Novel mutagenesis and screening technologies for food microorganisms: advances and prospects

High-throughput screening method for glycolipids based on substrate modification and their efficient biomanufacturing

The development of a high-throughput screening (HTS) method is crucial for boosting microbial synthesis. However, in non-model strains, genetic editing-based HTS is often not feasible. Here, a substrate-modified HTS strategy using Starmerella bombicola PL0120, a sophorolipids (SLs)-producing strain, was designed. First, the medium was optimized to increase the SLs yield to 248 g/L. Then, 2-benzylstearic acid was synthesized, which PL0120 can use to make SLs analogs. Subsequently, by selecting dark-phenotype strains and using 254 nm absorption, a 51.1 % high-yielding SLs strain screening rate was achieved. Among these strains, strain A6 yielded a concentration of 324 g/L. Moreover, this method has been extended to rhamnolipids (RLs). By engineering a microbubble reactor, the yield of RLs was increased to 70.3 g/L. This HTS methodology is instrumental in augmenting the production output of microbial fermentation products, which in turn, facilitates cost-effective biomanufacturing.

Assembly of a lignocellulose-degrading synthetic community from the strong-flavor Daqu by a stepwise method

The lignocellulose in Daqu plays an important role during the Baijiu fermentation, such as providing energy for microbial metabolism and precursors for flavor compounds. However, due to the complexity of the Daqu microbial community and the fermentation environment, the regulation of lignocellulose degradation efficiency is limited. In such cases, artificial intervention can be achieved through the application of synthetic communities. Here, we studied the structure of the lignocellulose-degrading microbial communities in Daqu. Based on the characteristics of lignocellulose composition, we developed three high-throughput screening methods and used a stepwise assembly approach to construct a synthetic community composed of Bacillus stercori, Bacillus paramycoides, Klebsiella pneumoniae, and Cyberlindnera fabianii. After fermentation, 54.71 % of the bran was degraded and 11 substances were uniquely produced. 4-vinylguaiacol and 2-ethyl-3,5(6)-dimethylpyrazine were considered to be the key aroma compounds of the synthetic community. This synthetic community offers a new approach to control Daqu fermentation.

Unveiling the genetic basis and metabolic rewiring behind the galactose-positive phenotype in a Streptococcus thermophilus mutant

Streptococcus thermophilus (S. thermophilus) is a widely used starter culture in dairy fermentation, but most strains are galactose-negative and only metabolize glucose from lactose hydrolysis. In this study, we aimed to uncover the mechanisms underlying the acquisition of a stable galactose-positive (Gal+) phenotype in a mutant strain of S. thermophilus IMAU10636. By treating the wild-type strain with the mutagenic agent N-methyl-N-nitro-N-nitrosoguanidine, we successfully isolated a Gal+ mutant, S. thermophilus IMAU10636Y. Comparative enzyme activity assays revealed that the mutant exhibited higher β-galactosidase and galactokinase activities, but lower glucokinase and pyruvate kinase activities compared to the wild-type. High-performance liquid chromatography analysis confirmed the mutant's enhanced ability to utilize lactose and galactose, leading to increased glucose secretion. Integrated genome and transcriptomics analyses provided deeper insights into the underlying genetic and metabolic mechanisms. We found that the metabolism regulatory network of the glycolysis / Leloir pathway was altered in the mutant, possibly due to the upregulation of the gene expression in the galR-galK intergenic region. This likely led to increased RNA polymerase binding and transcription of the gal operon, ultimately promoting the Gal+ phenotype. Additionally, we identified a mutation in the scrR gene, encoding a LacI family transcriptional repressor, which also contributed to the Gal+ phenotype. These findings offer new perspectives on the metabolic rewiring and regulatory mechanisms that enable S. thermophilus to acquire the ability to metabolize galactose. This knowledge can inform strategies for engineering and selecting Gal+ strains with desirable fermentation characteristics for dairy applications.

Engineering industrial yeast for improved tolerance and robustness

As an important cell factory, industrial yeast has been widely used for the production of compounds ranging from bulk chemicals to complex natural products. However, various adverse conditions including toxic products, extreme pH, and hyperosmosis etc., severely restrict microbial growth and metabolic performance, limiting the fermentation efficiency and diminishing its competitiveness. Therefore, enhancing the tolerance and robustness of yeasts is critical to ensure reliable and sustainable production of metabolites in complex industrial production processes. In this review, we provide a comprehensive review of various strategies for improving the tolerance of yeast cells, including random mutagenesis, system metabolic engineering, and material-mediated immobilization cell technology. It is expected that this review will provide a new perspective to realize the response and intelligent regulation of yeast cells to environmental stresses.

Recent advances in the biosynthesis and production optimization of gentamicin: A critical review

Gentamicin, an aminoglycoside antibiotic, is generated by a few species within the genus Micromonospora and has garnered significant attention due to its broad-spectrum efficacy in combating numerous infectious diseases. Comprising a complex array of closely related aminoglycoside compounds, the gentamicin B and C complexes emerge as particularly pertinent in clinical contexts. This review outlines the latest advancements in the biosynthesis and production of gentamicin, commencing with a comprehensive overview of its biosynthetic pathway. Subsequently, the article encapsulates a spectrum of strategies currently deployed to augment gentamicin yields. These strategies include mutation screening, molecular biological techniques, and optimization of the fermentation process. Moreover, numerous methods have been documented for detecting gentamicin across a range of matrices, underscoring the significance of precise quantitative analysis. Finally, the review furnishes an exhaustive market analysis and future outlook, elucidating prevailing trends and challenges within the gentamicin industry. Overall, this article serves as a pivotal resource for researchers and professionals engaged in gentamicin research, furnishing a meticulous introduction to efficient synthesis technologies and diverse applications, alongside presenting innovative concepts and methodologies aimed at increasing gentamicin production.

