Food-related applications of Yarrowia lipolytica

Inoculation of Yarrowia lipolytica promotes the growth of lactic acid bacteria, Debaryomyces udenii and the formation of ethyl esters in sour meat

Yarrowia lipolytica N12 and A13 with high lipase activity obtained by mutagenesis were inoculated into sour meat, and their effects on physicochemical properties, microbial community succession, free amino acids, and volatile compounds of sour meat were investigated. Inoculation fermentation increased the contents of free amino acids observably, rapidly reduced pH, promoted the accumulation of total acids, decreased 2-thiobarbituric acid reactive substances (TBARS) values. In addition, the addition of Y. lipolytica might contribute to the growth of lactic acid bacteria, Candida spp., and Debaryomyces udenii, which play an important role in production of volatile compounds. It was shown that inoculation promoted the production of esters, aldehydes, and alcohols, especially ethyl esters, giving sour meat a better meat flavor. Besides, it was found that Y. lipolytica A13 had better fermenting property. Sample of A13 group had higher contents of ethyl esters, free amino acids and dominant microorganisms. The results may help to provide new strains for sour meat fermentation.

Rapid Acidification and Off-Flavor Reduction of Pea Protein by Fermentation with Lactic Acid Bacteria and Yeasts

Pea protein is widely used as an alternative protein source in plant-based products. In the current study, we fermented pea protein to reduce off-flavor compounds, such as hexanal, and to produce a suitable fermentate for further processing. Laboratory fermentations using 5% (w/v) pea protein suspension were carried out using four selected lactic acid bacteria (LAB) strains, investigating their growth and acidification capabilities in pea protein. Rapid acidification of pea protein was achieved with Lactococcus lactis subsp. lactis strain LTH 7123. Next, this strain was co-inoculated together with either the yeasts Kluyveromyces lactis LTH 7165, Yarrowia lipolytica LTH 6056, or Kluyveromyces marxianus LTH 6039. Fermentation products of the mixed starter cultures and of the single strains were further analyzed by gas chromatography coupled with mass spectrometry to quantify selected volatile flavor compounds. Fermentation with L. lactis LTH 7123 led to an increase in compounds associated with the "beany" off-flavors of peas, including hexanal. However, significant reduction in those compounds was achieved after fermentation with Y. lipolytica LTH 6056 with or without L. lactis LTH 7123. Thus, fermentation using co-cultures of LAB and yeasts strains could prove to be a valuable method for enhancing quality attributes of pea protein-based products.

Innovative beverage creation through symbiotic microbial communities inspired by traditional fermented beverages: current status, challenges and future directions

Fermented beverages (FBs) are facing challenges in functional performance and flavor complexity, necessitating the development of new multi-functional options. Traditional fermented beverages (TFBs), both alcoholic and nonalcoholic, have gained increased attention for their health-promoting effects during the COVID-19 pandemic. This review summarized the primary commercially available probiotics of FBs, along with the limitations of single and mixed probiotic FBs. It also examined the recent research progress on TFBs, emphasizing the typical microbial communities (MC) of TFBs, and TFBs made from crops (grains, vegetables, fruits, etc.) worldwide and their associated functions and health benefits. Furthermore, the construction, technical bottlenecks of the synthetic MC involved in developing innovative FBs were presented, and the promising perspective of FBs was described. Drawing inspiration from the MC of TFBs, developing of stable and multifunctional FBs using synthetic MC holds great promise for beverage industry. However, synthetic MC suffers from structural instability and poorly acknowledged interaction mechanisms, resulting in disappointing results in FBs. Future researches should prioritize creating synthetic MC fermentation that closely resemble natural fermentation, tailored to meet the needs of different consumers. Creating personalized FBs with high-tech intelligence is vital in attracting potential consumers and developing novel beverages for the future.

Microbial meat: A sustainable vegan protein source produced from agri-waste to feed the world

In the modern world, animal and plant protein may not meet the sustainability criteria due to their high need for arable land and potable water consumption, among other practices. Considering the growing population and food shortage, finding alternative protein sources for human consumption is an urgent issue that needs to be solved, especially in developing countries. In this context, microbial bioconversion of valuable materials in nutritious microbial cells represent a sustainable alternative to the food chain. Microbial protein, also known as single-cell protein (SCP), consist of algae biomass, fungi or bacteria that are currently used as food source for both humans and animals. Besides contributing as a sustainable source of protein to feed the world, producing SCP, is important to reduce waste disposal problems and production costs meeting the sustainable development goals. However, for microbial protein as feed or food to become an important and sustainable alternative, addressing the challenges of raising awareness and achieving wider public regulatory acceptance is real and must be addressed with care and convenience. In this work, we critically reviewed the potential technologies for microbial protein production, its benefits, safety, and limitations associated with its uses, and perspectives for broader large-scale implementation. We argue that the information documented in this manuscript will assist in developing microbial meat as a major protein source for the vegan world.

