16 years research on lactic acid production with yeast – ready for the market?

Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1

BACKGROUND

Lignocellulosic biomass as feedstock has a huge potential for biochemical production. Still, efficient utilization of hydrolysates derived from lignocellulose is challenged by their complex and heterogeneous composition and the presence of inhibitory compounds, such as furan aldehydes. Using microbial consortia where two specialized microbes complement each other could serve as a potential approach to improve the efficiency of lignocellulosic biomass upgrading.

RESULTS

This study describes the simultaneous inhibitor detoxification and production of lactic acid and wax esters from a synthetic lignocellulosic hydrolysate by a defined coculture of engineered Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. A. baylyi ADP1 showed efficient bioconversion of furan aldehydes present in the hydrolysate, namely furfural and 5-hydroxymethylfurfural, and did not compete for substrates with S. cerevisiae, highlighting its potential as a coculture partner. Furthermore, the remaining carbon sources and byproducts of S. cerevisiae were directed to wax ester production by A. baylyi ADP1. The lactic acid productivity of S. cerevisiae was improved approximately 1.5-fold (to 0.41 ± 0.08 g/L/h) in the coculture with A. baylyi ADP1, compared to a monoculture of S. cerevisiae.

CONCLUSION

The coculture of yeast and bacterium was shown to improve the consumption of lignocellulosic substrates and the productivity of lactic acid from a synthetic lignocellulosic hydrolysate. The high detoxification capacity and the ability to produce high-value products by A. baylyi ADP1 demonstrates the strain to be a potential candidate for coculture to increase production efficiency and economics of S. cerevisiae fermentations.

Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation

While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.

Schwanniomyces etchellsii, acid-thermotolerant yeasts from urban city soil

Acid-tolerant yeasts are one of the important keys to producing ethanol from acidic substrates, especially from molasses and agricultural waste. In this study, selected cultivars of yeasts isolated from a variety of locations such as botanical gardens in Thailand urban areas, which are often found highly polluted in the air such as carbon dioxide which is a cause of acid rain. There is limited information about how tolerant yeasts, are or their functional properties related to the environment. Yeast species were determined by using the 18S rDNA sequence guide. The level of acid tolerance was evaluated by adding to the culture medium lactic acid (300-900 mM), acetic acid (100-400 mM), and propionic acid (25-100 mM). 18S rDNA analysis has shown a %similarity of the nucleotide sequence higher than 98.65% compared to the database. Schwanniomyces etchellsii strains found in urban city soil were notable for their tolerance of lactic acid up to 100 mM. There are two main types of yeasts in overall acid tolerance: S. etchellsii, which is recognized as an osmotic pressure-resistant species that is highly resistant to fermentation inhibitors and produces ethanol; and Schizosaccharomyces pombe, which cell wall has been reported to be characterized by accumulation of α-(1,3)-glucan and malic acid can be used in metabolic pathways. The results show that S. pombe, isolated from rice paddy fields, can grow efficiently in acetic and propionic acid up to 400 mM and 100 mM, respectively. This species could be cultured in ethanol at a concentration of 12.5% (v/v). Moreover, it presented high ethanol and acetic acid production of 14.5-15.9 g/L and 7-10 g/L, respectively, with or without acidic conditions. In comparison, S. etchellsii, isolated from the botanical garden soil, which is grown in acetic, propionic, and lactic acid, was also indicated to be an organic acid-tolerant species.

Construction of fully biodegradable poly(L-lactic acid)/poly(D-lactic acid)-poly(lactide-co-caprolactone) block polymer films: Viscoelasticity, processability and flexibility

Development of biodegradable polymer films is essential for sustainable energy conservation and ecological protection. In this work, to improve the processability and toughness of poly(lactic acid) (PLA) films, poly(lactide-co-caprolactone) (PLCL) segments were introduced into poly(L-lactic acid) (PLLA)/poly(D-lactic acid) (PDLA) chains via chain branching reactions during reactive processing, and fully biodegradable/flexible PLLA/D-PLCL block polymer with long-chain branches and stereocomplex (SC) crystalline structure was prepared. Compared with neat PLLA, PLLA/D-PLCL exhibited much higher complex viscosity/storage modulus, lower tanδ values in terminal region and obvious strain-hardening behavior. Through biaxial drawing, PLLA/D-PLCL films were prepared, which showed improved uniformity and non-preferred orientation. With increasing draw ratio, the total crystallinity (X_c) and X_c for SC crystal both increased. By introduction of PDLA, the two phases of PLLA and PLCL penetrated and entangled with each other, and the phase structure transformed from "sea-island" structure to "co-continuous network" structure, which was beneficial for exerting the toughening effect of flexible PLCL molecules on PLA matrix. The tensile strength and elongation at break of PLLA/D-PLCL films increased from 51.87 MPa and 28.22 % of neat PLLA film to 70.82 MPa and 148.28 %. This work provided a new strategy for developing fully biodegradable polymer films with high performance.