Enhancement of non-oleaginous green microalgae Ulothrix for bio-fixing CO2 and producing biofuels by ARTP mutagenesis

Oleaginous green microalgae are often mentioned in algae-based biodiesel industry, but most of them belong to specific genus (Chlorella, Scenedesmus, Botryococcus and Desmodesmus). Thus, the microalgal germplasm resources for biodiesel production are limited. Mutagenesis is regarded as an important technology for expanding germplasm resources. The main purpose of this study is to screen microalgae strains with high carbon dioxide tolerance and high lipid content from mutants derived from indigenous non-oleaginous green microalgae species-Ulothrix SDJZ-17. Two mutants with high CO2 tolerance and high lipid content genetic stability were obtained from the mutants by high-throughput screening, named Ulothrix SDJZ-17-A20 and Ulothrix SDJZ-17-A23. In order to evaluate the potential of CO2 fixation and biofuel production, A20 and A23 were cultured under air and 15% CO2 (v/v) conditions, and their wild-type strains (WT) were used as controls. Under the condition of high CO2 concentration, the growth performance and lipid production capacity of mutant strains A20 and A23 were not only significantly better than those of wild strains, but also better than those of their own cultured under air conditions. Among them, A23 obtained the highest LCE (light conversion efficiency) (14.79%), Fv/Fm (maximal photochemical efficiency of photosystem II) (71.04%) and biomass productivity (81.26 mg L-1 d-1), while A20 obtained the highest lipid content (22.45%). Both mutants can be used as candidate strains for CO2 fixation and biofuel production. By ARTP (atmospheric and room temperature plasma) mutagenesis with high-throughput screening, the mutants with higher CO2 tolerance, photosynthetic efficiency and lipid productivity can be obtained, even if they are derived from non-oleaginous microalgae, which is of great significance for enriching the energy microalgae germplasm bank, alleviating the global warming and energy crisis.

Multilevel systemic engineering of Bacillus licheniformis for efficient production of acetoin from lignocellulosic hydrolysates

Bio-refining lignocellulosic resource offers a renewable and sustainable approach for producing biofuels and biochemicals. However, the conversion efficiency of lignocellulosic resource is still challenging due to the intrinsic inefficiency in co-utilization of xylose and glucose. In this study, the industrial bacterium Bacillus licheniformis was engineered for biorefining lignocellulosic resource to produce acetoin. First, adaptive evolution was conducted to improve acetoin tolerance, leading to a 19.6 % increase in acetoin production. Then, ARTP mutagenesis and 60Co-γ irradiation was carried out to enhance the production of acetoin, obtaining 73.0 g/L acetoin from glucose. Further, xylose uptake and xylose utilization pathway were rewired to facilitate the co-utilization of xylose and glucose, enabling the production of 60.6 g/L acetoin from glucose and xylose mixtures. Finally, this efficient cell factory was utilized for acetoin production from lignocellulosic hydrolysates with the highest titer of 68.3 g/L in fed-batch fermentation. This strategy described here holds great applied potential in the biorefinery of lignocellulose for the efficient synthesis of high-value chemicals.

Improving Beneficial Traits in Bacillus cabrialesii subsp. cabrialesii TE3T through UV-Induced Genomic Changes

It is essential to hunt for new technologies that promote sustainable practices for agroecosystems; thus, the bioprospecting of beneficial microorganisms complementing with mutation induction techniques to improve their genomic, metabolic, and functional traits is a promising strategy for the development of sustainable microbial inoculants. Bacillus cabrialesii subsp. cabrialesii strain TE3T, a previously recognized plant growth-promoting and biological control agent, was subjected to UV mutation induction to improve these agro-biotechnological traits. Dilutions were made which were spread on Petri dishes and placed under a 20 W UV lamp at 10-min intervals for 60 min. After the UV-induced mutation of this strain, 27 bacterial colonies showed morphological differences compared to the wild-type strain; however, only a strain named TE3T-UV25 showed an improvement in 53.6% of the biocontrol against Bipolaris sorokiniana vs. the wild-type strain, by competition of nutrient and space (only detected in the mutant strain), as well as diffusible metabolites. Furthermore, the ability to promote wheat growth was evaluated by carrying out experiments under specific greenhouse conditions, considering un-inoculated, strain TE3T, and strain TE3T-UV25 treatments. Thus, after 120 days, biometric traits in seedlings were quantified and statistical analyses were performed, which showed that strain TE3T-UV25 maintained its ability to promote wheat growth in comparison with the wild-type strain. On the other hand, using bioinformatics tools such as ANI, GGDC, and TYGS, the Overall Genome Relatedness Index (OGRI) and phylogenomic relationship of mutant strain TE3T-UV25 were performed, confirming that it changed its taxonomic affiliation from B. cabrialesii subsp. cabrialesii to Bacillus subtilis. In addition, genome analysis showed that the mutant, wild-type, and B. subtilis strains shared 3654 orthologous genes; however, a higher number of shared genes (3954) was found between the TE3T-UV25 mutant strain and B. subtilis 168, while the mutant strain shared 3703 genes with the wild-type strain. Genome mining was carried out using the AntiSMASH v7.0 web server and showed that mutant and wild-type strains shared six biosynthetic gene clusters associated with biocontrol but additionally, pulcherriminic acid cluster only was detected in the genome of the mutant strain and Rhizocticin A was exclusively detected in the genome of the wild-type strain. Finally, using the PlaBase tool, differences in the number of genes (17) associated with beneficial functions in agroecosystems were detected in the genome of the mutant vs. wild-type strain, such as biofertilization, bioremediation, colonizing plant system, competitive exclusion, phytohormone, plant immune response stimulation, putative functions, stress control, and biocontrol. Thus, the UV-induced mutation was a successful strategy to improve the bioactivity of B. cabrialesii subsp. cabrialesii TE3T related to the agro-biotecnology applications. The obtained mutant strain, B. subtilis TE3T-UV25, is a promising strain to be further studied as an active ingredient for the bioformulation of bacterial inoculants to migrate sustainable agriculture.