Comparative Analysis of the Alkaline Proteolytic Enzymes of Yarrowia Clade Species and Their Putative Applications

Proteolytic enzymes are commercially valuable and have multiple applications in various industrial sectors. The most studied proteolytic enzymes produced by Yarrowia lipolytica, extracellular alkaline protease (Aep) and extracellular acid protease (Axp), were shown to be good candidates for different biotechnological applications. In this study, we performed a comprehensive analysis of the alkaline proteolytic enzymes of Yarrowia clade species, including phylogenetic studies, synteny analysis, and protease production and application. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we reconstructed the evolutionary scenario of the XPR2 gene for species of the Yarrowia clade. Furthermore, except for the proteolytic activity of the analyzed Yarrowia clade strains, the brewers’ spent grain (BSG) was used as a substrate to obtain protein hydrolysates with antioxidant activity. For each culture, the degree of hydrolysis was calculated. The most efficient protein hydrolysis was observed in the cultures of Y. lipolytica, Y. galli, and Y. alimentaria. In contrast, the best results obtained using the 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) method were observed for the culture medium after the growth of Y. divulgata, Y. galli, and Y. lipolytica on BSG.

Large-Scale Production of Isocitric Acid Using Yarrowia lipolytica Yeast with Further Down-Stream Purification

Isocitric acid (ICA) refers to a group of promising regulators of energy metabolism which has antistress, antihypoxic, and antioxidant activities. In this paper, we reported a process of ICA production from rapeseed oil using yeast Yarrowia lipolytica VKM Y-2373 in a 500-L fermentor. The producer synthesized 64.1 g/L ICA with a product yield of 0.72 g/g and a productivity 0.54 g/L·h. We also developed an effective purification method, including a cell separation, clarification, concentration, acidification, and crystallization process, which resulted in the formation of the crystals of monopotassium salt of ICA with a purity of 99.0–99.9%. To the best of our knowledge, this is the first report on an ICA production process at an upscaled bioreactor level.

Homologous High-Level Lipase and Single-Cell Protein Production with Engineered Yarrowia lipolytica via Scale-Up Fermentation for Industrial Applications

Yarrowia lipolytica is a promising feed additives. Here, we aimed to produce extracellular lipases and single-cell proteins (SCPs) at high levels simultaneously through fed-batch fermentation of engineered Y. lipolytica. The parameters for 500 mL shake flask cultures were optimized with a single factorial design. The resultant activity of lipase reached 880.6 U/mL after 84 h of fermentation, and 32.0 g/L fermentation broth of dry SCP was obtained at 120 h. To attain high SCP and lipase productivity, the high-density fed-batch fermentation of Y. lipolytica was scaled up in 10 L, 30 L, and 100 L fermentors. Using glycerol as the sole carbon source, the lipase activity peaked to 8083.3 U/mL, and the final dry SCP weight was 183.1 g/L at 94.6 h in 10 L fermentors. The extracellular lipase activity and SCP weight reached 11,100.0 U/mL and 173.3 g of dry SCP/L at 136 h in 30 L fermentors, respectively. Following 136 h of fed-batch fermentation, the extracellular lipase activity and dry SCP weight reached 8532.0 U/mL and 170.3 g/L in 100 L fermentors, respectively. A balance between the lipase secretion and growth of Y. lipolytica recombinant strain was achieved, indicating that an efficient fermentation strategy could promote further scale-up for industrial SCP production from engineered Y. lipolytica.

Mycological evaluation of frozen meat with special reference to yeasts

Background and Aim

Fungi can play beneficial and detrimental roles in meat products; however, the diversity and significance of fungi in meat products are poorly understood. This study aimed to isolate and characterize fungal species from frozen beef samples collected from retail stores in the Qena Governorate, Egypt.

Materials and Methods

A total of 70 frozen beef samples were collected from retail stores in Qena, Egypt. All samples were subjected to mycological examination. Fungal colonies were identified using conventional approaches, as well as the VITEK 2 system and DNA sequencing of the internal transcribed spacer region. Analyses of enzymatic activity, biofilm formation ability, and the antimicrobial resistance profiles of the isolated yeasts were also conducted.

Results

Molds and yeasts were isolated from 40% and 60% of meat samples, respectively. Mold isolates were dominated by Aspergillus, Penicillium, and Cladosporium spp., whereas yeast isolates were identified as Candida albicans, Candida parapsilosis, Yarrowia lipolytica, Saccharomyces cerevisiae, and Rhodotorula mucilaginosa. Compared to other yeast species, the highest production of lipase and protease was observed in Candida species. The strongest ability to form biofilms was observed in Candida spp., followed by S. cerevisiae, Y. lipolytica, and R. mucilaginosa. The results of antimicrobial susceptibility testing revealed that all yeast isolates showed notable resistance to fluconazole and itraconazole.

Conclusion

A significant correlation between antimicrobial resistance and biofilm formation was observed in several species. This study highlights the importance of the dangers of yeasts in food products and the extent of their impact on public health.