Conversion of CO2 into organic acids by engineered autotrophic yeast

The increase of CO2 emissions due to human activity is one of the preeminent reasons for the present climate crisis. In addition, considering the increasing demand for renewable resources, the upcycling of CO2 as a feedstock gains an extensive importance to establish CO2-neutral or CO2-negative industrial processes independent of agricultural resources. Here we assess whether synthetic autotrophic Komagataella phaffii (Pichia pastoris) can be used as a platform for value-added chemicals using CO2 as a feedstock by integrating the heterologous genes for lactic and itaconic acid synthesis. 13C labeling experiments proved that the resulting strains are able to produce organic acids via the assimilation of CO2 as a sole carbon source. Further engineering attempts to prevent the lactic acid consumption increased the titers to 600 mg L-1, while balancing the expression of key genes and modifying screening conditions led to 2 g L-1 itaconic acid. Bioreactor cultivations suggest that a fine-tuning on CO2 uptake and oxygen demand of the cells is essential to reach a higher productivity. We believe that through further metabolic and process engineering, the resulting engineered strain can become a promising host for the production of value-added bulk chemicals by microbial assimilation of CO2, to support sustainability of industrial bioprocesses.

D-Lactic Acid Production from Sugarcane Bagasse by Genetically Engineered Saccharomyces cerevisiae

Lactic acid (LA) is a promising bio-based chemical that has broad applications in food, nutraceutical, and bioplastic industries. However, production of the D-form of LA (D-LA) from fermentative organisms is lacking. In this study, Saccharomyces cerevisiae harboring the D-lactate dehydrogenase (DLDH) gene from Leuconostoc mesenteroides was constructed (CEN.PK2_DLDH). To increase D-LA production, the CRISPR/Cas12a system was used for the deletion of gpd1, gpd2, and adh1 to minimize glycerol and ethanol production. Although an improved D-LA titer was observed for both CEN.PK2_DLDHΔgpd and CEN.PK2_DLDHΔgpdΔadh1, growth impairment was observed. To enhance the D-LA productivity, CEN.PK2_DLDHΔgpd was crossed with the weak acid-tolerant S. cerevisiae BCC39850. The isolated hybrid2 showed a maximum D-LA concentration of 23.41 ± 1.65 g/L, equivalent to the improvement in productivity and yield by 2.2 and 1.5 folds, respectively. The simultaneous saccharification and fermentation using alkaline pretreated sugarcane bagasse by the hybrid2 led to an improved D-LA conversion yield on both the washed solid and whole slurry (0.33 and 0.24 g/g glucan). Our findings show the exploitation of natural yeast diversity and the potential strategy of gene editing combined with conventional breeding on improving the performance of S. cerevisiae for the production of industrially potent products.

Potential of non-Saccharomyces yeast to produce non-alcoholic beer

Recently, non-Saccharomyces yeast have become very popular in wine and beer fermentation. Their interesting abilities introduce novel aromatic profiles to the fermented product. In this study, screening of eight non-Saccharomyces yeast (Starmerella bombicola, Lindnera saturnus, Lindnera jadinii, ZygoSaccharomyces rouxii, Torulaspora delbrueckii, Pichia kluyveri, Candida pulcherrima, and Saccharomycodes ludwigii) revealed their potential in non-alcoholic beer production. Conditions for non-alcoholic beer production were optimised for all strains tested (except T. delbrueckii) with the best results obtained at temperature 10 to 15 °C for maximum of 10 days. Starmerella bombicola, an important industrial producer of biosurfactants, was used for beer production for the first time and was able to produce non-alcoholic beer even at 20 °C after 10 days of fermentation. Aromatic profile of the beer fermented with S. bombicola was neutral with no negative impact on organoleptic properties of the beer. The most interesting organoleptic properties were evaluated in beers fermented with L. jadinii and L. saturnus, which produced banana-flavoured beers with low alcohol content. This work confirmed the suitability of mentioned yeast to produce non-alcoholic beers and could serve as a steppingstone for further investigation.