The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants

Microorganisms are widely used for the industrial production of various valuable products, such as pharmaceuticals, food and beverages, biofuels, enzymes, amino acids, vaccines, etc. Research is constantly carried out to improve their properties, mainly to increase their productivity and efficiency and reduce the cost of the processes. The selection of microorganisms with improved qualities takes a lot of time and resources (both human and material); therefore, this process itself needs optimization. In the last two decades, microfluidics technology appeared in bioengineering, which allows for manipulating small particles (from tens of microns to nanometre scale) in the flow of liquid in microchannels. The technology is based on small-volume objects (microdroplets from nano to femtolitres), which are manipulated using a microchip. The chip is made of an optically transparent inert to liquid medium material and contains a series of channels of small size (<1 mm) of certain geometry. Based on the physical and chemical properties of microparticles (like size, weight, optical density, dielectric constant, etc.), they are separated using microsensors. The idea of accelerated selection of microorganisms is the application of microfluidic technologies to separate mutants with improved qualities after mutagenesis. This article discusses the possible application and practical implementation of microfluidic separation of mutants, including yeasts like Yarrowia lipolytica and Phaffia rhodozyma after chemical mutagenesis will be discussed.

Selection and Genetic Analysis of High Polysaccharide-Producing Mutants in Inonotus obliquus

Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To enhance polysaccharide production of I. obliquus HS819, atmospheric and room temperature plasma (ARTP) technology was employed for mutagenesis of the protoplasts. Through liquid fermentation, 32 mutant strains exhibiting diverse characteristics in morphology, color of the fermentation broth, mycelial pellet size, and biomass were screened. Secondary screening identified mutant strain A27, which showed a significant increase in polysaccharide production up to 1.67 g/L and a mycelial dry weight of 17.6 g/L, representing 137.67% and 15% increases compared to the HS819 strain, respectively. Furthermore, the fermentation period was reduced by 2 days, and subsequent subculture cultivation demonstrated stable polysaccharide production and mycelial dry weight. The genome resequencing analysis of the HS819 strain and mutant strain A27 revealed 3790 InDel sites and mutations affecting 612 functional genes associated with polysaccharide synthesis. We predict that our findings will be helpful for high polysaccharide production through genetic engineering of I. obliquus.

Research progress on biosynthesis of erythritol and multi-dimensional optimization of production strategies

Erythritol, as a new type of natural sweetener, has been widely used in food, medical, cosmetics, pharmaceutical and other fields due to its unique physical and chemical properties and physiological functions. In recent years, with the continuous development of strategies such as synthetic biology, metabolic engineering, omics-based systems biology and high-throughput screening technology, people's understanding of the erythritol biosynthesis pathway has gradually deepened, and microbial cell factories with independent modification capabilities have been successfully constructed. In this review, the cheap feedstocks for erythritol synthesis are introduced in detail, the environmental factors affecting the synthesis of erythritol and its regulatory mechanism are described, and the tools and strategies of metabolic engineering involved in erythritol synthesis are summarized. In addition, the study of erythritol derivatives is helpful in expanding its application field. Finally, the challenges that hinder the effective production of erythritol are discussed, which lay a foundation for the green, efficient and sustainable production of erythritol in the future and breaking through the bottleneck of production.

Screening of Selenium/Glutathione-Enriched Candida utilis and Its Anti-inflammatory and Antioxidant Activities in Mice

This study aimed to screen a mutant of Candida utilis SE-172 with high selenite tolerance and glutathione (GSH) biosynthesis capability via 60Co γ-radiation mutagenesis to prepare selenium (Se)-enriched yeast. The maximal intracellular contents of GSH and organic Se of 22.94 mg/g and 1308.1 μg/g were obtained, respectively, under a batch culture of SE-172. The physiological mechanism underlying increased GSH and organic Se contents in Se/GSH-enriched C. utilis SE-172 was revealed based on assaying activities of γ-glutamylcysteine synthase (γ-GCS) involved in GSH biosynthesis and selenophosphate synthase (SPS) related to organic Se bioconversion, and by determining intracellular ATP and NADH contents and ATP/ADP and NADH/NAD+ ratios associated with energy supply and regeneration. Moreover, the effect of this selenized yeast on anti-inflammatory and antioxidant activities in mice with colitis was investigated. The supplementation of Se/GSH-enriched yeast decreased the dextran sodium sulfate-induced damage to colon tissues, reduced the expression of pro-inflammatory factors [interleukin (IL)-6, IL-1β, and tumor necrosis factor-α (TNF-α)] in serum, increased the antioxidant-related enzyme [superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px)] activities, and decreased the malondialdehyde content in colon. The Se/GSH-enriched C. utilis SE-172 showed potent anti-inflammatory and antioxidant activities in mice with colitis.

Effects of Cold Plasma Pretreatment on the Synthesis of Polysaccharide from Pleurotus ostreatus

Fungal polysaccharides have attracted wide attention because of their medical pharmaceutical and health care value. So far, many efforts have been made in strain improvement to produce polysaccharides on a large scale at low cost. Here, a novel cold plasma-induced strain improvement technology was employed to pretreat Pleurotus ostreatus CGMCC 5.374 by radio-frequency (RF) low-vacuum cold plasma (LVCP) for the purpose of obtaining a high-yield polysaccharide strain. The optimum pretreatment conditions including discharge power, treatment time, and working pressure were determined by single factor and orthogonal experiment in succession. Furthermore, transcriptome analysis was conducted to study the effects of RF-LVCP on cell metabolism and proliferation. Results showed that under the optimal condition of discharge power of 130 W, treatment time of 25 s and working pressure of 140 Pa, polysaccharide content in mycelium was increased by 3.16% after 6 days in comparison to the original strain. Transcriptome analysis showed that RF-LVCP is helpful for specific gene transcription profiles, Gene Ontology (GO) and KEGG pathways, of which the differentially expressed genes (DEGs) were mainly involve with the up-regulation of polysaccharide transport, physiology, synthesis and metabolism, as well as the down-regulation of polysaccharide hydrolysis and macromolecular degradation.

