Microbial Cell Factories最新文献

Background: Oleaginous filamentous fungi, such as Mucor circinelloides, are capable of accumulating high levels of single cell oil (SCO), making them attractive candidates for the production of biodiesel and other oleochemicals. Lignocellulosic feedstocks offer an abundant and cost-effective carbon source for SCO production due to their high polysaccharide content. However, most oleaginous microorganisms cannot directly utilize cellulose and hemicellulose polysaccharides, necessitating their conversion into monosaccharides. Lignocellulosic substrates can be saccharified either separately from fermentation (separate hydrolysis and fermentation; SHF) or simultaneously (simultaneous saccharification and fermentation; SSF). This study evaluated SSF using M. circinelloides, as well as SHF cultivations on two types of lignocellulosic hydrolysates, and two control fermentations, with process monitoring via four vibrational spectroscopy techniques: Fourier Transform Infrared (FTIR) spectrometer with fibre optic probe, FTIR microspectrometer, FTIR spectrometer with high throughput setting (HTS), and FT-Raman spectrometer with HTS.

Results: Quantitative estimation of glucose in the cultivation media and lipid content in the biomass was achieved using PLSR analysis of FT-Raman measurements from the cell suspension. FT-Raman spectroscopy demonstrated exceptional capability for online and at-line process monitoring among the tested techniques. It enabled direct and rapid analysis of raw cell suspensions (containing growth media, cellulose-rich pulp substrate, and fungal biomass) without the need for sample pre-treatment, purification, or modification. FT-Raman provided comprehensive biochemical profiles, effectively detecting key chemical changes in both the cellulose-rich pulp substrates and the fungal biomass, including lipid accumulation by the oleaginous fungi. FTIR with fiber optics is effective for monitoring glucose in SHF processes, but its accuracy is limited in SSF processes due to the very low glucose concentrations. The study demonstrates that FTIR microspectroscopy is a valuable tool for lab-scale fermentation process development, as well as for investigating the bioconversion of lignocellulosic biomass into fungal biomass and metabolites.

Conclusions: FT-Raman spectroscopy is highlighted as a powerful process analytical technology (PAT) tool for real-time or near-real-time monitoring of SSF processes for intracellular SCO production. Its ability to provide rich chemical information rapidly and without extensive sample preparation holds significant promise for optimizing industrial SCO production from lignocellulosic feedstocks.

Background: Mannose has wide-ranging applications but microbial fermentation remains underdeveloped compared to biotransformation for its production. The yeast Komagataella phaffii stands out as a premier synthetic biology platform, renowned for its safety profile and exceptional suitability for high-density fermentation. This established chassis organism is ideally positioned for large-scale mannose production through targeted rewiring of its mannose biosynthetic pathway via metabolic engineering.

Results: K. phaffii was metabolically engineered for efficient mannose production using a dual carbon source system: glycerol for biomass generation and glucose for mannose synthesis. To redirect carbon flux toward fructose-6-phosphate (F6P) accumulation at the glycolytic node, glycolytic flux was attenuated by knocking out the phosphofructokinase II (pfk2) gene and downregulating phosphofructokinase I (pfk1). Simultaneously, pentose phosphate pathway flux was reduced by downregulating glucose-6-phosphate dehydrogenase (zwf1). To enhance mannose biosynthesis, conversion of F6P into mannose was promoted by suppressing phosphomannose isomerase (PAS_chr3_1115) and overexpressing the Escherichia coli-derived phosphatase gene yniC. Additionally, three genes involved in arabinitol and ribitol production (PAS_chr2-2_0019, PAS_chr4_0754, and PAS_chr4_0988) were deleted to suppress byproduct accumulation. The engineered strain achieved ~ 121.1 g/L mannose in high-cell-density, fed-batch fermentation, representing the highest reported titer via microbial fermentation to date.

Conclusions: This study achieved efficient mannose production in K. phaffii by remodeling central metabolism. It not only offers a new route for mannose biosynthesis but also establishes a model framework for engineering K. phaffii to produce other high-value bioactive compounds.

