Journal of Industrial Microbiology & Biotechnology最新文献

{"title":"Valorizing waste streams to enhance sustainability and economics in microbial oil production.","authors":"Nicholas Renegar, Seth Rhoades, Anusha Nair, Anthony J Sinskey, John P Ward, David Ross Appleton","doi":"10.1093/jimb/kuae041","DOIUrl":"10.1093/jimb/kuae041","url":null,"abstract":"<p><p>Driven by the demand for more sustainable products, research and capital investment has been committed to developing microbially produced oils. While researchers have shown oleaginous yeasts and other microbes can produce low-carbon footprint oils by leveraging waste streams as energy sources, previous analyses have not fully explored the quantity of available waste streams and in turn economy-of-scale enabled on capital and operating expenses. This paper makes parallels to 2G ethanol facilities, enabling a data-driven understanding of large-scale production economics. Production costs are broken down for a variety of scenarios. The analysis finds that reaching price parity with large-scale commodity oils (e.g., palm oil, high-oleic cooking oils, biofuels feedstock oils, lauric acid) is not possible today and unlikely even under aggressive future assumptions about strain productivity. Instead, commercial production must be targeted at end markets where sustainability-conscious consumers are willing to pay the price premiums identified in this paper.</p><p><strong>One sentence summary: </strong>This paper makes parallels to 2G ethanol facilities, enabling a data-driven understanding of large-scale production economics for microbial lipids.</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/PMC11630272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583495","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}

{"title":"Identification of plasmids from thermophilic Streptomyces strains and development of a gene cloning system for thermophilic Streptomyces species.","authors":"Yuuki Yamada, Haruo Ikeda","doi":"10.1093/jimb/kuae042","DOIUrl":"10.1093/jimb/kuae042","url":null,"abstract":"<p><p>To develop a host-vector system for use in thermophilic Streptomyces, multi-copy plasmids were screened for thermophilic Streptomyces species using data from public bioresource centers (JCM and NBRC). Of 27 thermophilic Streptomyces strains, 3 harbored plasmids. One plasmid (pSTVU1), derived from S. thermovulgaris NBRC 16615 (= JCM 4520, ATCC 19284, DSM 40444, ISP 5444, NRRL B-12375, and NCIMB 10078), was multi-copy and relatively small in size. Analysis of the sequence of this multi-copy plasmid revealed that it was 7,838 bp and contained at least 10 predicted open reading frames. The plasmid was introduced into 14 thermophilic Streptomyces strains (of 18 strains examined) and several mesophilic Streptomyces strains (S.lividans, S.parvulus, and S.avermitilis). pSTVU1 can be transferred by mixed culture because the plasmid encodes the ORF that regulates the transfer function. Plasmid transfer was observed not only between strains within the same species but also between mesophilic Streptomyces and thermophilic Streptomyces (and vice versa); however, the efficiency of this transfer was extremely low. We also confirmed that a derivative of pSTVU1 can be used as a multi-copy vector in the gene expression system that is expected to exhibit gene-dosage effects, establishing a method for efficient production of thermophilic α-amylase.</p><p><strong>One-sentence summary: </strong>A multi-copy plasmid was identified in thermophilic Streptomyces and used to develop a gene cloning system for thermophilic Streptomyces species.</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/PMC11600335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622035","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}

{"title":"A discussion and evaluation of statistical procedures used by JIMB authors when comparing means.","authors":"K Thomas Klasson","doi":"10.1093/jimb/kuae001","DOIUrl":"10.1093/jimb/kuae001","url":null,"abstract":"<p><p>Out of the 166 articles published in Journal of Industrial Microbiology and Biotechnology (JIMB) in 2019-2020 (not including special issues or review articles), 51 of them used a statistical test to compare two or more means. The most popular test was the (Standard) t-test, which often was used to compare several pairs of means. Other statistical procedures used included Fisher's least significant difference (LSD), Tukey's honest significant difference (HSD), and Welch's t-test; and to a lesser extent Bonferroni, Duncan's Multiple Range, Student-Newman-Keuls, and Kruskal-Wallis tests. This manuscript examines the performance of some of these tests with simulated experimental data, typical of those reported by JIMB authors. The results show that many of the most common procedures used by JIMB authors result in statistical conclusions that are prone to have large false positive (Type I) errors. These error-prone procedures included the multiple t-test, multiple Welch's t-test, and Fisher's LSD. These multiple comparisons procedures were compared with alternatives (Fisher-Hayter, Tukey's HSD, Bonferroni, and Dunnett's t-test) that were able to better control Type I errors.</p><p><strong>Non-technical summary: </strong>The aim of this work was to review and recommend statistical procedures for Journal of Industrial Microbiology and Biotechnology authors who often compare the effect of several treatments on microorganisms and their functions.</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/PMC10845891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417298","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}