Recent progress of atmospheric and room-temperature plasma as a new and promising mutagenesis technology

At present, atmospheric and room-temperature plasma (ARTP) is regarded as a new and powerful mutagenesis technology with the advantages of environment-friendliness, operation under mild conditions, and fast mutagenesis speed. Compared with traditional mutagenesis strategies, ARTP is used mainly to change the structure of microbial DNA, enzymes, and proteins through a series of physical, chemical, and electromagnetic effects with the organisms, leading to nucleotide breakage, conversion or inversion, causing various DNA damages, so as to screen out the microbial mutants with better biological characteristics. As a result, in recent years, ARTP mutagenesis and the combination of ARTP with traditional mutagenesis have been widely used in microbiology, showing great potential for application. In this review, the recent progress of ARTP mutagenesis in different application fields and bottlenecks of this technology are systematically summarized, with a view to providing a theoretical basis and technical support for better application. Finally, the outlook of ARTP mutagenesis is presented, and we identify the challenges in the field of microbial mutagenesis by ARTP.

Random mutagenesis as a tool for industrial strain improvement for enhanced production of antibiotics: a review

Secondary metabolites are produced by microbes in minimal quantities in the natural environment out of necessity. However, in the pharmaceutical industry, their overproduction becomes essential. To achieve higher yields, genetic modifications are employed to create strains that surpass the productivity of the initially isolated strains. While rational screening and genetic engineering have emerged as valuable practices in recent years, the cost-effective technique of mutagenesis and selection, known as "random screening," remains a preferred method for efficient short-term strain development. This review aims to comprehensively explore all aspects of strain improvement, focusing on why random mutagenesis continues to be widely adopted.

Improvement of triterpenoid production in mycelia of Antrodia camphorata through mutagenesis breeding and amelioration of CCl4-induced liver injury in mice

Due to the scarcity of wild fruiting bodies, submerged fermentation of the medicinal fungus Antrodia camphorata is attracting much attention, but the production of bioactive triterpenoids is low. Therefore, there is an urgent need to improve the triterpenoid yield of submerged fermentation. Here, the A. camphorata mutant E3-64 was generated from strain AC16101 through random mutagenesis breeding, producing 172.8 mg triterpenoid per gram of dry mycelia. Further optimization of culture parameters resulted in a yield of 255.5 mg/g dry mycelia (i.e., an additional >1.4-fold increase), which is the highest reported yield thus far. Notably, mutant E3-64 produced 94% and 178% more of the triterpenoid components antcin A and antcamphin A, respectively, while it produced 52% and 15% less antcin B and G, respectively. Mutant E3-64 showed increased expression of key genes involved in triterpenoid biosynthesis, as well as different genome-wide single-nucleotide polymorphisms as compared with AC16101. Triterpenoids of the E3-64 mycelia exhibited remarkably protective activity against acute CCl4-induced liver injury in mice. This study shows the potential of A. camphorata for scientific research and commercial application.

New perspectives into Gluconobacter-catalysed biotransformations

Different from other aerobic microorganisms that oxidise carbon sources to water and carbon dioxide, Gluconobacter catalyses the incomplete oxidation of various substrates with regio- and stereoselectivity. This ability, as well as its capacity to release the resulting products into the reaction media, place Gluconobacter as a privileged member of a non-model microorganism class that may boost industrial biotechnology. Knowledge of new technologies applied to Gluconobacter has been piling up in recent years. Advancements in its genetic modification, application of immobilisation tools and careful designs of the transformations, have improved productivities and stabilities of Gluconobacter strains or enabled new bioconversions for the production of valuable marketable chemicals. In this work, the latest advancements applied to Gluconobacter-catalysed biotransformations are summarised with a special focus on recent available tools to improve them. From genetic and metabolic engineering to bioreactor design, the most recent works on the topic are analysed in depth to provide a comprehensive resource not only for scientists and technologists working on/with Gluconobacter, but for the general biotechnologist.

Improving tolerance and 1,3-propanediol production of Clostridium butyricum using physical mutagenesis, adaptive evolution and genome shuffling

Bioconversion efficiency of glycerol to 1,3-propanediol (1,3-PD) by Clostridium butyricum is bottlenecked by its low tolerance to various stressors, especially glycerol as the substrate, 1,3-PD as the end product, and butyric acid as a by-product, which eventually decreases 1,3-PD yield. This study aimed at improving the tolerance and 1,3-PD production capability of C. butyricum using random mutagenesis and evolutionary techniques. Mutagenesis of wild strain by atmospheric room temperature plasma (ARTP) provided the first population with maximum tolerance to 160 g/L glycerol, while microbial microdroplet culture system (MMC)-mediated adaptive laboratory evolution (ALE) generated the second population with tolerance to 100 g/L 1,3-PD. Subsequently, genome shuffling of both populations yielded a final strain, GJH-418, which generated 60.12 g/L1,3-PD with a productivity of 1.72 g/L/h. The transcript analysis of the mutant and wild strains revealed the possible involvement of 8 genes in high tolerance and high 1,3-PD production through either up- or down-regulation.

