Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316‐13

Insights into yeast response to chemotherapeutic agent through time series genome-scale metabolic models

Organism-specific genome-scale metabolic models (GSMMs) can unveil molecular mechanisms within cells and are commonly used in diverse applications, from synthetic biology, biotechnology, and systems biology to metabolic engineering. There are limited studies incorporating time-series transcriptomics in GSMM simulations. Yeast is an easy-to-manipulate model organism for tumor research. Here, a novel approach (TS-GSMM) was proposed to integrate time-series transcriptomics with GSMMs to narrow down the feasible solution space of all possible flux distributions and attain time-series flux samples. The flux samples were clustered using machine learning techniques, and the clusters' functional analysis was performed using reaction set enrichment analysis. A time series transcriptomics response of Yeast cells to a chemotherapeutic reagent-doxorubicin-was mapped onto a Yeast GSMM. Eleven flux clusters were obtained with our approach, and pathway dynamics were displayed. Induction of fluxes related to bicarbonate formation and transport, ergosterol and spermidine transport, and ATP production were captured. Integrating time-series transcriptomics data with GSMMs is a promising approach to reveal pathway dynamics without any kinetic modeling and detects pathways that cannot be identified through transcriptomics-only analysis. The codes are available at https://github.com/karabekmez/TS-GSMM.

In vitro human colonic fermentation of coffee arabinogalactan and melanoidin-rich fractions

Coffee beverage is a source of dietary fiber composed by arabinogalactans, which can also be associated to proteins and phenolic compounds, originating melanoidins. Human colonic in vitro fermentations of coffee fractions, one rich in melanoidins (Mel) and the other in its parental polysaccharide arabinogalactans (AG), were performed in order to evaluate the metabolites produced by microbiota, namely short-chain fatty acids (SCFA), phenolic compounds, and bile acids. After 48 h of fermentation, a higher fermentability of the carbohydrate fraction of AG (62 %) than that of Mel (27 %) was observed, resulting in a SCFA content of 63 mM and 22 mM, respectively. Supplementation with AG and Mel fractions decreased the acetate:propionate ratio from 4.7 (in the absence of coffee fractions) to 2.5 and 3.5, respectively, suggesting a potential inhibition of HMG-CoA reductase, a rate-limiting enzyme for cholesterol synthesis. The fermentation of coffee fractions yielded dihydroferulic and dihydrocaffeic acids, known to have antioxidant properties. In the presence of Mel, it was observed a decrease (from 0.25 to 0.16 mg/mL) in the production of secondary bile acids, whose high content is associated to the development of several diseases, such as colorectal cancer, neurodegenerative and cardiovascular.

Thraustochytrids as a promising source of fatty acids, carotenoids, and sterols: bioactive compound biosynthesis, and modern biotechnology

Thraustochytrids are eukaryotes and obligate marine protists. They are increasingly considered to be a promising feed additive because of their superior and sustainable application in the production of health-benefiting bioactive compounds, such as fatty acids, carotenoids, and sterols. Moreover, the increasing demand makes it critical to rationally design the targeted products by engineering industrial strains. In this review, bioactive compounds accumulated in thraustochytrids were comprehensively evaluated according to their chemical structure, properties, and physiological function. Metabolic networks and biosynthetic pathways of fatty acids, carotenoids, and sterols were methodically summarized. Further, stress-based strategies used in thraustochytrids were reviewed to explore the potential methodologies for enhancing specific product yields. There are internal relationships between the biosynthesis of fatty acids, carotenoids, and sterols in thraustochytrids since they share some branches of the synthetic routes with some intermediate substrates in common. Although there are classic synthesis pathways presented in the previous research, the metabolic flow of how these compounds are being synthesized in thraustochytrids still remains uncovered. Further, combined with omics technologies to deeply understand the mechanism and effects of different stresses is necessary, which could provide guidance for genetic engineering. While gene-editing technology has allowed targeted gene knock-in and knock-outs in thraustochytrids, efficient gene editing is still required. This critical review will provide comprehensive information to benefit boosting the commercial productivity of specific bioactive substances by thraustochytrids.