{"title":"Arts, cultural heritage, sciences, and micro-/bio-/technology: Impact of biomaterials and biocolorants from antiquity till today!","authors":"Maarten L De Mol, Erick J Vandamme","doi":"10.1093/jimb/kuae049","DOIUrl":"10.1093/jimb/kuae049","url":null,"abstract":"<p><p>Nature has inspired and provided humans with ideas, concepts, and thoughts on design, art, and performance for millennia. From early societies when humankind often took shelter in caves, until today, many materials and colorants to express feelings or communicate with one another were derived from plants, animals, or microbes. In this manuscript, an overview of these natural products used in the creation of art is given, from paintings on rocks to fashionable dresses made from bacterial cellulose. Besides offering many examples of art works, the origin and application of various biomaterials and colorants are discussed. While many facets of our daily lives have changed over millennia, one certainty has been that humans have an intrinsic need to conceptualize and create to express themselves. Driven by technological advances in the past decades and in the light of global warming, new and often more sustainable materials and colorants have been discovered and implemented. The impact of art on human societies remains relevant and powerful.</p><p><strong>One-sentence summary: </strong>This manuscript discusses the use of biomaterials and biocolorants in art from a historical perspective, spanning 37,000 bc until today.</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/PMC11664188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828806","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}

{"title":"Cultivation of recombinant Aspergillus niger strains on dairy whey as a carbohydrate source.","authors":"Teagan C Crament, Kayline Arendsen, Shaunita H Rose, Trudy Jansen","doi":"10.1093/jimb/kuae007","DOIUrl":"10.1093/jimb/kuae007","url":null,"abstract":"<p><p>Agricultural waste valorisation provides a sustainable solution to waste management, and combining waste utilisation with commodity production allows for responsible production processes. Recombinant Aspergillus niger D15 strains expressing fungal endoglucanases (Trichoderma reesei eg1 and eg2 and Aspergillus carneus aceg) were evaluated for their ability to utilise lactose as a carbon source to determine whether dairy waste could be used as a feedstock for enzyme production. The recombinant A. niger D15[eg1]PyrG, D15[eg2]PyrG, and D15[aceg]PyrG strains produced maximum endoglucanase activities of 34, 54, and 34 U/mL, respectively, on lactose and 23, 27, and 22 U/mL, respectively, on whey. The A. niger D15[eg2]PyrG strain was used to optimise the whey medium. Maximum endoglucanase activity of 46 U/mL was produced on 10% whey medium containing 0.6% NaNO3. The results obtained indicate that dairy whey can be utilised as a feedstock for recombinant enzyme production. However, variations in enzyme activities were observed and require further investigation.</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/PMC10863410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650954","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}

{"title":"CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces.","authors":"Yongjae Lee, Soonkyu Hwang, Woori Kim, Ji Hun Kim, Bernhard O Palsson, Byung-Kwan Cho","doi":"10.1093/jimb/kuae009","DOIUrl":"10.1093/jimb/kuae009","url":null,"abstract":"<p><p>The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.</p><p><strong>One-sentence summary: </strong>This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.</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/PMC10949845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028225","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}

{"title":"Characterization of the exopolysaccharides produced by the industrial yeast Komagataella phaffii.","authors":"Amanda Fischer, Vanessa Castagna, Shafraz Omer, Micah Marmorstein, Junqi Wu, Shannon Ceballos, Emma Skoog, Carlito B Lebrilla, Chris Suarez, Aletta Schnitzler","doi":"10.1093/jimb/kuae046","DOIUrl":"10.1093/jimb/kuae046","url":null,"abstract":"<p><p>The yeast Komagataella phaffii has become a popular host strain among biotechnology start-up companies for producing recombinant proteins for food and adult nutrition applications. Komagataella phaffii is a host of choice due to its long history of safe use, open access to protocols and strains, a secretome free of host proteins and proteases, and contract manufacturing organizations with deep knowledge in bioprocess scale-up. However, a recent publication highlighted the abundance of an unknown polysaccharide that accumulates in the supernatant during fermentation. This poses a significant challenge in using K. phaffii as a production host. This polysaccharide leads to difficulties in achieving high purity products and requires specialized and costly downstream processing steps for removal. In this study, we describe the use of the common K. phaffii host strain YB-4290 for production of the bioactive milk protein lactoferrin. Upon purification of lactoferrin using membrane-based separation methods, significant amounts of carbohydrate were copurified with the protein. It was determined that the carbohydrate is mostly composed of mannose residues with minor amounts of glucose and glucosamine. The polysaccharide fraction has an average molecular weight of 50 kDa and consists mainly of mannan, galactomannan, and amylose. In addition, a large fraction of the carbohydrate has an unknown structure likely composed of oligosaccharides. Additional strains were tested in fermentation to further understand the source of the carbohydrates. The commonly used industrial hosts, BG10 and YB-4290, produce a basal level of exopolysaccharide; YB-4290 producing slightly more than BG10. Overexpression of recombinant protein stimulates exopolysaccharide production well above levels produced by the host strains alone. Overall, this study aims to provide a foundation for developing methods to improve the economics of recombinant protein production using K. phaffii as a production host.</p><p><strong>One-sentence summary: </strong>Overexpression of recombinant protein stimulates the hyperproduction of high-molecular-weight, mannose-based, exopolysaccharides by the industrial yeast Komagataella phaffii.</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/PMC11630240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693114","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}