Study of the persistence and dynamics of recombinant mCherry-producing Yarrowia lipolytica strains in the mouse intestine using fluorescence imaging

Yarrowia lipolytica is a dimorphic oleaginous non-conventional yeast widely used as a powerful host for expressing heterologous proteins, as well as a promising source of engineered cell factories for various applications. This microorganism has a documented use in Feed and Food and a GRAS (generally recognized as safe) status. Moreover, in vivo studies demonstrated a beneficial effect of this yeast on animal health. However, despite the focus on Y. lipolytica for the industrial manufacturing of heterologous proteins and for probiotic effects, its potential for oral delivery of recombinant therapeutic proteins has seldom been evaluated in mammals. As the first steps towards this aim, we engineered two Y. lipolytica strains, a dairy strain and a laboratory strain, to produce the model fluorescent protein mCherry. We demonstrated that both Y. lipolytica strains transiently persisted for at least 1 week after four daily oral administrations and they maintained the active expression of mCherry in the mouse intestine. We used confocal microscopy to image individual Y. lipolytica cells of freshly collected intestinal tissues. They were found essentially in the lumen and they were rarely in contact with epithelial cells while transiting through the ileum, caecum and colon of mice. Taken as a whole, our results have shown that fluorescent Y. lipolytica strains constitute novel tools to study the persistence and dynamics of orally administered yeasts which could be used in the future as oral delivery vectors for the secretion of active therapeutic proteins in the gut.

Fungi as a Source of Edible Proteins and Animal Feed

It is expected that the world population will reach 9 billion by 2050. Thus, meat, dairy or plant-based protein sources will fail to meet global demand. New solutions must be offered to find innovative and alternative protein sources. As a natural gift, edible wild mushrooms growing in the wet and shadow places and can be picked by hand have been used as a food. From searching mushrooms in the forests and producing single cell proteins (SCP) in small scales to mega production, academia, United Nations Organizations, industries, political makers and others, play significant roles. Fermented traditional foods have also been reinvestigated. For example, kefir, miso, and tempeh, are an excellent source for fungal isolates for protein production. Fungi have unique criteria of consuming various inexpensive wastes as sources of carbon and energy for producing biomass, protein concentrate or amino acids with a minimal requirement of other environmental resources (e.g., light and water). Fungal fermented foods and SCP are consumed either intentionally or unintentionally in our daily meals and have many applications in food and feed industries. This review addresses fungi as an alternative source of edible proteins and animal feed, focusing mainly on SCP, edible mushrooms, fungal fermented foods, and the safety of their consumption.

Tailoring and optimizing fatty acid production by oleaginous yeasts through the systematic exploration of their physiological fitness

Background

The use of palm oil for our current needs is unsustainable. Replacing palm oil with oils produced by microbes through the conversion of sustainable feedstocks is a promising alternative. However, there are major technical challenges that must be overcome to enable this transition. Foremost among these challenges is the stark increase in lipid accumulation and production of higher content of specific fatty acids. Therefore, there is a need for more in-depth knowledge and systematic exploration of the oil productivity of the oleaginous yeasts. In this study, we cultivated Cutaneotrichosporon oleaginosus and Yarrowia lipolytica at various C/N ratios and temperatures in a defined medium with glycerol as carbon source and urea as nitrogen source. We ascertained the synergistic effect between various C/N ratios of a defined medium at different temperatures with Response Surface Methodology (RSM) and explored the variation in fatty acid composition through Principal Component Analysis.

Results

By applying RSM, we determined a temperature of 30 °C and a C/N ratio of 175 g/g to enable maximal oil production by C. oleaginosus and a temperature of 21 °C and a C/N ratio of 140 g/g for Y. lipolytica. We increased production by 71% and 66% respectively for each yeast compared to the average lipid accumulation in all tested conditions. Modulating temperature enabled us to steer the fatty acid compositions. Accordingly, switching from higher temperature to lower cultivation temperature shifted the production of oils from more saturated to unsaturated by 14% in C. oleaginosus and 31% in Y. lipolytica. Higher cultivation temperatures resulted in production of even longer saturated fatty acids, 3% in C. oleaginosus and 1.5% in Y. lipolytica.

Conclusions

In this study, we provided the optimum C/N ratio and temperature for C. oleaginosus and Y. lipolytica by RSM. Additionally, we demonstrated that lipid accumulation of both oleaginous yeasts was significantly affected by the C/N ratio and temperature. Furthermore, we systematically analyzed the variation in fatty acids composition and proved that changing the C/N ratio and temperature steer the composition. We have further established these oleaginous yeasts as platforms for production of tailored fatty acids.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01956-5.