Background: Fermented bamboo shoots, locally known as Khorisa, are a traditional food widely consumed in Assam, India, valued for their distinctive tangy flavour and potential probiotic benefits. This study aimed to isolate, identify, and characterize microbial strains from Khorisa, assessing their probiotic potential, safety, and flavour-producing capabilities for application in functional food products.

Methods: Fifteen Khorisa samples were collected from five districts of Assam. Fifty-two microbial isolates were obtained and screened for proteolytic, lipolytic, and carbohydrate-fermenting activities. Six strains (Khorisa/NA/1-Khorisa/NA/6) showing positive enzymatic activity were evaluated for safety (haemolysis, DNase activity, antibiotic susceptibility) and probiotic attributes, including acid, bile, salt, and phenol tolerance, auto-aggregation, and epithelial cell adhesion. Sensory evaluation of curd and rice beverage fermented with these isolates was performed by a trained panel. Derivatized compounds were profiled using gas chromatography-mass spectrometry (GC-MS). Molecular identification was conducted via 16 S rRNA sequencing.

Results: Strain Khorisa/NA/3 was identified as Bacillus sp. strain FPIK1. It exhibited outstanding probiotic-like potential, maintaining 59.2% survival at pH 2, 92.5% at pH 4, and 40% bile salt tolerance. It demonstrated notable halotolerance (20.6% viability at 8% NaCl), phenol resistance (97% at 0.4%), high auto-aggregation (29%), and strong epithelial adhesion (69%). Thermal adaptability was evident with 91.5% viability at 37 °C and 83.4% at 40 °C. Safety evaluation confirmed a non-haemolytic, DNase-negative phenotype with broad antibiotic susceptibility, showing resistance to only one tested antibiotic. Sensory trials revealed that curd and rice beverage fermented with FPIK1 achieved the highest scores for flavour, aroma, and overall acceptability. GC-MS profiling revealed a diverse array of esters, alcohols, ketones, and organic acids that imparted sweet and lemony-sour notes. These volatiles were absent in both uninoculated controls and products prepared with non-flavour-producing strains, underscoring the strain's inherent ability to enhance organoleptic quality through natural flavour biosynthesis.

Conclusion: Bacillus sp. FPIK1, isolated from traditional Khorisa, combines robust probiotic-like attributes, a favourable safety profile, and diverse flavour-producing capabilities, underscoring its suitability as a natural starter culture for probiotic-like, flavour-enhanced fermented foods. These findings support its potential incorporation into functional dairy and non-dairy products, offering both sensory and health benefits while valorizing an indigenous fermented food resource.

Background: Oxalate oxidase (OxOx) is an important enzyme commonly used in the determination of urine oxalate concentration. It is naturally expressed by a variety of plants and microorganisms and recombinant OxOx enzyme has been successfully expressed in yeast, but not in Escherichia coli (E. coli) due to its aggregation in insoluble inclusion bodies. This study aimed to (1) develop a method for purification of active OxOx following expression in E. coli and (2) demonstrate the feasibility of using filter paper coated with recombinant OxOx as a method to measure oxalate concentration in solution.

Results: A synthetic gene optimized for E. coli codon bias expression was derived from barley and cloned into the pRSET expression vector. Phenyl-Sepharose CL-4B and Q-Sepharose Fast Flow chromatography purified the active enzyme to over 90% purity. Using these methods, 21 mg of purified active OxOx enzyme was obtained from a 1 L culture. The purified OxOx exhibited an activity of 3.4 U/mg with the minimum oxalate concentration needed for visual detection on filter paper of 25 µM (range 25-500 µM).

Conclusion: Our study highlights the feasibility of using E. coli for the expression and purification of OxOx, providing a promising approach for future applications in the field of healthcare. Our study has also laid the foundation for further developing an oxalate test strip for urinary oxalate assays based on OxOx.

