Journal of Industrial Microbiology & Biotechnology最新文献_第7页

Fungi as a source of eumelanin: current understanding and prospects. 真菌作为真黑色素的来源：目前的认识和展望。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad014

William Beeson, Kyle Gabriel, Christopher Cornelison

{"title":"Fungi as a source of eumelanin: current understanding and prospects.","authors":"William Beeson, Kyle Gabriel, Christopher Cornelison","doi":"10.1093/jimb/kuad014","DOIUrl":"10.1093/jimb/kuad014","url":null,"abstract":"Melanins represent a diverse collection of pigments with a variety of structures and functions. One class of melanin, eumelanin, is recognizable to most as the source of the dark black color found in cephalopod ink. Sepia officinalis is the most well-known and sought-after source of non-synthetic eumelanin, but its harvest is limited by the availability of cuttlefish, and its extraction from an animal source brings rise to ethical concerns. In recent years, these limitations have become more pressing as more applications for eumelanin are developed-particularly in medicine and electronics. This surge in interest in the applications of eumelanin has also fueled a rise in the interest of alternative, bio-catalyzed production methods. Many culinarily-utilized fungi are ideal candidates in this production scheme, as examples exist which have been shown to produce eumelanin, their growth at large scales is well understood, and they can be cultivated on recaptured waste streams. However, much of the current research on the fungal production of eumelanin focuses on pathogenic fungi and eumelanin's role in virulence. In this paper, we will review the potential for culinary fungi to produce eumelanin and provide suggestions for new research areas that would be most impactful in the search for improved fungal eumelanin producers.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/44/2f/kuad014.PMC10569377.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662015","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

Production of S-methyl-methionine using engineered Saccharomyces cerevisiae sake K6. 利用工程酿酒酵母K6生产s -甲基蛋氨酸。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad026

Jun-Min Lee, Min-Ho Park, Bu-Soo Park, Min-Kyu Oh

{"title":"Production of S-methyl-methionine using engineered Saccharomyces cerevisiae sake K6.","authors":"Jun-Min Lee, Min-Ho Park, Bu-Soo Park, Min-Kyu Oh","doi":"10.1093/jimb/kuad026","DOIUrl":"https://doi.org/10.1093/jimb/kuad026","url":null,"abstract":"S-methyl-methionine (SMM), also known as vitamin U, is an important food supplement produced by various plants. In this study, we attempted to produce it in an engineered microorganism, Saccharomyces cerevisiae, by introducing an MMT gene encoding a methionine S-methyltransferase from Arabidopsis thaliana. The S. cerevisiae sake K6 strain, which is a Generally Recognized as Safe (GRAS) strain, was chosen as the host because it produces a significant amount of S-adenosylmethionine (SAM), a precursor of SMM. To increase SMM production in the host, MHT1 and SAM4 genes encoding homocysteine S-methyltransferase were knocked out to prevent SMM degradation. Additionally, MMP1, which encodes S-methyl-methionine permease, was deleted to prevent SMM from being imported into the cell. Finally, ACS2 gene encoding acetyl-CoA synthase was overexpressed, and MLS1 gene encoding malate synthase was deleted to increase SAM availability. Using the engineered strain, 1.92 g/L of SMM was produced by fed-batch fermentation.One-sentence summary: Introducing a plant-derived MMT gene encoding methionine S-methyltransferase into engineered Saccharomyces cerevisiae sake K6 allowed microbial production of S-methyl-methionine (SMM).","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10495038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10586662","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

Perkinsus marinus in bioreactor: growth and a cost-reduced growth medium. 生物反应器中的海洋刺柏：生长和成本降低的生长培养基。

IF 3.2 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad023

Caitlin Murphy, José A Fernández Robledo, G Peter van Walsum

{"title":"Perkinsus marinus in bioreactor: growth and a cost-reduced growth medium.","authors":"Caitlin Murphy, José A Fernández Robledo, G Peter van Walsum","doi":"10.1093/jimb/kuad023","DOIUrl":"10.1093/jimb/kuad023","url":null,"abstract":"Perkinsus marinus (Perkinsea) is an osmotrophic facultative intracellular marine protozoan responsible for \"Dermo\" disease in the eastern oyster, Crassostrea virginica. In 1993 in vitro culture of P. marinus was developed in the absence of host cells. Compared to most intracellular protozoan parasites, the availability of P. marinus to grow in the absence of host cells has provided the basis to explore its use as a heterologous expression system. As the genetic toolbox is becoming available, there is also the need for larger-scale cultivation and lower-cost media formulations. Here, we took an industrial approach to scaled-up growth from a small culture flask to bioreactors, which required developing new cultivation parameters, including aeration, mixing, pH, temperature control, and media formulation. Our approach also enabled more real-time data collection on growth. The bioreactor cultivation method showed similar or accelerated growth rates of P. marinus compared to culture in T-flasks. Redox measurements indicated sufficient oxygen availability throughout the cultivation. Replacing fetal bovine serum with chicken serum showed no differences in the growth rate and a 60% reduction in the medium cost. This study opens the door to furthering P. marinus as a valid heterologous expression system by showing the ability to grow in bioreactors.One-sentence summary: Perkinsus marinus, a microbial parasite of oysters that could be useful for developing vaccines for humans, has been shown to grow well in laboratory equipment that can be expanded to commercial scale using a less expensive growth formula than usual laboratory practice.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10314872","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