The Consumption of Amino Acids and Production of Volatile Aroma Compounds by Yarrowia lipolytica in Brewers’ Wort

The yeast Yarrowia lipolytica is well known for its versatile production of metabolites from various substrates, but, although isolated from, e.g., wild-fermented Belgian Sour beers, it is rarely considered a starter culture in fermented beverages. In this study, we aimed to elucidate the ability of Y. lipolytica to ferment brewers’ wort containing iso-α-acid for 7 days at low and high aeration and at 20 °C and 30 °C, with a special focus on amino acid consumption and production of volatile aroma compounds. Y. lipolytica was able to grow in the wort under all four conditions, although the growth was inhibited. Furthermore, it only consumed glucose and fructose, and no ethanol was formed. Moreover, under high aeration conditions, Y. lipolytica consumed 75–80% of the amino acids in the wort. Interestingly, no esters were produced during the fermentations, and only five higher alcohols (1-propanol, 2-methyl-1-propanol, 3-methyl-1-butanol, 3-methyl-3-buten-1-ol, and 2-phenylethanol), two aldehydes (3-methylbutanal and (E)-2-nonenal), two ketones (cyclopentanone and 9-oxabicyclo [6.1.0]nonan-4-one), one fatty acid (3-methyl-butanoic acid), and one benzene derivate (1,2,4-trimethyl-benzene) were produced. These results may contribute to the potential use of Y. lipolytica in a traditional brewery for the production of novel beers; e.g., alcohol-free beer.

Overview on the Infections Related to Rare Candida species

Atypical Candida spp. infections are rising, mostly due to the increasing numbers of immunocompromised patients. The most common Candida spp. is still Candida albicans; however, in the last decades, there has been an increase in non-Candida albicans Candida species infections (e.g., Candida glabrata, Candida parapsilosis, and Candida tropicalis). Furthermore, in the last 10 years, the reports on uncommon yeasts, such as Candida lusitaniae, Candida intermedia, or Candida norvegensis, have also worryingly increased. This review summarizes the information, mostly related to the last decade, regarding the infections, diagnosis, treatment, and resistance of these uncommon Candida species. In general, there has been an increase in the number of articles associated with the incidence of these species. Additionally, in several cases, there was a suggestive antifungal resistance, particularly with azoles, which is troublesome for therapeutic success.

Single Cell Protein for Foods and Feeds: A Review of Trends

Introduction:

Predictions on the world’s population in the next few decades suggest that the global demand for animal-derived proteins may not be met if current conventional agriculture approaches are used. One promising solution to this complex crisis lies in the use of single-cell proteins (SCP). SCP refers to the edible biomass of unicellular microorganisms and can be developed as animal feeds or human foods. This paper provides a detailed overview on research towards the production and utilisation of SCPs and trends within the field.

Study Design:

A bibliometric based study was conducted on 425 SCP research articles collected from the Web of Science database, analysing the most cited papers using VOSviewer software, and contributing authors, affiliations and country of origin. Research publications on SCP started in 1961 and has grown steadily over the years.

Discussion:

Emerging research topics within SCP production focused on the use of improved fungal strains, the composition and characteristics of SCPs based on the type of substrates used, industrial production processes and the use of waste for SCP production, which serves the dual purpose of mitigating the cost associated with waste disposal and production of a valuable product.

Selection of Producer of α-Ketoglutaric Acid from Ethanol-Containing Wastes and Impact of Cultivation Conditions

Ester–aldehyde fraction (EAF) is a by-product of ethyl-alcohol-producing companies whose purification requires an expensive process. The results of this study illustrate the environmentally friendly and alternative possibility of using EAF to increase their value as substrate to produce α-ketoglutaric acid (KGA) using different yeasts. It was found that some species of the genera Babjeviella, Diutina, Moesziomyces, Pichia, Saturnispora, Sugiyamaella, Yarrowia and Zygoascus grown under thiamine deficiency accumulate KGA in the medium with an EAF as the sole carbon source. The strain Y. lipolytica VKM Y-2412 was selected as the producer. To reach the maximum production of KGA, the cultivation medium should contain 0.3 µg/L thiamine during cultivation in flasks and 2 µg/L in the fermentor; the concentration of (NH4)2SO4 should range from 3 to 6 g/L; and the optimal concentrations of Zn2+, Fe2+ and Cu2+ ions should be 1.2, 0.6 and 0.05 mg/L, respectively. EAF concentration should not exceed 1.5 g/L in the growth phase and 3 g/L in the KGA synthesis phase. At higher EAF concentrations, acetic acid was accumulated and inhibited yeast growth and KGA production. Under optimal conditions, the producer accumulated 53.8 g/L KGA with a yield (Yp/s) of 0.68 g/g substrate consumed.

