Biotechnological production of value-added compounds by ustilaginomycetous yeasts

The Short-Term Variation of Human Gut Mycobiome in Response to Dietary Intervention of Different Macronutrient Distributions

While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria, with relatively little attention given to the gut mycobiome. This study aims to investigate how diets with different dietary macronutrient distributions impact the gut mycobiome. We investigated gut mycobiome response to high-carbohydrate, low-fat (HC) and low-carbohydrate high-fat (LC) diet interventions based on a series of 72-day feeding-based n-of-1 clinical trials. A total of 30 participants were enrolled and underwent three sets of HC and LC dietary interventions in a randomized sequence. Each set lasted for 24 days with a 6-day washout period between dietary interventions. We collected and analyzed the fungal composition of 317 stool samples before and after each intervention period. To account for intra-individual variation across the three sets, we averaged the mycobiome data from the repeated sets for analysis. Of the 30 participants, 28 (aged 22-34 years) completed the entire intervention. Our results revealed a significant increase in gut fungal alpha diversity (p < 0.05) and significant changes in fungal composition (beta diversity, p < 0.05) after the HC dietary intervention. Specifically, we observed the enrichment of five fungal genera (Pleurotus, Kazachstania, Auricularia, Paraphaeosphaeria, Ustilaginaceae sp.; FDR < 0.052) and depletion of one fungal genus (Blumeria; FDR = 0.03) after the HC intervention. After the LC dietary intervention, one fungal genus was enriched (Ustilaginaceae sp.; FDR = 0.003), and five fungal genera were depleted (Blumeria, Agaricomycetes spp., Malassezia, Rhizopus, and Penicillium; FDR < 0.1). This study provides novel evidence on how the gut mycobiome structure and composition change in response to the HC and LC dietary interventions and reveals diet-specific changes in the fungal genera.

Renewable carbon sources to biochemicals and -fuels: contributions of the smut fungi Ustilaginaceae

The global demand for food, fuels, and chemicals increases annually. Using renewable C-sources (i.e. biomass, CO₂, and organic waste) is a prerequisite for a future free of fossil carbon. The smut fungi Ustilaginaceae naturally produce a versatile spectrum of valuable products, such as organic acids, polyols, and glycolipids, applicable in the food, energy, chemistry, and pharmaceutical sector. Combined with the use of alternative (co-)substrates (e.g. acetate, butanediol, formate, and glycerol), these microorganisms offer excellent potential for industrial biotechnology, thereby overcoming central challenges humankind faces, including CO₂ release and land use. Here, we provide insight into fundamental production capacities, present genetic modifications that improve the biotechnical application, and review recent high-performance engineering of Ustilaginaceae toward relevant platform chemicals.

Nonconventional yeasts to produce aroma compounds by using agri-food waste materials

Nowadays, biotechnological applications are emphasized to ensure sustainable development by reutilizing waste materials to prevent ecological problems and to produce or recover compounds that may have positive effects on health. Yeasts are fascinating microorganisms that play a key role in several traditional and innovative processes. Although Saccharomyces is the most important genus of yeasts, and they are major producers of biotechnological products worldwide, a variety of other yeast genera and species than Saccharomyces that are called 'non-Saccharomyces' or 'nonconventional' yeasts also have important potential for use in biotechnological applications. Some of the nonconventional yeast strains offer a unique potential for biotechnological applications to produce valuable secondary metabolites due to their characteristics of surviving and growing in such extreme conditions, e.g. wide substrate range, rapid growth, thermotolerance, etc. In this review, we aimed to summarize potential biotechnological applications of some nonconventional yeasts (Kluyveromyces spp., Yarrowia spp., Pichia spp., Candida spp., etc.) to produce industrially important aroma compounds (phenylethyl alcohol, phenylethyl acetate, isobutyl acetate, diacetyl, etc.) by reutilizing agri-food waste materials in order to prevent ecological problems and to produce or recover compounds that may have positive effects on health.

Current Status and Future Perspectives of Supports and Protocols for Enzyme Immobilization

The market for industrial enzymes has witnessed constant growth, which is currently around 7% a year, projected to reach $10.5 billion in 2024. Lipases are hydrolase enzymes naturally responsible for triglyceride hydrolysis. They are the most expansively used industrial biocatalysts, with wide application in a broad range of industries. However, these biocatalytic processes are usually limited by the low stability of the enzyme, the half-life time, and the processes required to solve these problems are complex and lack application feasibility at the industrial scale. Emerging technologies create new materials for enzyme carriers and sophisticate the well-known immobilization principles to produce more robust, eco-friendlier, and cheaper biocatalysts. Therefore, this review discusses the trending studies and industrial applications of the materials and protocols for lipase immobilization, analyzing their advantages and disadvantages. Finally, it summarizes the current challenges and potential alternatives for lipases at the industrial level.