Background: Microbial anti-inflammatory molecule (MAM) is a key effector of the next-generation probiotic Faecalibacterium duncaniae A2-165, a species whose depletion in the gut microbiota is strongly linked to inflammatory bowel disease (IBD) and other conditions. Despite its importance, the direct anti-inflammatory effects of purified MAM have never been evaluated in vitro or in intestinal inflammation models. Prior studies have relied on bacterial supernatants, synthetic peptides, or DNA delivery systems, each with inherent limitations.

Results: In this study, we produced and purified recombinant MAM (R-MAM) under denaturing conditions and, for the first time, demonstrated its direct anti-inflammatory activity in vitro and its protective effects in a colitis murine model. Despite numerous attempts, we were not able to obtain a non-aggregated R-MAM. Therefore, we can assume that the R-MAM used here is partly or totally denatured. Nevertheless, in vitro assays with human intestinal epithelial cells (HT-29) and peripheral blood mononuclear cells (PBMCs) confirmed the ability of MAM to induce an anti-inflammatory cytokine profile. In addition, in a DNBS-induced colitis model, oral administration of R-MAM significantly prevented weight loss and reduced colon weight and thickness, key macroscopic indicators of inflammation.

Conclusions: These findings provide a critical validation step for the therapeutic potential of MAM in intestinal inflammation, despite its purification under denaturing conditions. Future studies should focus on optimizing protein stability and conformational integrity to increase its therapeutic potential as a biotherapeutic agent.

Background: The abyssal environment is characterized by extreme conditions such as high hydrostatic pressure (HHP), low temperature, and high salinity, which affects the protein synthesis of filamentous fungi. The targeted extracellular enzyme regulation mechanism plays a key role in maintaining its survival and colonization in extreme environments. Compared to prokaryotes, studies on the characteristics of extracellular enzymes in abyssal fungi and their role in carbon-nitrogen coupling metabolism remain limited. In this study, we systematically explored the chitinase-producing activity and catalytic efficiency of Purpureocillium lilacinum FDZ8Y1, a filamentous fungus derived from sediments in the Mariana Trench, in different environments. Transcriptome analysis was used to further investigate the changes of chitinase-related energy metabolism in response to HHP.

Results: Through gradient environmental stress assays (temperature/salinity/HHP) and comparative enzymatic profiling with congeneric strains, P. lilacinum FDZ8Y1 demonstrates remarkable cold tolerance, salt tolerance, and pressure-responsive characteristics in both enzyme production and catalytic efficiency. Transcriptomic analysis revealed that the genes encoding chitinases and the metabolic activities related to chitin degradation and utilization play a pivotal role in the response of this fungus to HHP. HHP stimulation activated the expression of chitinase gene in this fungus, the regulation of cell wall components, as well as key metabolic pathways such as glycolytic - galactose metabolism, fatty acid β -oxidation, and nitrate reductase-mediated nitrogen metabolism.

Conclusions: Our research identified the excellent chitinase activity characteristics of P. lilacinum FDZ8Y1 under low temperature and high pressure, identified the metabolic pathway transformation of this fungus in response to HHP, explored the metabolic response models related to chitin degradation and utilization under these conditions, and further analyzed the functional correlations of these metabolic adaptations. This information provides a new idea and direction for further understanding the functional adaptability of deep-sea fungi and exploring the enzyme resources of deep-sea microorganisms.

Background: Friedelin is a pharmacologically valuable pentacyclic triterpenoid with anti-inflammatory, anticancer, antiviral, and antiobesity properties. Conventional methods of friedelin production rely on solvent-intensive extraction from plant biomass, which is often expensive, inefficient, and environmentally unsustainable. Phaeodactylum tricornutum, a model marine diatom with a unique chimeric sterol biosynthetic pathway and native oxidosqualene accumulation, presents a promising platform for heterologous triterpenoid biosynthesis.