A comprehensive assessment of Yarrowia lipolytica and its interactions with metals: Current updates and future prospective

The non-conventional yeast Yarrowia lipolytica has been popular as a model system for understanding biological processes such as dimorphism and lipid accumulation. The organism can efficiently utilize hydrophobic substrates (hydrocarbons and triglycerides) thereby rendering it relevant in bioremediation of oil polluted environments. The current review focuses on the interactions of this fungus with metal pollutants and its potential application in bioremediation of metal contaminated locales. This fungus is intrinsically equipped with a variety of physiological and biochemical features that enable it to tide over stress conditions induced by the presence of metals. Production of enzymes such as phosphatases, reductases and superoxide dismutases are worth a special mention. In the presence of metals, levels of inherently produced metal binding proteins (metallothioneins) and the pigment melanin are seen to be elevated. Morphological alterations with respect to biofilm formation and dimorphic transition from yeast to mycelial form are also induced by certain metals. The biomass of Y. lipolytica is inherently important as a biosorbent and cell surface modification, process optimization or whole cell immobilization techniques have aided in improving this capability. In the presence of metals such as mercury, cadmium, copper and uranium, the culture forms nanoparticulate deposits. In addition, on account of its intrinsic reductive ability, Y. lipolytica is being exploited for synthesizing nanoparticles of gold, silver, cadmium and selenium with applications as antimicrobial compounds, location agents for bioimaging and as feed supplements. This versatile organism thus has great potential in interacting with various metals and addressing problems related to their pollutant status.

Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil

Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.

Biomolecules from Plant Wastes Potentially Relevant in the Management of Irritable Bowel Syndrome and Co-Occurring Symptomatology

During and following the processing of a plant’s raw material, considerable amounts are wasted, composted, or redistributed in non-alimentary sectors for further use (for example, some forms of plant waste contribute to biofuel, bioethanol, or biomass production). However, many of these forms of waste still consist of critical bioactive compounds used in the food industry or medicine. Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders. The primary treatment is based on symptomatology alleviation and controlled dietary management. Thus, this review aimed to describe the possible relevance of molecules residing in plant waste that can be used to manage IBS and co-occurring symptoms. Significant evidence was found that many forms of fruit, vegetable, and medicinal plant waste could be the source of some molecules that could be used to treat or prevent stool consistency and frequency impairments and abdominal pain, these being the main IBS symptoms. While many of these molecules could be recovered from plant waste during or following primary processing, the studies suggested that enriched food could offer efficient valorization and prevent further changes in properties or stability. In this way, root, stem, straw, leaf, fruit, and vegetable pomaces were found to consist of biomolecules that could modulate intestinal permeability, pain perception, and overall gastrointestinal digestive processes.

Exploitation of Yeasts with Probiotic Traits for Kefir Production: Effectiveness of the Microbial Consortium

Kefir is a fermented milk made by beneficial lactic acid bacteria and yeasts inoculated as grains or free cultures. In this work, five yeast strains with probiotic aptitudes belonging to Candida zeylanoides, Yarrowia lipolytica, Kluyveromyces lactis, and Debaryomyces hansenii species were assessed in a defined consortium, in co-culture with a commercial strain of Lactobacillus casei, in order to evaluate the yeasts’ fermentation performance during kefir production, using different milks. The concentration of each yeast was modulated to obtain a stable consortium that was not negatively affected by the bacteria. Furthermore, all yeasts remained viable for five weeks at 4 °C, reaching about 8.00 Log CFU in 150 mL of kefir, a volume corresponding to a pot of a commercial product. The yeasts consortium showed a suitable fermentation performance in all milks, conferring peculiar and distinctive analytical and aromatic properties to the kefirs, confirmed by a pleasant taste. Overall, the panel test revealed that the cow’s and sheep’s kefir were more appreciated than the others; this evaluation was supported by a distinctive fermentation by-products’ content that positively influences the final aroma, conferring to the kefir exalted taste and complexity. These results allow us to propose the yeasts consortium as a versatile and promising multistarter candidate able to affect industrial kefir with both recognizable organoleptic properties and probiotic aptitudes.

Effect of Metabolic Regulators and Aeration on Isocitric Acid Synthesis by Yarrowia lipolytica Grown on Ester-Aldehyde Fraction

Isocitric acid (ICA) has found wide application in medicine as a promising compound with powerful antioxidant activity to combat oxidative stress. In the known microbiological processes of ICA production by non-conventional yeast Yarrowia lipolytica, the pure carbon sources are commonly used. ICA can be also synthetized by Y. lipolytica from ester-aldehyde fraction (EAF)-waste of the ethanol production process. A highly effective method of ICA production from EAF based on regulation of key enzymes (aconitate hydratase and isocitrate lyase) by metabolic regulators (iron and itaconic acid) and aeration was developed. It is recommended to cultivate Y. lipolytica VKM Y-2373 under nitrogen deficiency conditions, a high aeration (60% of air saturation), an addition of 15 mM itaconic acid, and 2.4 mg/L iron. Under optimal conditions, Y. lipolytica VKM Y-2373 produced 83 g/L ICA with isocitrate to citrate ratio of 4.1:1 and mass yield of 1.1 g/g. The putative mechanism of ICA overproduction from EAF by Y. lipolytica was suggested.