Genomic, phenotypic, and clinical safety of Limosilactobacillus reuteri ATCC PTA 4659. 罗伊氏乳酸杆菌ATCC PTA 4659的基因组学、表型和临床安全性。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad041

Malin Sendelius, Jakob Axelsson, Peidi Liu, Stefan Roos

{"title":"Genomic, phenotypic, and clinical safety of Limosilactobacillus reuteri ATCC PTA 4659.","authors":"Malin Sendelius, Jakob Axelsson, Peidi Liu, Stefan Roos","doi":"10.1093/jimb/kuad041","DOIUrl":"10.1093/jimb/kuad041","url":null,"abstract":"Evaluating the safety of probiotic microorganisms is an important part of the development of probiotic products. In this study, we have performed a systematic safety assessment of Limosilactobacillus reuteri American Type Culture Collection (ATCC) PTA 4659 based on genome analysis, antibiotic susceptibility testing, phenotypic characterization, and a human clinical safety study. Genome sequence analysis showed that the strain is free from virulence and antibiotic resistance genes. Connected to this, phenotypic characterization showed that the strain is susceptible to the main classes of antibiotics. Limosilactobacillus reuteri ATCC PTA 4659 was shown to produce histamine, which has previously been described as an anti-inflammatory mediator produced by certain L. reuteri strains. However, the amount of histamine, a biogenic amine, poses no safety concern of a potential product. The strain was investigated in a human clinical safety study and was shown to survive passage through the gastrointestinal tract, both when administered at high [1 × 1011 colony-forming units (CFU)/day] and low doses (1 × 109 CFU/day). The clinical safety evaluation showed that the doses administered are safe for human consumption. Furthermore, carbohydrate utilization, mucus adhesion, and tolerance to acid and bile were studied. It was shown that L. reuteri ATCC PTA 4659 has a very high adhesion to mucus and tolerance to both gastric pH and bile, all potentially important properties for a probiotic strain. Altogether, this study has demonstrated that Limosilactobacillus reuteri ATCC PTA 4659 is safe for human consumption and along with its phenotypic characteristics and previously described anti-inflammatory effects, makes it a promising strain for future probiotic development. NCT01033539.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10689046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136397768","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

Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae. 酿酒酵母代谢调控的天然启动子及启动子工程策略。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuac029

Shifan He, Zhanwei Zhang, Wenyu Lu

{"title":"Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae.","authors":"Shifan He, Zhanwei Zhang, Wenyu Lu","doi":"10.1093/jimb/kuac029","DOIUrl":"https://doi.org/10.1093/jimb/kuac029","url":null,"abstract":"Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/50/9d/kuac029.PMC9936215.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9299135","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: 2

The effect of CO2 concentration on yeast fermentation: rates, metabolic products, and yeast stress indicators. 二氧化碳浓度对酵母发酵的影响：速率、代谢产物和酵母应激指标。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad001

Mario Guadalupe-Daqui, Renee M Goodrich-Schneider, Paul J Sarnoski, John C Carriglio, Charles A Sims, Brian J Pearson, Andrew J MacIntosh

{"title":"The effect of CO2 concentration on yeast fermentation: rates, metabolic products, and yeast stress indicators.","authors":"Mario Guadalupe-Daqui, Renee M Goodrich-Schneider, Paul J Sarnoski, John C Carriglio, Charles A Sims, Brian J Pearson, Andrew J MacIntosh","doi":"10.1093/jimb/kuad001","DOIUrl":"10.1093/jimb/kuad001","url":null,"abstract":"This research aimed to assess how the partial removal of carbon dioxide affects fermentations to provide a better understanding of how the manipulation of carbon dioxide concentration can be used to optimize industrial fermentations. To achieve this, fermentation kinetics, fermentation metabolic products, and yeast stress indicators were analyzed throughout ongoing brewing fermentations conducted under partial vacuum with atmospheric pressure controls. The partial vacuum reduced the solubility of carbon dioxide in the media and decreased the time necessary to reach carbon dioxide saturation. The effect was an increased rate of fermentation, and significantly more viable cells produced under vacuum pressure compared to controls. Ethanol, glycerol, and volatile organic compound concentrations were all significantly increased under partial vacuum, while indicators of yeast stress (trehalose) were reduced. Additionally, as the number of yeast cells was higher under partial vacuum, less sugar was consumed per volume of yeast cell. This study measured fermentation kinetics, metabolic products, and yeast health to holistically assess the effect of partial vacuum during a batch fermentation and found significant differences in each that can be individually exploited by researchers and industry.Summary: An exploration of batch yeast fermentation in a low-pressure environment, with a focus on the health and productivity of the yeast cells.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/47/3a/kuad001.PMC10124126.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9402875","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: 5