Genome-scale metabolic modeling of Thraustochytrium sp. RT2316-16: Effects of nutrients on metabolism

Marine thraustochytrids produce metabolically important lipids such as the long-chain omega-3 polyunsaturated fatty acids, carotenoids, and sterols. The growth and lipid production in thraustochytrids depends on the composition of the culture medium that often contains yeast extract as a source of amino acids. This work discusses the effects of individual amino acids provided in the culture medium as the only source of nitrogen, on the production of biomass and lipids by the thraustochytrid Thraustochytrium sp. RT2316-16. A reconstructed metabolic network based on the annotated genome of RT2316-16 in combination with flux balance analysis was used to explain the observed growth and consumption of the nutrients. The culture kinetic parameters estimated from the experimental data were used to constrain the flux via the nutrient consumption rates and the specific growth rate of the triacylglycerol-free biomass in the genome-scale metabolic model (GEM) to predict the specific rate of ATP production for cell maintenance. A relationship was identified between the specific rate of ATP production for maintenance and the specific rate of glucose consumption. The GEM and the derived relationship for the production of ATP for maintenance were used in linear optimization problems, to successfully predict the specific growth rate of RT2316-16 in different experimental conditions.

Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of Genome-Scale Metabolic Models in the Context of Pharma 4.0

Schizochytrium sp. is a microorganism cultured for producing docosahexaenoic acid (DHA). Genome-scale metabolic modeling (GEM) is a promising technique for describing gen-protein-reactions in cells, but with still limited industrial application due to its complexity and high computation requirements. In this work, we simplified GEM results regarding the relationship between the specific oxygen uptake rate (−rO2), the specific growth rate (µ), and the rate of lipid synthesis (rL) using an evolutionary algorithm for developing a model that can be used by a soft sensor for fermentation monitoring. The soft sensor estimated the concentration of active biomass (X), glutamate (N), lipids (L), and DHA in a Schizochytrium sp. fermentation using the dissolved oxygen tension (DO) and the oxygen mass transfer coefficient (kLa) as online input variables. The soft sensor model described the biomass concentration response of four reported experiments characterized by different kLa values. The average range normalized root-mean-square error for X, N, L, and DHA were equal to 1.1, 1.3, 1.1, and 3.2%, respectively, suggesting an acceptable generalization capacity. The feasibility of implementing the soft sensor over a low-cost electronic board was successfully tested using an Arduino UNO, showing a novel path for applying GEM-based soft sensors in the context of Pharma 4.0.

In Vitro Digestibility and Bioaccessibility of Nutrients and Non-Nutrients Composing Extruded Brewers' Spent Grain

This study aimed to evaluate the effect of the extrusion process on the bioaccessibility of brewers’ spent grain (BSG) nutrients (carbohydrates and proteins) and non-nutrients (bioactive compounds). BSG and extruded BSG (EBSG) were digested in vitro simulating human oral-gastro-intestinal digestion and colonic fermentation. The duodenal bioaccessibility of glucose, amino acids and phenolic compounds was analyzed. The fermentability of the dietary fiber was assessed by analysis of short-chain fatty acids. Additionally, assessment of the bioaccessibility of phenolic compounds after colonic fermentation was undertaken. The antioxidant, anti-inflammatory and antidiabetic properties of the bioaccessible compounds were studied. Extrusion caused no change in the digestibility of gluten and glucose bioaccessibility (p > 0.05). Moreover, the bioaccessibility of amino acids and phenolic compounds significantly increased (p < 0.05) due to extrusion. However, higher short-chain fatty acid content was formed in colonic fermentation of BSG (p < 0.05) compared to EBSG. The latter inhibited intracellular ROS formation in IEC-6 cells and showed anti-inflammatory properties in RAW264.7 cells. With respect to antidiabetic properties, glucose absorption was lower, and the inhibition of carbohydrases higher (p < 0.05), in the presence of EBSG compared to BSG. The effects of EBSG and BSG digests on glucose transporters were not significantly different (p > 0.05). In conclusion, extrusion positively affected the nutritional value and health-promoting properties of BSG.

Production, Biosynthesis, and Commercial Applications of Fatty Acids From Oleaginous Fungi

Oleaginous fungi (including fungus-like protists) are attractive in lipid production due to their short growth cycle, large biomass and high yield of lipids. Some typical oleaginous fungi including Galactomyces geotrichum, Thraustochytrids, Mortierella isabellina, and Mucor circinelloides, have been well studied for the ability to accumulate fatty acids with commercial application. Here, we review recent progress toward fermentation, extraction, of fungal fatty acids. To reduce cost of the fatty acids, fatty acid productions from raw materials were also summarized. Then, the synthesis mechanism of fatty acids was introduced. We also review recent studies of the metabolic engineering strategies have been developed as efficient tools in oleaginous fungi to overcome the biochemical limit and to improve production efficiency of the special fatty acids. It also can be predictable that metabolic engineering can further enhance biosynthesis of fatty acids and change the storage mode of fatty acids.