Isocitric Acid Production from Ethanol Industry Waste by Yarrowia lipolytica

There is ever increasing evidence that isocitric acid can be used as a promising compound with powerful antioxidant activity to combat oxidative stress. This work demonstrates the possibility of using waste product from the alcohol industry (so-called ester-aldehyde fraction) for production of isocitric acid by yeasts. The potential producer of isocitric acid from this fraction, Yarrowia lipolytica VKM Y-2373, was selected by screening of various yeast cultures. The selected strain showed sufficient growth and good acid formation in media with growth-limiting concentrations of nitrogen, sulfur, phosphorus, and magnesium. A shortage of Fe2+ and Ca2+ ions suppressed both Y. lipolytica growth and formation of isocitric acid. The preferential synthesis of isocitric acid can be regulated by changing the nature and concentration of nitrogen source, pH of cultivation medium, and concentration of ester-aldehyde fraction. Experiments in this direction allowed us to obtain 65 g/L isocitric acid with a product yield (YICA) of 0.65 g/g in four days of cultivation.

Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement

Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.

Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products

Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

Background

Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica.

Results

To investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations.

Conclusions

The genomic characterization of five yeast strains isolated from N. vespilloides resulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07597-z.

Metabolically engineering of Yarrowia lipolytica for the biosynthesis of naringenin from a mixture of glucose and xylose

Xylose-inducible modules simultaneously expressing xylose utilization and naringenin biosynthesis pathways were developed in Yarrowia lipolytica to produce naringenin from a mixture of glucose and xylose. The naringenin synthetic pathway was constructed using a constitutive expression to yield 239.1 ± 5.1 mg/L naringenin. Furthermore, the introduction of an inducible pathway realized the dual function of xylose as a substrate and synthetic inducer, which coupled the xylose utilization with naringenin biosynthesis and increased production. Interestingly, the simultaneous enhancement of xylose reductase and xylose transporter expression along with that of xylitol dehydrogenase and xylulokinase can further improve the xylose utilization ability of Y. lipolytica. As expected, xylose-inducible synthesis of naringenin could achieved a titer of 715.3 ± 12.8 mg/L through the shake-flask cultivation level. Therefore, xylose-induced activation of both the xylose utilization and product biosynthesis pathway is considered to be an effective strategy for the biosynthesis of xylose-derived chemicals in yeast.

Optimization of medium composition and fermentation conditions for α-ketoglutaric acid production from biodiesel waste by Yarrowia lipolytica

This work demonstrates the ability of the yeast Yarrowia lipolytica cultivated on biodiesel waste to synthesize α-ketoglutaric acid with a minimal content of pyruvic acid as the main byproduct. The key factor promoting the microbial production of α-ketoglutaric acid from the waste is a strong deficiency of thiamine in the cultivation medium. The production of α-ketoglutaric acid by the yeast can be regulated by changing the concentration of nitrogen, iron, zinc, copper, and manganese in the medium, as well as by pH medium and the aeration rate. The optimization of these parameters in flask experiments allowed us to increase the concentration of α-ketoglutaric acid in the medium by 2.6 times and to shift the α-ketoglutaric acid/pyruvic acid ratio from 5:1 to 30:1. During cultivation in a fermentor under optimized conditions, Y. lipolytica produced 80.4 g/L α-ketoglutaric acid with a process selectivity of 96.7% and the product yield (Y_KGA) equal to 1.01 g/g. KEY POINTS: • α-Ketoglutaric acid is commercially important biotechnological product. • Biosynthesis of α-ketoglutaric acid from biodiesel waste. • Optimization of cultivation medium and nutrition medium.

Uptake and detoxification of diesel oil by a tropical soil Actinomycete Gordonia amicalis HS-11: Cellular responses and degradation perspectives

A tropical soil Actinomycete, Gordonia amicalis HS-11, has been previously demonstrated to degrade unsaturated and saturated hydrocarbons (squalene and n-hexadecane, respectively) in an effective manner. In present study, G. amicalis HS-11 degraded 92.85 ± 3.42% of the provided diesel oil [1% (v/v)] after 16 days of aerobic incubation. The effect of different culture conditions such as carbon source, nitrogen source, pH, temperature, and aeration on degradation was studied. During degradation, this Actinomycete synthesized surface active compounds (SACs) in an extracellular manner that brought about a reduction in surface tension from 69 ± 2.1 to 30 ± 1.1 mN m^-1 after 16 days. The morphology of cells grown on diesel was monitored by using a Field Emission Scanning Electron Microscope. Diesel-grown cells were longer and clumped with smooth surfaces, possibly due to the secretion of SACs. The interaction between the cells and diesel oil was studied by Confocal Laser Scanning Microscope. Some cells were adherent on small diesel droplets and others were present in the non-attached form thus confirming the emulsification ability of this organism. The fatty acid profiles of the organism grown on diesel oil for 48 h were different from those on Luria Bertani Broth. The genotoxicity and cytotoxicity of diesel oil before and after degradation were determined. Cytogenetic parameters such as mitotic index (MI); mitosis distribution and chromosomal aberration (type and frequency) were assessed. Oxidative stress was evaluated by measuring levels of catalase, superoxide dismutase and concentration of malondialdehyde. On the basis of these studies it was deduced that the degradation metabolites were relatively non-toxic.

