Repeated fed-batch strategy and metabolomic analysis to achieve high docosahexaenoic acid productivity in Crypthecodinium cohnii

Oleaginous Heterotrophic Dinoflagellates—Crypthecodiniaceae

The heterotrophic Crypthecodinium cohnii is a major model for dinoflagellate cell biology, and a major industrial producer of docosahexaenoic acid, a key nutraceutical and added pharmaceutical compound. Despite these factors, the family Crypthecodiniaceae is not fully described, which is partly attributable to their degenerative thecal plates, as well as the lack of ribotype-referred morphological description in many taxons. We report here significant genetic distances and phylogenetic cladding that support inter-specific variations within the Crypthecodiniaceae. We describe Crypthecodinium croucheri sp. nov. Kwok, Law and Wong, that have different genome sizes, ribotypes, and amplification fragment length polymorphism profiles when compared to the C. cohnii. The interspecific ribotypes were supported by distinctive truncation-insertion at the ITS regions that were conserved at intraspecific level. The long genetic distances between Crypthecodiniaceae and other dinoflagellate orders support the separation of the group, which includes related taxons with high oil content and degenerative thecal plates, to be ratified to the order level. The current study provides the basis for future specific demarcation-differentiation, which is an important facet in food safety, biosecurity, sustainable agriculture feeds, and biotechnology licensing of new oleaginous models.

Early Warning of Ischemic Stroke Based on Atherosclerosis Index Combined With Serum Markers

CONTEXT

Ischemic stroke (IS) is a serious public health problem worldwide, threatening human life and health. Atherosclerosis is the cause of stroke. At present, there are few selective indexes that can be used to evaluate atherosclerosis in the clinic; providers rely mainly on the atherosclerotic index (AI). Disturbance of lipid metabolism is considered to be a key event leading to IS.

OBJECTIVE

The purpose of this study was to discover potential biomarkers in the serum of atherosclerosis-induced IS, combined with the AI to provide early warning for the diagnosis of IS.

METHODS

In this study, we used nontargeted metabolomics based on ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) to measure the changes in serum metabolites in a group of patients with IS. To verify the reproducibility of candidate biomarkers in the population, we expanded the sample size.

RESULTS

Five metabolites were identified, including sphingomyelin (18:0/14:0), 1-Methylpyrrolinium, PC (18:0/18:0), LysoPC (18:0/0:0), and PC (18: 2/18:2). The combination of these 5 metabolic markers has good diagnostic and predictive ability, and the change level of these metabolites is significantly related to IS. Our results also indicate that changes in glycerophospholipid metabolism may indicate an early risk of IS development.

CONCLUSION

These findings may contribute to the development of new diagnostic methods of potential biomarkers in serum combined with the AI, thereby providing early warning for the diagnosis of atherosclerosis-induced IS, and may provide a new insights for pathogenesis in IS.

Rewiring the Metabolic Network to Increase Docosahexaenoic Acid Productivity in Crypthecodinium cohnii by Fermentation Supernatant-Based Adaptive Laboratory Evolution

Docosahexaenoic acid (DHA, 22:6n-3) plays significant roles in enhancing human health and preventing human diseases. The heterotrophic marine dinoflagellate Crypthecodinium cohnii is a good candidate to produce high-quality DHA. To overcome the inhibition caused by the fermentation supernatant in the late fermentation stage of DHA-producing C. cohnii, fermentation supernatant-based adaptive laboratory evolution (FS-ALE) was conducted. The cell growth and DHA productivity of the evolved strain (FS280) obtained after 280 adaptive cycles corresponding to 840 days of evolution were increased by 161.87 and 311.23%, respectively, at 72 h under stress conditions and increased by 19.87 and 51.79% without any stress compared with the starting strain, demonstrating the effectiveness of FS-ALE. In addition, a comparative proteomic analysis identified 11,106 proteins and 910 differentially expressed proteins, including six stress-responsive proteins, as well as the up- and downregulated pathways in FS280 that might contribute to its improved cell growth and DHA accumulation. Our study demonstrated that FS-ALE could be a valuable solution to relieve the inhibition of the fermentation supernatant at the late stage of normal fermentation of heterotrophic microalgae.