A two-prong mutagenesis and adaptive evolution strategy to enhance the temperature tolerance and productivity of Nannochloropsis oculata

Incorporation of microalgae in biorefineries intended to help society reach carbon neutrality is hindered by algal growth inhibition at high temperatures, necessitating the use of costly and carbon-intensive cooling systems. In the present study, a two-prong strategy of random mutagenesis and adaptive laboratory evolution to generate robust thermotolerant strains of Nannochloropsis oculata, was used. The best mutants demonstrated increased productivity at 35 °C, which was 10 °C higher than the optimal temperature of the wild type. In a 2-L photobioreactor at 35 °C, biomass and lipid productivity were 1.43-fold and 2.24-fold higher, respectively, than wild type at 25 °C. Higher pigment and carbohydrate content contributed to the mutants' rapid growth and enhanced photosynthetic efficiency. Metabolomics and lipidomics showed rewiring of the central carbon metabolism and membrane lipid synthesis in thermotolerant strains to ensure cellular homeostasis without compromising productivity. Tagatose and phosphatidylethanolamine upregulation were identified as future genetic targets for further enhancing lipid production.

Insecticidal characteristics and structural identification of the potential active compounds from Streptomyces sp. KR0006: Strain improvement through mutagenesis

Pest control by biological means is an effective, eco-friendly, and promising method that typically involves compounds naturally derived from actinomycetes. Thus, the present study aimed to screen, characterize, and identify the structure of insecticidal compounds from Streptomyces sp. KR0006 and increase the activity through mutagenesis. In the examination of the insecticidal activity level of the isolates, Streptomyces sp. KR0006 metabolite showed significant activity against larvae and moths of Plutella xylostella. Taxonomic analyses of the 16S rRNA gene sequences revealed that the isolated KR0006 strain tended to be 99% consistent with Streptomyces cinereoruber strain NBRC 12756. Three active compounds isolated from the culture filtrate of KR0006 were purified by solvent partition, mid-pressure liquid chromatography (MPLC), Sephadex LH20 column chromatography, and high-performance liquid chromatography (HPLC). By performing ¹H-NMR, ¹³C-NMR, and 2D-NMR experiments, and high-resolution electrospray ionization mass spectrometry analysis, the 316-HP2, 316-HP3, and 316-HP5 compounds were inferred as antimycin A3a (MW, 519.; C₂₆H₃₆N₂O₉), antimycin A8a (MW, 534; C₂₇H₃₈N₂O₉), and antimycin A1a (MW, 548; C₂₈H₄₀N₂O₉) respectively. Mutant U67 obtained from exposure to ultraviolet (UV) irradiation (254 nm, height 17 cm) for 70 seconds resulted in a 70% more larval mortality than that of the initial wild culture. The second mutation of the culture broth enhanced insecticidal activity by 80 and 100% compared with the first mutation and initial medium, respectively. Our study found that Streptomyces sp. KR0006 strain produces insecticidal active compounds and could be used for practical pest management.

Curcumin-Loaded Self-Assembly Constructed by Octenylsuccinate Fish (Cyprinus carpio L.) Scale Gelatin: Preparation and Characterization

Curcumin loaded octenylsuccinate fish scale gelatin (OFSG) was prepared in this study, to explore the potential of FSG for delivering hydrophobic nutrients. The effects of molecule weight (M_w, 22,677-369 g/mol) and degree of substitution (DS, 0-0.116) on the curcumin loading efficiency (CLE, μg/mL) of OFSG (6.98-26.85 mg/mL) were evaluated. The expose of interior hydrophobic groups in FSG and increased intermolecular hydrophobic area contributed to the loading of curcumin in two phases, respectively. The interaction between OFSG and curcumin showed a decreased absorption in FTIR and an increased crystallinity in XRD. The loading of curcumin into OFSG caused a significant decrease of the particle size (from 350-12,070 to 139-214 nm), PDI (from 0.584-0.659 to 0.248-0.347) and ζ-potential (-12.2 or -11.4 to -21.0 or -20.3). OFSG showed a significantly higher stability and lower release of curcumin than FSG at the end of the simulated gastrointestinal digestion. Thus, OFSG showed great potential in the construction of a carrier for hydrophobic nutrients.

Modulating Gene Expression within a Microbiome Based on Computational Models

Simple Summary

Development of computational biology methodologies has provided comprehensive understanding of the complexity of microbiomes, and the extensive ways in which they influence their environment. This has awakened a new research goal, aiming to not only understand the mechanisms in which microbiomes function, but to actively modulate and engineer them for various purposes. However, current microbiome engineering techniques are usually manually tailored for a specific system and neglect the different interactions between the new genetic information and the bacterial population, turning a blind eye to processes such as horizontal gene transfer, mutations, and other genetic alterations. In this work, we developed a generic computational method to automatically tune the expression of heterologous genes within a microbiome according to given preferences, to allow the functionality of the engineering process to propagate in longer periods of time. This goal was achieved by treating each part of the gene individually and considering long term fitness effects on the environment, providing computational and experimental evidence for this approach.

Abstract

Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core property influencing this process is horizontal gene transfer between members of the bacterial community used to maintain genetic variation. The essential effect of this mechanism is the exposure of genetic information to a wide array of members of the community, creating an additional “layer” of information in the microbiome named the “plasmidome”. From an engineering perspective, introduction of genetic information to an environment must be facilitated into chosen species which will be able to carry out the desired effect instead of competing and inhibiting it. Moreover, this process of information transfer imposes concerns for the biosafety of genetic engineering of microbiomes as exposure of genetic information into unwanted hosts can have unprecedented ecological impacts. Current technologies are usually experimentally developed for a specific host/environment, and only deal with the transformation process itself at best, ignoring the impact of horizontal gene transfer and gene-microbiome interactions that occur over larger periods of time in uncontrolled environments. The goal of this research was to design new microbiome-specific versions of engineered genetic information, providing an additional layer of compatibility to existing engineering techniques. The engineering framework is entirely computational and is agnostic to the selected microbiome or gene by reducing the problem into the following set up: microbiome species can be defined as wanted or unwanted hosts of the modification. Then, every element related to gene expression (e.g., promoters, coding regions, etc.) and regulation is individually examined and engineered by novel algorithms to provide the defined expression preferences. Additionally, the synergistic effect of the combination of engineered gene blocks facilitates robustness to random mutations that might occur over time. This method has been validated using both computational and experimental tools, stemming from the research done in the iGEM 2021 competition, by the TAU group.

Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies

The global market demand for natural astaxanthin is rapidly increasing owing to its safety, the potential health benefits, and the diverse applications in food and pharmaceutical industries. The major native producers of natural astaxanthin on industrial scale are the alga Haematococcus pluvialis and the yeast Xanthopyllomyces dendrorhous. However, the natural production via these native producers is facing challenges of limited yield and high cost of cultivation and extraction. Alternatively, astaxanthin production via metabolically engineered non-native microbial cell factories such as Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica is another promising strategy to overcome these limitations. In this review we summarize the recent scientific and biotechnological progresses on astaxanthin biosynthetic pathways, transcriptional regulations, the interrelation with lipid metabolism, engineering strategies as well as fermentation process control in major native and non-native astaxanthin producers. These progresses illuminate the prospects of producing astaxanthin by microbial cell factories on industrial scale.

Edible mushroom industry in China: current state and perspectives

China is one of the largest producers and exporters of wild edible fungi in the world. Cultivation mushroom production value ranks within the top five after grain, vegetable, fruit, and edible oil plantation, greater than sugar, cotton, and tobacco business. More than 40 new varieties of high market value mushrooms from our group were highlighted in this article. Mushroom cultivations have a high impact on China's poverty alleviation program, with earnings at least ten times higher than rice and corn. The products were exported to 137 countries and regions, mainly to Japan, South Korea, ASEAN, the USA, and the European Union, among these, Japan is the biggest import market for cultivated mushrooms from China. Rapid development in the market and an increased demand for edible fungi generally enhance the economy of domestic edible fungi. We are the leading research group in logical farm design that is HACCP-certified to reduce the cost of investment for agriculture, thus broadening the consumption market of edible mushrooms and forming a demand-oriented leading industry for the promotion of human health. The enterprise needs to re-examine the operation plan and the strategic thinking to improve the fundamental drivers based on the available resources of the locality. Mushrooms growing intergrate with upgraded technologies and equipment to become smart agriculture which have smart production and intelligent factories. The purpose of suitable products will not change: delicious, nutritious, healthy, and modern. KEY POINTS: • Cultivation mushroom production value ranks within the top five after grain, vegetable, fruit, and edible oil plantation, greater than sugar, cotton, and tobacco business. • Mushroom cultivations have a high impact on China's poverty alleviation program, with earnings at least ten times higher than rice and corn. • The development of transportation and industrialization of mushrooms facilitate the modernization of mushroom industry in China.

Improved Productivity of Astaxanthin from Photosensitive Haematococcus pluvialis Using Phototaxis Technology

Haematococcus pluvialis is a microalgae actively studied for the production of natural astaxanthin, which is a powerful antioxidant for human application. However, it is economically disadvantageous for commercialization owing to the low productivity of astaxanthin. This study reports an effective screening strategy using the negative phototaxis of the H. pluvialis to attain the mutants having high astaxanthin production. A polydimethylsiloxane (PDMS)-based microfluidic device irradiated with a specific light was developed to efficiently figure out the phototactic response of H. pluvialis. The partial photosynthesis deficient (PP) mutant (negative control) showed a 0.78-fold decreased cellular response to blue light compared to the wild type, demonstrating the positive relationship between the photosynthetic efficiency and the phototaxis. Based on this relationship, the Haematococcus mutants showing photosensitivity to blue light were selected from the 10,000 random mutant libraries. The M1 strain attained from the phototaxis-based screening showed 1.17-fold improved growth rate and 1.26-fold increases in astaxanthin production (55.12 ± 4.12 mg g⁻¹) in the 100 L photo-bioreactor compared to the wild type. This study provides an effective selection tool for industrial application of the H. pluvialis with improved astaxanthin productivity.

Production of Vitamin K by Wild-Type and Engineered Microorganisms

Vitamin K is a fat-soluble vitamin that mainly exists as phylloquinone or menaquinone in nature. Vitamin K plays an important role in blood clotting and bone health in humans. For use as a nutraceutical, vitamin K is produced by natural extraction, chemical synthesis, and microbial fermentation. Natural extraction and chemical synthesis methods for vitamin K production have limitations, such as low yield of products and environmental concerns. Microbial fermentation is a more sustainable process for industrial production of natural vitamin K than two other methods. Recent advanced genetic technology facilitates industrial production of vitamin K by increasing the yield and productivity of microbial host strains. This review covers (i) general information about vitamin K and microbial host, (ii) current titers of vitamin K produced by wild-type microorganisms, and (iii) vitamin K production by engineered microorganisms, including the details of strain engineering strategies. Finally, current limitations and future directions for microbial production of vitamin K are also discussed.

Cellulase production and efficient saccharification of biomass by a new mutant Trichoderma afroharzianum MEA-12

BACKGROUND

Cellulase plays a key role in converting cellulosic biomass into fermentable sugar to produce chemicals and fuels, which is generally produced by filamentous fungi. However, most of the filamentous fungi obtained by natural breeding have low secretory capacity in cellulase production, which are far from meeting the requirements of industrial production. Random mutagenesis combined with adaptive laboratory evolution (ALE) strategy is an effective method to increase the production of fungal enzymes.