Influence of detergents and sodium hypochlorite on Yarrowia lipolytica biofilms in utensils used in industrial production of colonial cheese

The formation of microbial biofilms in materials used in the industrial production of dairy may lead to deterioration of these foods. Yarrowia lipolytica biofilms are widely found in dairy products and can modify the final characteristics of these products. Thus, this study investigated the effectiveness of hygienization by detergents and sodium hypochlorite on the formation of Y. lipolytica biofilms in different utensils usually employed during industrial cheese production, like polypropylene, hoses, and nylon/polyethylene. The utensils were sanitized using solutions of mild and alkaline detergents, and sodium hypochlorite, according to the cheese industry Standard Operation Procedure. Results showed that in all coupons there was biofilm formation with Y. lipolytica isolates. The contact angle measurements were favored to promote the adhesion of the biofilm in the evaluated surfaces. Even after treatment with sanitizers, a significant survival rate of planktonic cells was observed in all coupons tested. These results indicate that Y. lipolytica biofilms show a significant ability to adhere to polypropylene, presenting an important impact on the quality of colonial cheese.

Microbiological Production of Isocitric Acid from Biodiesel Waste and Its Effect on Spatial Memory

Within this work, the microbial synthesis of (2R,3S)-isocitric acid (ICA), a metabolite of the nonconventional yeast Yarrowia lipolytica, from biodiesel waste, has been studied. The selected strain Y. lipolytica VKM Y-2373 synthesized ICA with citric acid (CA) as a byproduct. This process can be regulated by changing cultivation conditions. The maximal production of ICA with the minimal formation of the byproduct was provided by the use of a concentration of (NH4)2SO4 (6 g/L); the addition of biodiesel waste to cultivation medium in 20-60 g/L portions; maintaining the pH of the cultivation medium at 6, and degree of aeration between 25% and 60% of saturation. Itaconic acid at a concentration of 15 mM favorably influenced the production of ICA by the selected strain. The optimization of cultivation conditions allowed us to increase the concentration of ICA in the culture liquid from 58.32 to 90.2 g/L, the product yield (Y) by 40%, and the ICA/CA ratio from 1.1:1 to 3:1. Research on laboratory animals indicated that ICA counteracted the negative effect of ammonium molybdate (10-5 М) and lead diacetate (10-7 М) on the learning and spatial memory of rats, including those exposed to emotional stress.

Engineering Oleaginous Yeast as the Host for Fermentative Succinic Acid Production From Glucose

Oleaginous yeast Yarrowia lipolytica is a prospective host for production of succinic acid. The interruption of tricarboxylic acid cycle through succinate dehydrogenase gene (SDH) deletion was reported to result in strains incapable of glucose utilization and this ability had to be restored by chemical mutation or long adaptive laboratory evolution. In this study, a succinate producing strain of Y. lipolytica was engineered by truncating the promoter of SDH1 gene, which resulted in 77% reduction in SDH activity but did not impair the ability of the strain to grow on glucose. The flux toward succinic acid was further improved by overexpressing the genes in the glyoxylate pathway and the oxidative TCA branch, and expressing phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes. A short adaptation on glucose reduced the lag phase of the strain and increased its tolerance to high glucose concentrations. The resulting strain produced 7.8 ± 0.0 g/L succinic acid with a yield of 0.105 g/g glucose in shake flasks without pH control, while mannitol (11.8 ± 0.8 g/L) was the main by-product. Further investigations showed that mannitol accumulation was caused by low pH stress and buffering the fermentation medium eliminated mannitol formation. In a fed-batch bioreactor in mineral medium at pH 5, at which point according to K_a values of succinic acid, the major fraction of product was in acidic form rather than dissociated form, the strain produced 35.3 ± 1.5 g/L succinic acid with 0.26 ± 0.00 g/g glucose yield.

Understanding the regulation of extracellular protease gene expression in fungi: a key step towards their biotechnological applications

The secretion of proteases by certain species of yeast and filamentous fungi is of importance not only for their biological function and survival, but also for their biotechnological application to various processes in the food, beverage, and bioprocessing industries. A key step towards understanding the role that these organisms play in their environment, and how their protease-secreting ability may be optimally utilised through industrial applications, involves an evaluation of those factors which influence protease production. The objective of this review is to provide an overview of the findings from investigations directed at elucidating the regulatory mechanisms underlying extracellular protease secretion in yeast and filamentous fungi, and the environmental stimuli that elicit these responses. The influence of nitrogen-, carbon-, and sulphur-containing compounds, as well as proteins, temperature, and pH, on extracellular protease regulation, which is frequently exerted at the transcriptional level, is discussed in particular depth. Protease-secreting organisms of biotechnological interest are also presented in this context, in an effort to explore the areas of industrial significance that could possibly benefit from such knowledge. In this way, the establishment of a platform of existing knowledge regarding fungal protease regulation is attempted, with the particular goal of aiding in the practical application of these organisms to processes that require secretion of this enzyme.