The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts

In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.

Multiparametric Approach to Interactions between Saccharomyces cerevisiae and Lachancea thermotolerans during Fermentation

The aim of a significant part of current wine technology research is to better understand and monitor mixed culture fermentations and optimize the microbiological processes and characteristics of the final wine. In this context, the yeast couple formed by Lachancea thermotolerans and Saccharomyces cerevisiae is of particular interest. The diverse results observed in the literature have shown that wine characteristics are dependent on both interactions between yeasts and environmental and fermentation parameters. Here, we took a multiparametric approach to study the impact of fermentation parameters on three different but related aspects of wine fermentation: population dynamics, fermentation, and volatile compound production. An experimental design was used to assess the effects of four independent factors (temperature, oxygenation, nitrogen content, inoculum ratio) on variables representing these three aspects. Temperature and, to a lesser extent, oxygenation and the inoculum ratio, were shown to constitute key factors in optimizing the presence of Lachancea thermotolerans during fermentation. The inoculum ratio also appeared to greatly impact lactic acid production, while the quantity of nitrogen seemed to be involved more in the management of aroma compound production. These results showed that a global approach to mixed fermentations is not only pertinent, but also constitutes an important tool for controlling them.

Biomodulation of Physicochemical Parameters, Aromas, and Sensory Profile of Craft Beers by Using Non-Saccharomyces Yeasts

Beer is an alcoholic beverage produced by the metabolism of yeasts and made from water, malt, and hops. In recent years, the interest in craft beers has increased considerably due to the demand for new beverages and the consumer's willingness to pay higher prices. This article explores the sensorial changes produced in craft beers by using different Saccharomyces and non-Saccharomyces yeasts with several instrumental and sensory analyses performed. After a primary fermentation process with Saccharomyces cerevisiae or Lachancea thermotolerans, it was observed that green beer brewed with L. thermotolerans had a lower pH (3.41) due to the significant production of l-lactic acid (3.98 g/L) compared to that brewed with S. cerevisiae. Following, the bottle conditioning was carried out with a culture of S. cerevisiae, L. thermotolerans, Hanseniaspora vineae, or Schizosaccharomyces pombe. Of note is the increased production of aromatic esters, including 2-phenylethyl acetate in the H. vineae conditioning, which is associated with a high aromatic quality, as well as ethyl lactate in all samples, whose main fermentation was carried out with L. thermotolerans. Although this research is at an early stage, future complementary studies may shed more light on this topic.

Impact of Lachancea thermotolerans on Chemical Composition and Sensory Profiles of Viognier Wines

Viognier is a warm climate grape variety prone to loss of acidity and accumulation of excessive sugars. The yeast Lachancea thermotolerans can improve the stability and balance of such wines due to the partial conversion of sugars to lactic acid during alcoholic fermentation. This study compared the performance of five L. thermotolerans strains in co-inoculations and sequential inoculations with Saccharomyces cerevisiae in high sugar/pH Viognier fermentations. The results highlighted the dichotomy between the non-acidified and the bio-acidified L. thermotolerans treatments, with either comparable or up to 0.5 units lower pH relative to the S. cerevisiae control. Significant differences were detected in a range of flavour-active yeast volatile metabolites. The perceived acidity mirrored the modulations in wine pH/TA, as confirmed via “Rate-All-That-Apply” sensory analysis. Despite major variations in the volatile composition and acidity alike, the varietal aromatic expression (i.e., stone fruit aroma/flavour) remained conserved between the treatments.

Hypersymbiotics™: An artistic reflection on the ethical and environmental implications of microbiome research and new technologies

This essay describes my ongoing series "Hypersymbiotics™," which began in 2012 and explores the potential ways in which our microbiome, genetics, epigenetics and even our environment could potentially be enhanced to turn us into human 'super-organisms.' The series includes performances and installations involving BioArt, as well as photographic documentation of ephemeral artworks and takes the form of a vehicle for public discussion about new healthcare technologies. The essay discusses artworks made using synthetic biology techniques including CRISPR genetic modification in bacteria and yeasts, and gene editing in plants, as well as using artificial intelligence and stem cell research. It critiques the role of the media and advertising in the promotion of complex new biomedical technologies. The "Hypersymbiotics™" series is deeply concerned with promoting public understanding of the ethical implications of new scientific developments and enabling reflection and debate. At its core the artwork is about knowledge, power, and control and where that resides.