{"title":"Biosensors for the detection of chorismate and cis,cis-muconic acid in Corynebacterium glutamicum.","authors":"Jeanette C Velasquez-Guzman, Herbert M Huttanus, Demosthenes P Morales, Tara S Werner, Austin L Carroll, Adam M Guss, Chris M Yeager, Taraka Dale, Ramesh K Jha","doi":"10.1093/jimb/kuae024","DOIUrl":"10.1093/jimb/kuae024","url":null,"abstract":"<p><p>Corynebacterium glutamicum ATCC 13032 is a promising microbial chassis for industrial production of valuable compounds, including aromatic amino acids derived from the shikimate pathway. In this work, we developed two whole-cell, transcription factor based fluorescent biosensors to track cis,cis-muconic acid (ccMA) and chorismate in C. glutamicum. Chorismate is a key intermediate in the shikimate pathway from which value-added chemicals can be produced, and a shunt from the shikimate pathway can divert carbon to ccMA, a high value chemical. We transferred a ccMA-inducible transcription factor, CatM, from Acinetobacter baylyi ADP1 into C. glutamicum and screened a promoter library to isolate variants with high sensitivity and dynamic range to ccMA by providing benzoate, which is converted to ccMA intracellularly. The biosensor also detected exogenously supplied ccMA, suggesting the presence of a putative ccMA transporter in C. glutamicum, though the external ccMA concentration threshold to elicit a response was 100-fold higher than the concentration of benzoate required to do so through intracellular ccMA production. We then developed a chorismate biosensor, in which a chorismate inducible promoter regulated by natively expressed QsuR was optimized to exhibit a dose-dependent response to exogenously supplemented quinate (a chorismate precursor). A chorismate-pyruvate lyase encoding gene, ubiC, was introduced into C. glutamicum to lower the intracellular chorismate pool, which resulted in loss of dose dependence to quinate. Further, a knockout strain that blocked the conversion of quinate to chorismate also resulted in absence of dose dependence to quinate, validating that the chorismate biosensor is specific to intracellular chorismate pool. The ccMA and chorismate biosensors were dually inserted into C. glutamicum to simultaneously detect intracellularly produced chorismate and ccMA. Biosensors, such as those developed in this study, can be applied in C. glutamicum for multiplex sensing to expedite pathway design and optimization through metabolic engineering in this promising chassis organism.</p><p><strong>One-sentence summary: </strong>High-throughput screening of promoter libraries in Corynebacterium glutamicum to establish transcription factor based biosensors for key metabolic intermediates in shikimate and β-ketoadipate pathways.</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/PMC11258901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468541","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}

{"title":"Optimizing dsRNA engineering strategies and production in E. coli HT115 (DE3).","authors":"Juliana da Rosa, Américo José Carvalho Viana, Fernando Rafael Alves Ferreira, Alessandra Koltun, Liliane Marcia Mertz-Henning, Silvana Regina Rockenbach Marin, Elibio Leopoldo Rech, Alexandre Lima Nepomuceno","doi":"10.1093/jimb/kuae028","DOIUrl":"10.1093/jimb/kuae028","url":null,"abstract":"<p><p>Producing double-stranded RNA (dsRNA) represents a bottleneck for the adoption of RNA interference technology in agriculture, and the main hurdles are related to increases in dsRNA yield, production efficiency, and purity. Therefore, this study aimed to optimize dsRNA production in E. coli HT115 (DE3) using an in vivo system. To this end, we designed a new vector, pCloneVR_2, which resulted in the efficient production of dsRNA in E. coli HT115 (DE3). We performed optimizations in the culture medium and expression inducer in the fermentation of E. coli HT115 (DE3) for the production of dsRNA. Notably, the variable that had the greatest effect on dsRNA yield was cultivation in TB medium, which resulted in a 118% increase in yield. Furthermore, lactose induction (6 g/L) yielded 10 times more than IPTG. Additionally, our optimized up-scaled protocol of the TRIzol™ extraction method was efficient for obtaining high-quality and pure dsRNA. Finally, our optimized protocol achieved an average yield of 53.3 µg/mL after the production and purification of different dsRNAs, reducing production costs by 72%.</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/PMC11375590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995902","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}

{"title":"Using design of experiments to guide genetic optimization of engineered metabolic pathways.","authors":"Seonyun Moon, Anna Saboe, Michael J Smanski","doi":"10.1093/jimb/kuae010","DOIUrl":"10.1093/jimb/kuae010","url":null,"abstract":"<p><p>Design of experiments (DoE) is a term used to describe the application of statistical approaches to interrogate the impact of many variables on the performance of a multivariate system. It is commonly used for process optimization in fields such as chemical engineering and material science. Recent advances in the ability to quantitatively control the expression of genes in biological systems open up the possibility to apply DoE for genetic optimization. In this review targeted to genetic and metabolic engineers, we introduce several approaches in DoE at a high level and describe instances wherein these were applied to interrogate or optimize engineered genetic systems. We discuss the challenges of applying DoE and propose strategies to mitigate these challenges.</p><p><strong>One-sentence summary: </strong>This is a review of literature related to applying Design of Experiments for genetic optimization.</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/PMC10981448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140136911","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}