Perspectives for the application of Ustilaginaceae as biotech cell factories

Basidiomycetes fungi of the family Ustilaginaceae are mainly known as plant pathogens causing smut disease on crops and grasses. However, they are also natural producers of value-added substances like glycolipids, organic acids, polyols, and harbor secretory enzymes with promising hydrolytic activities. These attributes recently evoked increasing interest in their biotechnological exploitation. The corn smut fungus Ustilago maydis is the best characterized member of the Ustilaginaceae. After decades of research in the fields of genetics and plant pathology, a broad method portfolio and detailed knowledge on its biology and biochemistry are available. As a consequence, U. maydis has developed into a versatile model organism not only for fundamental research but also for applied biotechnology. Novel genetic, synthetic biology, and process development approaches have been implemented to engineer yields and product specificity as well as for the expansion of the repertoire of produced substances. Furthermore, research on U. maydis also substantially promoted the interest in other members of the Ustilaginaceae, for which the available tools can be adapted. Here, we review the latest developments in applied research on Ustilaginaceae towards their establishment as future biotech cell factories.

Innovations in CAZyme gene diversity and its modification for biorefinery applications

For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.

Growth Behavior of Selected Ustilaginaceae Fungi Used for Mannosylerythritol Lipid (MEL) Biosurfactant Production - Evaluation of a Defined Culture Medium

Fungi of the Ustilaginaceae family are a promising source for many biotechnologically relevant products. Among these, mannosylerythritol lipid (MEL) biosurfactants have drawn a special interested over the last decades due to their manifold application possibilities. Nevertheless, there is still a knowledge gap regarding process engineering of MEL production. As an example, no reports on the use of a chemically defined culture medium have been published yet, although such a defined medium might be beneficial for scaling-up the production process toward industrial scale. Our aim therefore was to find a mineral medium that allows fast biomass growth and does not negatively affect the successive MEL production from plant oils. The results showed comparable growth performance between the newly evaluated mineral medium and the established yeast extract medium for all seven investigated Ustilaginaceae species. Final biomass concentrations and specific growth rates of 0.16-0.25 h^–1 were similar for the two media. Oxygen demand was generally higher in the mineral medium than in the yeast extract medium. It was shown that high concentrations of vitamins and trace elements were necessary to support the growth. Increasing starting concentrations of the media by a factor of 10 resulted in proportionally increasing final biomass concentrations and up to 2.3-times higher maximum growth rates for all species. However, it could also lead to oxygen limitation and stagnant growth rates when too high medium concentrations were used, which was observed for Ustilago siamensis and Moesziomyces aphidis. Successive MEL production from rapeseed oil was effectively shown for 4 out of 7 organisms when the mineral medium was used for cell growth, and it was even enhanced for two organisms, M. aphidis and Pseudozyma hubeiensis pro tem., as compared to the established yeast extract medium. Conversion of rapeseed oil into MEL was generally improved when higher biomass concentrations were achieved during the initial growth phase, indicating a positive relationship between biomass concentration and MEL production. Overall, this is the first report on the use of a chemically defined mineral medium for the cell growth of Ustilaginaceae fungi and successive MEL production from rapeseed oil, as an alternative to the commonly employed yeast extract medium.

Could squalene be an added value to use olive by-products?

Squalene (SQ) is an intermediate hydrocarbon in the biosynthesis of phytosterols and terpenes in plants. It is widely used for applications such as skin moisturizers, vaccines, or in carriers for active lipophilic molecules. It has commonly been obtained from sharks, but restrictions on their use have created a need to find alternative sources. We present a review of studies concerning SQ in olive groves to characterize its content and to provide new aspects that may increase the circular economy of the olive tree. There is a large variation in SQ content in virgin olive oil due to cultivars and agronomic issues such as region, climate, types of soil, crop practices, and harvest date. Cultivars with the highest SQ content in their virgin olive oil were 'Nocellara de Belice', 'Drobnica', 'Souri', and 'Oblica'. An interaction between cultivar and aspects such as irrigation practices or agricultural season is frequently observed. Likewise, the production of high SQ content needs precise control of fruit maturation. Leaves represent an interesting source, if its extraction and yield compensate for the expenses of their disposal. Supercritical carbon dioxide extraction from olive oil deodorizer distillates offers an opportunity to obtain high-purity SQ from this derivative. Exploiting SQ obtained from olive groves for the pharmaceutical or cosmetic industries poses new challenges and opportunities to add value and recycle by-products. © 2019 Society of Chemical Industry.