Palm Oil Mill Effluent for Lipid Production by the Diatom Thalassiosira pseudonana

Biomass and lipid production by the marine centric diatom Thalassiosira pseudonana were characterized in media based on palm oil mill effluent (POME) as a source of key nutrients. The optimal medium comprised 20% by volume POME, 80 µM Na2SiO3, and 35 g NaCl L−1 in water at pH ~7.7. In 15-day batch cultures (16:8 h/h light–dark cycle; 200 µmol photons m−2 s−1, 26 ± 1 °C) bubbled continuously with air mixed with CO2 (2.5% by vol), the peak concentration of dry biomass was 869 ± 14 mg L−1 corresponding to a productivity of ~58 mg L−1 day−1. The neutral lipid content of the biomass was 46.2 ± 1.1% by dry weight. The main components of the esterified lipids were palmitoleic acid methyl ester (31.6% w/w) and myristic acid methyl ester (16.8% w/w). The final biomass concentration and the lipid content were affected by the light–dark cycle. Continuous (24 h light) illumination at the above-specified irradiance reduced biomass productivity to ~54 mg L−1 day−1 and lipid content to 38.1%.

Production of polyunsaturated fatty acids by Schizochytrium (Aurantiochytrium) spp

Diverse health benefits are associated with dietary consumption of omega-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFA), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Traditionally, these fatty acids have been obtained from fish oil, but limited supply, variably quality, and an inability to sustainably increase production for a rapidly growing market, are driving the quest for alternative sources. DHA derived from certain marine protists (heterotrophic thraustochytrids) already has an established history of commercial production for high-value dietary use, but is too expensive for use in aquaculture feeds, a much larger potential market for ω-3 LC-PUFA. Sustainable expansion of aquaculture is prevented by its current dependence on wild-caught fish oil as the source of ω-3 LC-PUFA nutrients required in the diet of aquacultured animals. Although several thraustochytrids have been shown to produce DHA and EPA, there is a particular interest in Schizochytrium spp. (now Aurantiochytrium spp.), as some of the better producers. The need for larger scale production has resulted in development of many strategies for improving productivity and production economics of ω-3 PUFA in Schizochytrium spp. Developments in fermentation technology and metabolic engineering for enhancing LC-PUFA production in Schizochytrium spp. are reviewed.

Progress of metabolic engineering for the production of eicosapentaenoic acid

Eicosapentaenoic Acid (EPA) is an essential ω-3 polyunsaturated fatty acid for human health. Currently, high-quality EPA production is largely dependent on the extraction of fish oil, but this unsustainable approach cannot meet its rising market demand. Biotechnological approaches for EPA production from microorganisms have received increasing attention due to their suitability for large-scale production and independence of the seasonal or climate restrictions. This review summarizes recent research on different microorganisms capable of producing EPA, such as microalgae, bacteria, and fungi, and introduces the different EPA biosynthesis pathways. Notably, some novel engineering strategies have been applied to endow and improve the abilities of microorganisms to synthesize EPA, including the construction and optimization of the EPA biosynthesis pathway, an increase in the acetyl-CoA pool supply, the increase of NADPH and the inhibition of competing pathways. This review aims to provide an updated summary of EPA production.

Multiproduct biorefinery from marine thraustochytrids towards a circular bioeconomy

Microalgal biotechnology research continues to expand due to largely unexplored marine environments and growing consumer interest in healthy products. Thraustochytrids, which are marine oleaginous protists, are known for their production of bioactives with significant applications in nutraceuticals, pharmaceuticals, and aquaculture. A wide range of high-value biochemicals, such as nutritional supplements (omega-3 fatty acids), squalene, exopolysaccharides (EPSs), enzymes, aquaculture feed, and biodiesel and pigment compounds, have been investigated. We discuss thraustochytrids as potential feedstocks to produce various bioactive compounds and advocate developing a biorefinery to offset production costs. We anticipate that future advances in cell manufacturing, lipidomic analysis, and nanotechnology-guided lipid extraction would facilitate large-scale cost-competitive production through these microbes.