Results: In this study, the TwOSC4 gene from Tripterygium wilfordii, which encodes friedelin synthase, was successfully expressed in P. tricornutum via biolistic transformation. As a result, two transgenic strains, Pt-OSC4-20 and Pt-OSC4-48, were confirmed to express TwOSC4 at both transcript and protein levels. Liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) analysis validated friedelin production in these strains, with a baseline accumulation of 26 ng/mL under standard conditions. Upon treatment with Ro 48-8071, an oxidosqualene cyclase inhibitor that suppresses endogenous sterol biosynthesis, friedelin production increased up to 55 ng/mL. Nile red staining revealed increased lipid droplet formation in the transgenic strains, suggesting the possible intracellular storage of friedelin. Importantly, transgene expression did not impair cell growth, indicating the metabolic compatibility of the host with exogenous triterpenoid synthesis.

Conclusions: This is the first study to demonstrate successful biosynthesis of friedelin in a microalgal system, highlighting the potential of P. tricornutum as a sustainable phototrophic chassis for the production of plant-derived triterpenoids. Unlike yeast-based systems, which require extensive metabolic amplification, P. tricornutum enables simpler genetic engineering and simultaneous coproduction of valuable compounds, such as fucoxanthin and Omega-3 Eicosapentaenoic Acid (EPA). These findings lay the groundwork for further strain optimization aimed at increasing friedelin yield and broadening the scope of triterpenoid biosynthesis in microalgae.

Background: Foot-and-mouth disease (FMD) is a highly infectious disease that mainly affects cloven-hoofed animals. The rapid spread of this disease hinders the success of control measures. This necessitates the urgent development of a vaccine to ensure the safe rearing of affected animals. However, traditional vaccines have some drawbacks including partial protection against persistent infection and a lack of cross-protection against different strains.

Results: We developed an oral vaccine that targets VP1, the major immunogenic protein of the causative FMD virus (FMDV). We expressed this protein using the surface display method and subsequently analyzed its immune efficacy. Western blot analysis and confocal imaging confirmed that our constructs effectively expressed VP1 on the surface of yeast cells. However, the expression of surface-displayed VP1 was substantially lower than that of intracellular VP1. The immune response of mice fed with cells expressing surface-displayed VP1 was greater than that of mice fed with an equal number of cells expressing intracellular VP1.

Conclusions: Our study indicates that yeast surface expressed VP1 elicits a superior immune response against FMDV than intracellularly expressed VP1 for immune response against FMDV, which offers a potential breakthrough in the effort to provide a simple and highly effective oral vaccine.

Background: Corn bran arabinoxylan (CBAX) is one of the most structurally complex xylans in nature. The bioconversion of CBAX into value-added products remains challenging because the substrate is resistant to pure xylanases and commercial enzyme cocktails. The carbohydrate-active enzymes (CAZymes) of Penicillium parvum 4-14 have been shown to efficiently hydrolyze CBAX. This study aimed to investigate the expression patterns and functional roles of CAZymes involved in the degradation of complex arabinoxylans in the fungus using transcriptomic and proteomic technologies.

Results: P. parvum 4-14 grew on CBAX and corn cob arabinoxylan (CCAX) with different substitution patterns and produced secretomes with varied compositions. The CBAX- or CCAX-induced fungal secretomes showed similar ratios (76.2% and 75.1%) on monosaccharide release from CBAX, but the former has a 12% higher ratio on monosaccharide release from CCAX than the latter. Integrated transcriptomic and proteomic analyses revealed distinct patterns of functional gene expression and CAZyme secretion in P. parvum cells induced by the two types of arabinoxylans, implying that the fungus has a complex regulatory system for CAZyme synthesis. A total of 26 CAZymes were inferred to be involved in the degradation of CBAX on the basis of multi-omics data and substrate structures. At the same fungal growth stage (48 h), 24 of these 26 CAZyme showed 0.42- to 5.74-fold higher gene transcription levels under CBAX culture than under CCAX culture.

Conclusions: Different sources of arabinoxylans significantly affect the production of extracellular CAZymes in P. parvum. These findings are valuable for understanding the key CBAX-degrading enzymes and engineering tailored enzyme systems to valorize complex hemicelluloses.