Monitoring of the enzymatic activity of intracellular lipases of

Under nitrogen starvation, Ustilago maydis forms lipid droplets (LDs). Although the dynamics of these organelles are known in the literature, the identity of the lipases implicated in their degradation is unknown. We determined lipase activity and identified the intracellular lipases expressed during growth under nitrogen starvation and YPD media by zymograms. The results showed that cytosolic extracts exhibited higher lipase activity when cells were grown in YPD. Under nitrogen starvation, lipase activity was not detected after 24 h of culture, resulting in lipid accumulation in LDs. This suggests that these lipases could be implicated in LD degradation. In the zymogram, two bands, one of 25 and the other of 37 kDa, presented lipase activity. The YPD extracts showed lipase activity in olive and almond oils, which contain triacylglycerols with mono and polyunsaturated fatty acids. This is the first report about U. maydis cytosolic lipases involved in LD degradation.

Influence of microorganism and plant oils on the structure of mannosylerythritol lipid (MEL) biosurfactants revealed by a novel thin layer chromatography mass spectrometry method

Mannosylerythritol lipids (MEL) are microbial glycolipid biosurfactants with great potential for application in cosmetics and household detergents. In current biotechnological processes, they are produced by basidiomycetous fungi, the Ustilaginaceae, as a complex mixture of different chemical structures. It was the aim of this paper to study the influence of producer organisms and substrates on the resulting MEL structures with a novel high-resolution HPTLC-MALDI-TOF method. Given the seven different microbes and four plant oils, our analysis revealed that the product concentrations varied strongly between organisms, while they were similar for the different substrates. Coconut oil presented an exception, since only one organism was able to synthesize MEL from this substrate in considerable yields. Analysis by GC-FID further showed that the chain length pattern of hydrophobic fatty acid side-chains was very specific for individual organisms, while substrates had only a minor influence on the chain length. Our novel HPTLC-MALDI-TOF combination method finally demonstrated the presence of multiple MEL sub-variants with differing acetylation and fatty acid chain lengths. It also revealed the production of a more hydrophilic biosurfactant mannosylmannitol lipid (MML) as a side-product in certain fungi. Overall, it was concluded that the pattern of produced biosurfactant structures are mainly governed by producer organisms rather than substrates.

Triacylglycerols accumulation and glycolipids secretion by the oleaginous yeast Rhodotorula babjevae Y-SL7: Structural identification and biotechnological applications

The newly isolated oleaginous yeast, Rhodotorula babjevae Y-SL7, was shown to accumulate high intracellular content of microbial oil (mainly triacylglycerols) and to secret, under the same culture conditions, an atypical glycolipid. This unusual behavior was induced when the strain was subjected to nitrogen limitation and high amount of carbon. A series of analytical methods was adopted in order to structurally characterize the secreted glycolipid. The latter consists of a mixture of 9 molecules formed by a polyol head group, bound through the carboxyl end of an acetylated 3-hydroxy fatty acid with C18 or C16 chain length. In addition of their physicochemical properties such as emulsifying activity on hydrophobic substrates, Y-SL7 glycolipids have shown a therapeutically promising cytotoxic effect against different cancer cell lines. In fact, Y-SL7 strain can be used for the production of triacylglycerols as energetic molecules and for the secretion of a biosurfactant of therapeutic and environmental interest.

Online evaluation of the metabolic activity of Ustilago maydis on (poly)galacturonic acid

Background

Pectin is a rather complex and highly branched polysaccharide strengthening the plant cell wall. Thus, many different pectinases are required for an efficient microbial conversion of biomass waste streams with a high pectin content like citrus peel, apple pomace or sugar beet pulp. The screening and optimization of strains growing on pectic substrates requires both, quantification of the residual substrate and an accurate determination of the enzymatic activity. Galacturonic acid, the main sugar unit of pectin, is an uncommon substrate for microbial fermentations. Thus, growth and enzyme production of the applied strain has to be characterized in detail to understand the microbial system. An essential step to reach this goal is the development of online monitoring tools.

Results

In this study, a method for the online determination of residual substrate was developed for the growth of the plant pathogenic fungus Ustilago maydis on pectic substrates such as galacturonic acid. To this end, an U. maydis strain was used that expressed a heterologous exo-polygalacturonase for growth on polygalacturonic acid. The growth behavior on galacturonic acid was analyzed by online measurement of the respiration activity. A method for the online prediction of the residual galacturonic acid concentration during the cultivation, based on the overall oxygen consumption, was developed and verified by offline sampling. This sensitive method was extended towards polygalacturonic acid, which is challenging to quantify via offline measurements. Finally, the enzymatic activity in the culture supernatant was calculated and the enzyme stability during the course of the cultivation was confirmed.

Conclusion

The introduced method can reliably predict the residual (poly)galacturonic acid concentration based on the overall oxygen consumption. Based on this method, the enzymatic activity of the culture broth of an U. maydis strain expressing a heterologous exo-polygalacturonase could be calculated. It was demonstrated that the method is especially advantageous for determination of low enzymatic activities. In future, it will be applied to U. maydis strains in which the number of produced hydrolytic enzymes is increased for more efficient degradation.

Electronic supplementary material

The online version of this article (10.1186/s13036-018-0128-1) contains supplementary material, which is available to authorized users.