Effects of glycerol and glucose on docosahexaenoic acid synthesis in Aurantiochyrium limacinum SFD-1502 by transcriptome analysis

Docosahexaenoic acid (DHA) has numerous functions in adjusting the organic health and pragmatic value in medicine and food field. In this study, we compared glycerol and glucose as the only carbon source for DHA production by Aurantiochytrium. When the glycerol concentration was 120 g/L, the maximum DHA yield was 11.08 g/L, and the DHA yield increased significantly, reaching 47.67% of the total lipid content. When the cells grew in glucose, the DHA proportion was 37.39%. Transcriptome data showed that the glycolysis pathway and tricarboxylic acid cycle in Aurantiochytrium were significantly inhibited during glycerol culture, which promoted the tricarboxylic acid transport system and was conducive to the synthesis of fatty acids by acetyl coenzyme A; glucose as substrate activated fatty acid synthesis (FAS)pathway and produced more saturated fatty acids, while glycerol as substrate activated polyketide synthase (PKS)pathway and produced more long-chain polyunsaturated fatty acids. This laid a foundation for fermentation metabolism regulation and molecular transformation.

Biotechnological Enhancement of Probiotics through Co-Cultivation with Algae: Future or a Trend?

The diversity of algal species is a rich source of many different bioactive metabolites. The compounds extracted from algal biomass have various beneficial effects on health. Recently, co-culture systems between microalgae and bacteria have emerged as an interesting solution that can reduce the high contamination risk associated with axenic cultures and, consequently, increase biomass yield and synthesis of active compounds. Probiotic microorganisms also have numerous positive effects on various aspects of health and represent potent co-culture partners. Most studies consider algae as prebiotics that serve as enhancers of probiotics performance. However, the extreme diversity of algal organisms and their ability to produce a plethora of metabolites are leading to new experimental designs in which these organisms are cultivated together to derive maximum benefit from their synergistic interactions. The future success of these studies depends on the precise experimental design of these complex systems. In the last decade, the development of high-throughput approaches has enabled a deeper understanding of global changes in response to interspecies interactions. Several studies have shown that the addition of algae, along with probiotics, can influence the microbiota, and improve gut health and overall yield in fish, shrimp, and mussels aquaculture. In the future, such findings can be further explored and implemented for use as dietary supplements for humans.

A comprehensive review on carbon source effect of microalgae lipid accumulation for biofuel production

Energy is a major driving force for the economic development. Due to the scarcity of fossil fuels and negative impact on the environment, it is important to develop renewable and sustainable energy sources for humankind. Microalgae as the primary feedstock for biodiesel has shown great application potential. However, lipid yield from microalgae is limited by the upstream cost, which restrain the realization of large-scale biofuel production. The modification of lipid-rich microalgae cell has become the focus over the last few decades to improve the lipid content and productivity of microalgae. Carbon is a vital nutrient that regulates the growth and metabolism of microalgae. Different carbon sources are assimilated by microalgae cells via different pathways. Inorganic carbon sources are mainly used through the CO₂-concentrating mechanisms (CCMs), while organic carbon sources are absorbed by microalgae mainly through the Pentose Phosphate (PPP) Pathway and the Embden-Meyerhof-Pranas (EMP) pathway. Therefore, the addition of carbon source has a significant impact on the production of microalgae biomass and lipid accumulation. In this paper, mechanisms of lipid synthesis and carbon uptake of microalgae were introduced, and the effects of different carbon conditions (types, concentrations, and addition methods) on lipid accumulation in microalgal biomass production and biodiesel production were comprehensively discussed. This review also highlights the recent advances in microalgae lipid cultivation with large-scale commercialization and the development prospects of biodiesel production. Current challenges and constructive suggestions are proposed on cost-benefit concerns in large-scale production of microalgae biodiesel.

Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.

Combined Metabolome and Lipidome Analyses for In-Depth Characterization of Lipid Accumulation in the DHA Producing Aurantiochytrium sp. T66

Thraustochytrids are marine heterotrophic microorganisms known for their potential to accumulate docosahexaenoic acid (DHA)-enriched lipids. There have been many attempts to improve thraustochytrid DHA bioprocesses, especially through traditional optimization of cultivation and media conditions. Nevertheless, thraustochytrid-based bioprocesses are still not commercially competitive for high volume-low cost production of DHA. Thus, it is realized that genetic and metabolic engineering strategies are needed for the development of commercially competitive thraustochytrid DHA cell factories. Here, we present an analytical workflow for high resolution phenotyping at metabolite and lipid levels to generate deeper insight into the thraustochytrid physiology, with particular focus on central carbon and redox metabolism. We use time-series sampling during unlimited growth and nitrogen depleted triggering of DHA synthesis and lipid accumulation (LA) to show-case our methodology. The mass spectrometric absolute quantitative metabolite profiling covered glycolytic, pentose phosphate pathway (PPP) and tricarboxylic acid cycle (TCA) metabolites, amino acids, complete (deoxy)nucleoside phosphate pools, CoA and NAD metabolites, while semiquantitative high-resolution supercritical fluid chromatography MS/MS was applied for the lipid profiling. Interestingly, trace amounts of a triacylglycerols (TG) with DHA incorporated in all three acyl positions was detected, while TGs 16:0_16:0_22:6 and 16:0_22:6_22:6 were among the dominant lipid species. The metabolite profiling data indicated that lipid accumulation is not limited by availability of the acyl chain carbon precursor acetyl-CoA nor reducing power (NADPH) but rather points to the TG head group precursor glycerol-3-phosphate as the potential cause at the metabolite level for the gradual decline in lipid production throughout the cultivation. This high-resolution phenotyping provides new knowledge of changes in the central metabolism during growth and LA in thraustochytrids and will guide target selection for metabolic engineering needed for further improvements of this DHA cell factory.

Repetitive Fed-Batch: A Promising Process Mode for Biomanufacturing With E. coli

Recombinant protein production with Escherichia coli is usually carried out in fed-batch mode in industry. As set-up and cleaning of equipment are time- and cost-intensive, it would be economically and environmentally favorable to reduce the number of these procedures. Switching from fed-batch to continuous biomanufacturing with microbials is not yet applied as these cultivations still suffer from time-dependent variations in productivity. Repetitive fed-batch process technology facilitates critical equipment usage, reduces the environmental fingerprint and potentially increases the overall space-time yield. Surprisingly, studies on repetitive fed-batch processes for recombinant protein production can be found for yeasts only. Knowledge on repetitive fed-batch cultivation technology for recombinant protein production in E. coli is not available until now. In this study, a mixed feed approach, enabling repetitive fed-batch technology for recombinant protein production in E. coli, was developed. Effects of the cultivation mode on the space-time yield for a single-cycle fed-batch, a two-cycle repetitive fed-batch, a three-cycle repetitive fed batch and a chemostat cultivation were investigated. For that purpose, we used two different E. coli strains, expressing a model protein in the cytoplasm or in the periplasm, respectively. Our results demonstrate that a repetitive fed-batch for E. coli leads to a higher space-time yield compared to a single-cycle fed-batch and can potentially outperform continuous biomanufacturing. For the first time, we were able to show that repetitive fed-batch technology is highly suitable for recombinant protein production in E. coli using our mixed feeding approach, as it potentially (i) improves product throughput by using critical equipment to its full capacity and (ii) allows implementation of a more economic process by reducing cleaning and set-up times.