RESULTS

This study obtained a mutant of Trichoderma afroharzianum by exposures to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), Ethyl Methanesulfonate (EMS), Atmospheric and Room Temperature Plasma (ARTP) and ALE with high sugar stress. The T. afroharzianum mutant MEA-12 produced 0.60, 5.47, 0.31 and 2.17 IU/mL FPase, CMCase, pNPCase and pNPGase, respectively. These levels were 4.33, 6.37, 4.92 and 4.15 times higher than those of the parental strain, respectively. Also, it was found that T. afroharzianum had the same carbon catabolite repression (CCR) effect as other Trichoderma in liquid submerged fermentation. In contrast, the mutant MEA-12 can tolerate the inhibition of glucose (up to 20 mM) without affecting enzyme production under inducing conditions. Interestingly, crude enzyme from MEA-12 showed high enzymatic hydrolysis efficiency against three different biomasses (cornstalk, bamboo and reed), when combined with cellulase from T. reesei Rut-C30. In addition, the factors that improved cellulase production by MEA-12 were clarified.

CONCLUSIONS

Overall, compound mutagenesis combined with ALE effectively increased the production of fungal cellulase. A super-producing mutant MEA-12 was obtained, and its cellulase could hydrolyze common biomasses efficiently, in combination with enzymes derived from model strain T. reesei, which provides a new choice for processing of bioresources in the future.

Tuning Microbial Activity via Programmatic Alteration of Cell/Substrate Interfaces

A wide portfolio of advanced programmable materials and structures has been developed for biological applications in the last two decades. Particularly, due to their unique properties, semiconducting materials have been utilized in areas of biocomputing, implantable electronics, and healthcare. As a new concept of such programmable material design, biointerfaces based on inorganic semiconducting materials as substrates introduce unconventional paths for bioinformatics and biosensing. In particular, understanding how the properties of a substrate can alter microbial biofilm behavior enables researchers to better characterize and thus create programmable biointerfaces with necessary characteristics on demand. Herein, the current status of advanced microorganism-inorganic biointerfaces is summarized along with types of responses that can be observed in such hybrid systems. This work identifies promising inorganic material types along with target microorganisms that will be critical for future research on programmable biointerfacial structures.

Intelligent host engineering for metabolic flux optimisation in biotechnology

Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.

Effective bioconversion of 1,3-propanediol from biodiesel-derived crude glycerol using organic acid resistance-enhanced Lactobacillus reuteri JH83

Organic acids produced during the fermentation of lactic acid bacteria inhibit cellular growth and the production of 1,3-propanediol (1,3-PDO). Lactobacillus reuteri JH83, which has an increase of 18.6% in organic acid resistance, was obtained through electron beam irradiation mutagenesis irrelevant to the problem of genetically modified organisms. The maximum bioconversion of 1,3-PDO in fed-batch fermentation using pure glycerol by L. reuteri JH83 was 93.2 g/L at 72 h, and the productivity was 1.29 g/L·h, which achieved an increase by 34.6%, compared to that of the wild-type strain. In addition, the result of fed-batch fermentation for the production of 1,3-PDO using crude glycerol was not significantly different from that of pure glycerol. Additionally, transcriptome analysis confirmed changes in the expression levels of sucrose phosphorylase, which is a major facilitator superfamily transporter, and muramyl ligase family proteins, which protect lactic acid bacteria from various stressors, such as organic acids.

Combination of mutagenesis and adaptive evolution to engineer salt-tolerant and aroma-producing yeast for soy sauce fermentation

BACKGROUND

The moromi fermentation of high-salt liquid-state fermentation (HLF) soy sauce is usually performed in high-brine solution (17-20%, w/w), which decreases the metabolic activity of aroma-producing yeast. To enhance the soy sauce flavors, increasing the salt tolerance of aroma-producing yeasts is very important for HLF soy sauce fermentation.

RESULTS

In the present study, atmospheric and room-temperature plasma (ARTP) was first used to mutate the aroma-producing yeast Wickerhamomyces anomalus, and the salt tolerant strains were obtained by selection of synthetic medium with a sodium chloride concentration of 18% (w/w). Furthermore, adaptive laboratory evolution (ALE) was used to improve the salt tolerance of the mutant strains. The results obtained indicated that the combination use of ARTP and ALE markedly increased the NaCl tolerance of the yeast by increasing the cellular accumulation of K+ and removal of cytosolic Na+ , in addition to promoting the production of glycerin and strengthening the integrity of the cell membrane and cell wall. In soy sauce fermentation, the engineered strains improved the physicochemical parameters of HLF soy sauce compared to those produced by the wild-type strain, and the engineered strains also increased the alcohol, acid and aldehyde production, and enriched the types of esters in the soy sauce.

CONCLUSION

The results of the present study indicated that the combination of ARTP mutagenesis and ALE significantly improved the salt tolerance of the aroma-producing yeast, and also enhanced the production of volatiles of HLF soy sauce. © 2021 Society of Chemical Industry.

Mutational property of newly identified mutagen l-glutamic acid γ-hydrazide in Escherichia coli

We previously found that an l-glutamine analog l-glutamic acid γ-hydrazide has high mutagenic activity through the high-throughput laboratory evolution of Escherichia coli. In this study, mutagenicity and mutational property of l-glutamic acid γ-hydrazide were examined by the Ames test and mutation accumulation experiments using E. coli. The Ames test revealed that l-glutamic acid γ-hydrazide showed higher mutagenic activity without metabolic activation than known mutagens 2-aminoanthracene, and cobalt(II) acetate tetrahydrate. This result indicates that l-glutamic acid γ-hydrazide does not require metabolic activation for mutagenic activity in E. coli. Mutation accumulation experiments and whole-genome sequencing analysis revealed the number and spectrum of the accumulated mutations with or without l-glutamic acid γ-hydrazide. In the presence of l-glutamic acid γ-hydrazide, MDS42 strain accumulated 392.3 ± 116.2 point mutations during 30 passages corresponding to 777 generations, while MDS42 strain accumulated 1.5 ± 2.5 point mutations without l-glutamic acid γ-hydrazide during 50 passages corresponding to 1341 generations. The mutational spectrum of l-glutamic acid γ-hydrazide was G/C to A/T transition (82.2 ± 4.3 %) and A/T to G/C transition (17.4 ± 4.3 %). These results indicated that l-glutamic acid γ-hydrazide has a strong mutagenic activity.