Analyzing CRISPR screens in non-conventional microbes. 分析非常规微生物中的CRISPR筛选。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad006

Varun Trivedi, Adithya Ramesh, Ian Wheeldon

{"title":"Analyzing CRISPR screens in non-conventional microbes.","authors":"Varun Trivedi, Adithya Ramesh, Ian Wheeldon","doi":"10.1093/jimb/kuad006","DOIUrl":"https://doi.org/10.1093/jimb/kuad006","url":null,"abstract":"Abstract The multifaceted nature of CRISPR screens has propelled advancements in the field of functional genomics. Pooled CRISPR screens involve creating programmed genetic perturbations across multiple genomic sites in a pool of host cells subjected to a challenge, empowering researchers to identify genetic causes of desirable phenotypes. These genome-wide screens have been widely used in mammalian cells to discover biological mechanisms of diseases and drive the development of targeted drugs and therapeutics. Their use in non-model organisms, especially in microbes to improve bioprocessing-relevant phenotypes, has been limited. Further compounding this issue is the lack of bioinformatic algorithms for analyzing microbial screening data with high accuracy. Here, we describe the general approach and underlying principles for conducting pooled CRISPR knockout screens in non-conventional yeasts and performing downstream analysis of the screening data, while also reviewing state-of-the-art algorithms for identification of CRISPR screening outcomes. Application of pooled CRISPR screens to non-model yeasts holds considerable potential to uncover novel metabolic engineering targets and improve industrial bioproduction. One-Sentence Summary This mini-review describes experimental and computational approaches for functional genomic screening using CRISPR technologies in non-conventional microbes.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10257789","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: 1

Diverse mechanisms of bioproduction heterogeneity in fermentation and their control strategies. 发酵过程中生物生产异质性的多种机制及其控制策略。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad033

Xinyue Mu, Fuzhong Zhang

引用次数: 0

Micrococcus spp. as a promising source for drug discovery: A review. 微球菌作为一种有前景的药物发现来源：综述。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad017

Daniela Tizabi, Russell T Hill

{"title":"Micrococcus spp. as a promising source for drug discovery: A review.","authors":"Daniela Tizabi, Russell T Hill","doi":"10.1093/jimb/kuad017","DOIUrl":"10.1093/jimb/kuad017","url":null,"abstract":"Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ef/fd/kuad017.PMC10548855.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9824219","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

Utilizing a divalent metal ion transporter to control biogenic nanoparticle synthesis. 利用二价金属离子转运蛋白控制生物纳米颗粒的合成。

IF 3.4 4区生物学

Journal of Industrial Microbiology & Biotechnology Pub Date : 2023-02-17 DOI: 10.1093/jimb/kuad020

Manasi Subhash Gangan, Kyle L Naughton, James Q Boedicker

{"title":"Utilizing a divalent metal ion transporter to control biogenic nanoparticle synthesis.","authors":"Manasi Subhash Gangan, Kyle L Naughton, James Q Boedicker","doi":"10.1093/jimb/kuad020","DOIUrl":"10.1093/jimb/kuad020","url":null,"abstract":"Biogenic synthesis of inorganic nanomaterials has been demonstrated for both wild and engineered bacterial strains. In many systems the nucleation and growth of nanomaterials is poorly controlled and requires concentrations of heavy metals toxic to living cells. Here, we utilized the tools of synthetic biology to engineer a strain of Escherichia coli capable of synthesizing cadmium sulfide nanoparticles from low concentrations of reactants with control over the location of synthesis. Informed by simulations of bacterially-assisted nanoparticle synthesis, we created a strain of E. coli expressing a broad-spectrum divalent metal transporter, ZupT, and a synthetic CdS nucleating peptide. Expression of ZupT in the outer membrane and placement of the nucleating peptide in the periplasm focused synthesis within the periplasmic space and enabled sufficient nucleation and growth of nanoparticles at sub-toxic levels of the reactants. This strain synthesized internal CdS quantum dot nanoparticles with spherical morphology and an average diameter of approximately 3.3 nm.One-sentence summary: Expression of a metal ion transporter regulates synthesis of cadmium sulfide nanoparticles in bacteria.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10481092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10177669","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: 1