strategy to boost the output of malonyl-CoA–dependent pathways in P. putida.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581547","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

Genome reduction improves octanoic acid production in scale down bioreactors 减少基因组可提高缩比生物反应器中辛酸的产量。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-06 DOI: 10.1111/1751-7915.70034

William T. Cordell, Gennaro Avolio, Ralf Takors, Brian F. Pfleger

{"title":"Genome reduction improves octanoic acid production in scale down bioreactors","authors":"William T. Cordell, Gennaro Avolio, Ralf Takors, Brian F. Pfleger","doi":"10.1111/1751-7915.70034","DOIUrl":"10.1111/1751-7915.70034","url":null,"abstract":"Microorganisms in large-scale bioreactors are exposed to heterogeneous environmental conditions due to physical mixing constraints. Nutritional gradients can lead to transient expression of energetically wasteful stress responses and as a result, can reduce the titres, rates and yields of a bioprocess at larger scales. To what extent these process parameters are impacted is often unknown and therefore bioprocess scale-up comes with major risk. Designing platform strains to account for these intermittent stresses before introducing synthesis pathways is one strategy for de-risking bioprocess development. For example, Escherichia coli strain RM214 is a derivative of wild-type MG1655 that has had several genes and whole operons removed from its genome based on their metabolic cost. In this study, we engineered E. coli strain RM214 (referred to as WG02) to produce octanoic acid from glycerol in batch-flask and fed-batch bioreactor cultivations and compared it to an octanoic acid-producing E. coli MG1655 (WG01). In batch flask cultivations, the two strains performed similarly. However, in carbon limited fed-batch bioreactor cultivations, WG02 provided a greater than 22% boost to biomass compared to WG01 while maintaining similar titres of octanoic acid. Reducing the biomass accumulation of WG02 with nitrogen limited fed-batch cultivation resulted in a 16% improvement in octanoic acid titre over WG01. Finally, in a scale-down system consisting of a stirred tank reactor (representing a well-mixed zone) and plug flow reactor (representing an intermittent carbon starvation zone), WG02 again improved octanoic acid titre by almost 18% while maintaining similar biomass concentrations as WG01.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 11","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589944","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

Thermodynamic constraints on the window of opportunity for direct interspecies electron transfer (DIET) 种间直接电子转移（DIET）机会窗口的热力学约束。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-11-02 DOI: 10.1111/1751-7915.70019

Jan Dolfing

引用次数: 0