State of the Art on the Microbial Production of Industrially Relevant Organic Acids

The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by many cells. They are the products, by-products or co-products of many primary metabolic processes of microbial cells. Thanks to the potential of microbial cell factories and to the development of industrial biotechnology, from the last decades of the previous century, the microbial-based production of these molecules has started to approach the market. This was possible because of a joint effort of microbial biotechnologists and biochemical and process engineers that boosted natural production up to the titer, yield and productivity needed to be industrially competitive. More recently, the possibility to utilize renewable residual biomasses as feedstock not only for biofuels, but also for organic acids production is further augmenting the sustainability of their production, in a logic of circular bioeconomy. In this review, we briefly present the latest updates regarding the production of some industrially relevant organic acids (citric fumaric, itaconic, lactic and succinic acid), discussing the challenges and possible future developments of successful production.

Molecular Tools for Leveraging the Potential of the Acid-Tolerant Yeast Zygosaccharomyces bailii as Cell Factory

Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycete budding yeast, is widely known for its peculiar tolerance to different stresses, among which are organic acids. Moreover, the recent reclassification of the species, including diverse hybrids, is further expanding both fundamental and applied interests. It is therefore reasonable that despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here we describe in detail the methods for determining chromosome number, size, and aneuploidy, transformation, classical target gene disruption or gene integration, and designing of episomal expression plasmids helpful for engineering the yeast Z. bailii .

Yeast Template-Derived Multielectron Reaction NASICON Structure Na3MnTi(PO4)3 for High-Performance Sodium-Ion Batteries

The sodium super ion conductor (NASICON) structure materials are essential for sodium-ion batteries (SIBs) due to their robust crystal structure, excellent ionic conductivity, and flexibility to regulate element and valence. However, the poor electronic conductivity and inferior energy density caused by the nature of these materials have always been obstacles to commercialization. Herein, using yeast as a template to derive NASICON structure Na₃MnTi(PO₄)₃ (NMTP) materials (noted as Yeast@NMTP/C) is presented. The Yeast@NMTP/C material retains the microsphere morphology of the yeast template and not only controls the particle size (around 2 μm) to shorten the Na⁺ diffusion pathways but also improves the electronic conductivity to optimize the electrochemical kinetics. The Yeast@NMTP/C cathode delivers reversible multielectron redox reactions including Ti^4+/3+, Mn^3+/2+, and Mn^4+/3+ and exhibits a high capacity of 108.5 mAh g^-1 with a 79.2% capacity retention after 1000 cycles at a 2C rate. The sodium storage mechanism of Yeast@NMTP/C reveals that the addition of Ti^4+/3+ redox plays a key role in improving the Na⁺ diffusion kinetics, and both solid-solution and two-phase reactions take place during the desodiation and sodiation process. Additionally, the high-rate and long-span cycle performance of Yeast@NMTP/C at 10C is ascribed to contribute to pseudocapacitance.

An Integrative View of the Role of Lachancea thermotolerans in Wine Technology

The interest in Lachancea thermotolerans, a yeast species with unusual characteristics, has notably increased in all ecological, evolutionary, and industrial aspects. One of the key characteristics of L. thermotolerans is the production of high quantities of lactic acid compared to other yeast species. Its evolution has mainly been driven by the influence of the environment and domestication, allowing several metabolic traits to arise. The molecular regulation of the fermentative process in L. thermotolerans shows interesting routes that play a complementary or protective role against fermentative stresses. One route that is activated under this condition is involved in the production of lactic acid, presenting a complete system for its production, showing the involvement of several enzymes and transporters. In winemaking, the use of L. thermotolerans is nowadays mostly focused in early–medium-maturity grape varieties, in which over-ripening can produce wines lacking acidity and with high concentrations of ethanol. Recent studies have reported new positive influences on quality apart from lactic acid acidification, such as improvements in color, glutathione production, aroma, malic acid, polysaccharides, or specific enzymatic activities that constitute interesting new criteria for selecting better strains. This positive influence on winemaking has increased the availability of commercial strains during recent years, allowing comparisons among some of those products. Initially, the management of L. thermotolerans was thought to be combined with Saccaharomyces cerevisiae to properly end alcoholic fermentation, but new studies are innovating and reporting combinations with other key enological microorganisms such as Schizosaccharomyces pombe, Oenocous oeni, Lactiplantibacillus plantarum, or other non-Saccharomyces.