Toward improvements for enhancement the productivity and color value of Monascus pigments: a critical review with recent updates

Monascus pigments are a kind of high-quality natural edible pigments fermented by Monascus filamentous fungi, which have been widely used in food, cosmetics, medicine, textiles, dyes and chemical industries as active functional ingredients. Moreover, Monascus pigments have a good application prospect because of a variety of biological functions such as antibacterial, antioxidation, anti-inflammatory, regulating cholesterol, and anti-cancer. However, the low productivity and color value of pigments restrict their development and application. In this review, we introduced the categories, structures, biosynthesis and functions of Monascus pigments, and summarized the current methods for improving the productivity and color value of pigments, including screening and mutagenesis of strains, optimization of fermentation conditions, immobilized fermentation, mixed fermentation, additives, gene knockout and overexpression technologies, which will help to develop the foundation for the industrial production of Monascus pigments.

Low-waste fermentation-derived organic acid production by bipolar membrane electrodialysis—an overview

Organic acids, e.g, citric acid, fumaric acid, lactic acid, malic acid, pyruvic acid and succinic acid, have important role in the food industry and are potential raw materials for the sustainable chemical industry. Their fermentative production based on renewable raw materials requires innovatively designed downstream processing to maintain low environmental impact and resource efficiency throughout the production process. The application of bipolar membranes offers clean and effective way to generate hydrogen ions required for free acid production from its salt. The water dissociation reaction inside the bipolar membrane triggered by electric field plays key role in providing hydrogen ion for the replacement of the cations in organic acid salts. Combined with monopolar ion-exchange membranes in a bipolar membrane electrodialysis process, material flow can be separated beside the product stream into additional reusable streams, thus minimizing the waste generation. This paper focuses on bipolar membrane electrodialysis applied for organic acid recovery from fermentation broth.

Advances in sophorolipid-producing strain performance improvement and fermentation optimization technology

Sophorolipids (SLs), currently one of the most promising biosurfactants, are secondary metabolites produced by many non-pathogenic yeasts, among which Candida bombicola ATCC 22214 is the main sophorolipid-producing strain. SLs have gained much attention since they exhibit anti-tumor, anti-bacterial, anti-inflammatory, and other beneficial biological activities. In addition, as biosurfactants, SLs have a low toxicity level and are easily degradable without polluting the environment. However, the production cost of SLs remains high, which hinders the industrialization process of SL production. This paper describes SL structure and the metabolic pathway of SL synthesis firstly. Furthermore, we analyze factors that contribute to the higher production cost of SLs and summarize current research status on the advancement of SL production based on two aspects: (1) the improvement of strain performance and (2) the optimization of fermentation process. Further prospects of lowering the cost of SL production are also discussed in order to achieve larger-scale SL production with a high yield at a low cost. KEY POINTS: • Review of advances in strain performance improvement and fermentation optimization. • High-throughput screening and metabolic engineering for high-performance strains. • Low-cost substrates and semi-continuous strategies for efficient SL production.

Tartary buckwheat protein hydrolysates enhance the salt tolerance of the soy sauce fermentation yeast Zygosaccharomyces rouxii

Supplementation of protein hydrolysate is an important strategy to improve the salt tolerance of soy sauce aroma-producing yeast. In the present study, Tartary buckwheat protein hydrolysates (BPHs) were prepared and separated by ultrafiltration into LM-1 (<1 kDa) and HM-2 (1-300 kDa) fractions. The supplementation of HM-2 fraction could significantly improve cell growth and fermentation of soy sauce aroma-producing yeast Zygosaccharomyces rouxii As2.180 under high salt (12%, w/w) conditions. However, the LM-1 fraction inhibited strain growth and fermentation. The addition of HM-2 promoted yeast cell accumulation of K⁺, removal of cytosolic Na⁺ and accumulation of glycerol. Furthermore, the HM-2 fraction improved the cell membrane integrity and mitochondrial membrane and decreased intracellular ROS accumulation of the strain. The above results indicated that the supplementation of BPHs with a molecular weight of 1-300 kDa is a potentially effective and feasible strategy for improving the salt tolerance of soy sauce aroma-producing yeast Z. rouxii.

Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production

Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.

Harnessing the Power of Mutagenesis and Adaptive Laboratory Evolution for High Lipid Production by Oleaginous Microalgae and Yeasts

Oleaginous microalgae and yeasts represent promising candidates for large-scale production of lipids, which can be utilized for production of drop-in biofuels, nutraceuticals, pigments, and cosmetics. However, low lipid productivity and costly downstream processing continue to hamper the commercial deployment of oleaginous microorganisms. Strain improvement can play an essential role in the development of such industrial microorganisms by increasing lipid production and hence reducing production costs. The main means of strain improvement are random mutagenesis, adaptive laboratory evolution (ALE), and rational genetic engineering. Among these, random mutagenesis and ALE are straight forward, low-cost, and do not require thorough knowledge of the microorganism’s genetic composition. This paper reviews available mutagenesis and ALE techniques and screening methods to effectively select for oleaginous microalgae and yeasts with enhanced lipid yield and understand the alterations caused to metabolic pathways, which could subsequently serve as the basis for further targeted genetic engineering.