Biosynthetic strategies to produce xylitol: an economical venture

Xylitol is a natural five-carbon sugar alcohol with potential for use in food and pharmaceutical industries owing to its insulin-independent metabolic regulation, tooth rehardening, anti-carcinogenic, and anti-inflammatory, as well as osteoporosis and ear infections preventing activities. Chemical and biosynthetic routes using D-xylose, glucose, or biomass hydrolysate as raw materials can produce xylitol. Among these methods, microbial production of xylitol has received significant attention due to its wide substrate availability, easy to operate, and eco-friendly nature, in contrast with high-energy consuming and environmental-polluting chemical method. Though great advances have been made in recent years for the biosynthesis of xylitol from xylose, glucose, and biomass hydrolysate, and the yield and productivity of xylitol are substantially improved by metabolic engineering and optimizing key metabolic pathway parameters, it is still far away from industrial-scale biosynthesis of xylitol. In contrary, the chemical synthesis of xylitol from xylose remains the dominant route. Economic and highly efficient xylitol biosynthetic strategies from an abundantly available raw material (i.e., glucose) by engineered microorganisms are on the hard way to forwarding. However, synthetic biology appears as a novel and promising approach to develop a super yeast strain for industrial production of xylitol from glucose. After a brief overview of chemical-based xylitol production, we critically analyzed and comprehensively summarized the major metabolic strategies used for the enhanced biosynthesis of xylitol in this review. Towards the end, the study is wrapped up with current challenges, concluding remarks, and future prospects for designing an industrial yeast strain for xylitol biosynthesis from glucose.

Biosynthesis of isocitric acid in repeated-batch culture and testing of its stress-protective activity

Biosynthesis of Ds(+)-threo-isocitric acid from ethanol in the Yarrowia lipolytica batch and repeated-batch cultures was studied. Repeated-batch cultivation was found to provide for a good biosynthetic efficiency of the producer for as long as 748 h, probably due to maintenance of high activities of enzymes involved in the biosynthesis of isocitric acid. Under optimal repeated-batch cultivation conditions, the producer accumulated 109.6 g/L Ds(+)-threo-isocitric acid with a production rate of 1.346 g/L h. The monopotassium salt of isocitric acid isolated from the culture liquid and purified to 99.9% was found to remove neurointoxication, to restore memory, and to improve the learning of laboratory rats intoxicated with lead and molybdenum salts. Taking into account the fact that the neurotoxic effect of heavy metals is mainly determined by oxidative stress, the aforementioned favorable action of isocitric acid on the intoxicated rats can be explained by its antioxidant activity among other pharmacological effects.

Established and Upcoming Yeast Expression Systems

Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.

An oleaginous yeast platform for renewable 1-butanol synthesis based on a heterologous CoA-dependent pathway and an endogenous pathway

Background

Microbial biofuel production provides a promising sustainable alternative to fossil fuels. 1-Butanol is recognized as an advanced biofuel and is gaining attention as an ideal green replacement for gasoline. In this proof-of-principle study, the oleaginous yeast Yarrowia lipolytica was first engineered with a heterologous CoA-dependent pathway and an endogenous pathway, respectively.

Results

The co-overexpression of two heterologous genes ETR1 and EutE resulted in the production of 1-butanol at a concentration of 65 μg/L. Through the overexpression of multiple 1-butanol pathway genes, the titer was increased to 92 μg/L. Cofactor engineering through endogenous overexpression of a glyceraldehyde-3-phosphate dehydrogenase and a malate dehydrogenase further led to titer improvements to 121 μg/L and 110 μg/L, respectively. In addition, the presence of an endogenous 1-butanol production pathway and a gene involved in the regulation of 1-butanol production was successfully identified in Y. lipolytica. The highest titer of 123.0 mg/L was obtained through this endogenous route by combining a pathway gene overexpression strategy.

Conclusions

This study represents the first report on 1-butanol biosynthesis in Y. lipolytica. The results obtained in this work lay the foundation for future engineering of the pathways to optimize 1-butanol production in Y. lipolytica.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1014-8) contains supplementary material, which is available to authorized users.

Biosynthesis of pyruvic acid from glycerol-containing substrates and its regulation in the yeast Yarrowia lipolytica

The ability of different yeasts to synthesize pyruvic acid (PA) from glycerol-containing substrates has been studied. The selected strain Yarrowia lipolytica VKM Y-2378 synthesized PA with α-ketoglutaric acid (KGA) as a byproduct. The content of KGA greatly depended on cultivation conditions. The minimal formation of the byproduct was provided by the limitation of yeast growth by thiamine (0.6 µg/g biomass); the use of ammonium sulfate (0.6%) as a nitrogen source; addition of glycerol to cultivation medium in 20 g/L portions; maintaining the cultivation temperature at 28 °C, pH of the cultivation medium at 4.5, and medium aeration between 55 and 60% of saturation; the optimal cultivation time was 48 h. The selected strain cultivated under such conditions in a fermenter with a waste glycerol from biodiesel production process synthesized 41 g/L PA with a yield of 0.82 g/g. The mechanism of PA production from glycerol-containing substrates in Y. lipolytica is discussed.

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.