Antarctic Thraustochytrids as Sources of Carotenoids and High-Value Fatty Acids

Eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and carotenoids are needed as human dietary supplements and are essential components in commercial feeds for the production of aquacultured seafood. Microorganisms such as thraustochytrids are potential natural sources of these compounds. This research reports on the lipid and carotenoid production capacity of thraustochytrids that were isolated from coastal waters of Antarctica. Of the 22 isolates, 21 produced lipids containing EPA+DHA, and the amount of these fatty acids exceeded 20% of the total fatty acids in 12 isolates. Ten isolates were shown to produce carotenoids (27.4-63.9 μg/g dry biomass). The isolate RT2316-16, identified as Thraustochytrium sp., was the best producer of biomass (7.2 g/L in five days) rich in carotenoids (63.9 μg/g) and, therefore, became the focus of this investigation. The main carotenoids in RT2316-16 were β-carotene and canthaxanthin. The content of EPA+DHA in the total lipids (34 ± 3% w/w in dry biomass) depended on the stage of growth of RT2316-16. Lipid and carotenoid content of the biomass and its concentration could be enhanced by modifying the composition of the culture medium. The estimated genome size of RT2316-16 was 44 Mb. Of the 5656 genes predicted from the genome, 4559 were annotated. These included genes of most of the enzymes in the elongation and desaturation pathway of synthesis of ω-3 polyunsaturated fatty acids. Carotenoid precursors in RT2316-16 were synthesized through the mevalonate pathway. A β-carotene synthase gene, with a different domain organization compared to the gene in other thraustochytrids, explained the carotenoid profile of RT2316-16.

High-quality genome-scale metabolic model of Aurantiochytrium sp. T66

The long-chain, ω-3 polyunsaturated fatty acids (PUFAs) (e.g., eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA]), are essential for humans and animals, including marine fish species. Presently, the primary source of these PUFAs is fish oils. As the global production of fish oils appears to be reaching its limits, alternative sources of high-quality ω-3 PUFAs is paramount to support the growing aquaculture industry. Thraustochytrids are a group of heterotrophic protists with the capability to synthesize and accrue large amounts of DHA. Thus, the thraustochytrids are prime candidates to solve the increasing demand for ω-3 PUFAs using microbial cell factories. However, a systems-level understanding of their metabolic shift from cellular growth into lipid accumulation is, to a large extent, unclear. Here, we reconstructed a high-quality genome-scale metabolic model of the thraustochytrid Aurantiochytrium sp. T66 termed iVS1191. Through iterative rounds of model refinement and extensive manual curation, we significantly enhanced the metabolic scope and coverage of the reconstruction from that of previously published models, making considerable improvements with stoichiometric consistency, metabolic connectivity, and model annotations. We show that iVS1191 is highly consistent with experimental growth data, reproducing in vivo growth phenotypes as well as specific growth rates on minimal carbon media. The availability of iVS1191 provides a solid framework for further developing our understanding of T66's metabolic properties, as well as exploring metabolic engineering and process-optimization strategies in silico for increased ω-3 PUFA production.

Production of lipids by Chaetoceros affinis in media based on palm oil mill effluent

Biomass and lipid production by the marine diatom Chaetoceros affinis were characterized under continuous light with aeration. Media based on palm oil mill effluent (POME; 10, 20 and 30 % v/v in distilled water) were used together with a standard control medium. The maximum biomass concentration on day 12 of batch cultures in control medium was 821 ± 71 mg L^-1. Under identical conditions, in the best POME medium (20 % POME v/v in distilled water with other inorganic components), the biomass concentration was reduced by ∼11 % to 734 ± 66 mg L^-1. The lipid content of the biomass grown in the control medium was 50.8 ± 4.5 % by dry weight, but was a little lower (48.9 ± 4.1 % by dry wt) in the above specified best POME medium. In the best POME medium, oleic acid was the major fatty acid (72.3 ± 5.2 % by weight) in the total lipids extracted from the biomass and monounsaturated fatty acids were the main type of fatty acids (74.6 ± 5.2 %). POME levels of >20 % in the medium suppressed both biomass and lipid production relative to the medium with 20 % POME.

Temperature Differentially Affects Gene Expression in Antarctic Thraustochytrid Oblongichytrium sp. RT2316-13

Oblongichytrium RT2316-13 synthesizes lipids rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The content of these fatty acids in the total lipids depended on growth temperature. Sequencing technology was used in this work to examine the thraustochytrid's response to a decrease in growth temperature from 15 °C to 5 °C. Around 4% (2944) of the genes were differentially expressed (DE) and only a few of the DE genes (533 upregulated; 206 downregulated) had significant matches to those in the SwissProt database. Most of the annotated DE genes were related to cell membrane composition (fatty acids, sterols, phosphatidylinositol), the membrane enzymes linked to cell energetics, and membrane structure (cytoskeletal proteins and enzymes). In RT2316-13, the synthesis of long-chain polyunsaturated fatty acids occurred through ω3- and ω6-pathways. Enzymes of the alternative pathways (Δ8-desaturase and Δ9-elongase) were also expressed. The upregulation of the genes coding for a Δ5-desaturase and a Δ5-elongase involved in the synthesis of EPA and DHA, explained the enrichment of total lipid with these two long-chain fatty acids at the low temperature. This molecular response has the potential to be used for producing microbial lipids with a fatty acids profile similar to that of fish oils.