Saccharomyces cerevisiae as host for the recombinant production of polyketides and nonribosomal peptides

As a robust, fast growing and genetically tractable organism, the budding yeast Saccharomyces cerevisiae is one of the most widely used hosts in biotechnology. Its applications range from the manufacturing of vaccines and hormones to bulk chemicals and biofuels. In recent years, major efforts have been undertaken to expand this portfolio to include structurally complex natural products, such as polyketides and nonribosomally synthesized peptides. These compounds often have useful pharmacological properties, which make them valuable drugs for the treatment of infectious diseases, cancer, or autoimmune disorders. In nature, polyketides and nonribosomal peptides are generated by consecutive condensation reactions of short chain acyl-CoAs or amino acids, respectively, with the substrates and reaction intermediates being bound to large, multidomain enzymes. For the reconstitution of these multistep catalytic processes, the enzymatic assembly lines need to be functionally expressed and the required substrates must be supplied in reasonable quantities. Furthermore, the production hosts need to be protected from the toxicity of the biosynthetic products. In this review, we will summarize and evaluate the status quo regarding the heterologous production of polyketides and nonribosomal peptides in S. cerevisiae. Based on a comprehensive literature analysis, prerequisites for a successful pathway reconstitution could be deduced, as well as recurring bottlenecks in this microbial host.

Potential Valorization of Organic Waste Streams to Valuable Organic Acids through Microbial Conversion: A South African Case Study

The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates the development of technologies that utilize sustainable feedstocks, have simple and robust operations, are feasible at small scale and produce a variety of valuable bioproducts, thus fitting the biorefinery concept. This case study focuses on the microbial production of higher-value products from selected organic waste streams abundant in the South African agricultural sector using microbes adapted to utilize different parts of biomass waste streams. A ruminant-based carboxylate platform based on mixed or undefined anaerobic co-cultures of rumen microorganisms can convert the carbohydrate polymers in the lignocellulosic part of organic waste streams to carboxylic acids that can be upgraded to biofuels or green chemicals. Furthermore, yeast and fungi can convert the simpler carbohydrates (such as the sugars and malic acid in grape and apple pomace) to ethanol and high-value carboxylic acids, such as lactic, fumaric, succinic and citric acid. This review will discuss the combinational use of the ruminal carboxylate platform and native or recombinant yeasts to valorize biomass waste streams through the production of higher-value organic acids with various applications.

Efficient conversion of hemicellulose sugars from spent sulfite liquor into optically pure L-lactic acid by Enterococcus mundtii

Spent sulfite liquor (SSL), a waste stream from wood pulp production, has great potential as carbon source for future industrial fermentations. In the present study, SSL was separated into a hemicellulose derived sugar syrup (HDSS) and a lignosulfonic fraction by simulated moving bed chromatography. The recovery of SSL sugars in the HDSS was 89% and the fermentation inhibitors furfural, 5-hydroxymethylfurfural and acetic acid were removed by 98.7%, 60.5% and 75.5%, respectively. The obtained sugars have been converted to L-lactic acid, a building block for bioplastics, by fermentation with the lactic acid bacterium Enterococcus mundtii DSM4838. Batch fermentations on HDSS produced up to 56.3 g/L L-lactic acid. Simultaneous conversion of pentose and hexose sugars during fed-batch fermentation of wildtype E. mundtii led to 87.9 g/L optically pure (>99%) L-lactic acid, with maximum productivities of 3.25 g/L.h and yields approaching 1.00 g/g during feeding phase from HDSS as carbon source.

Membrane transporters in the bioproduction of organic acids: state of the art and future perspectives for industrial applications

Organic acids such as monocarboxylic acids, dicarboxylic acids or even more complex molecules such as sugar acids, have displayed great applicability in the industry as these compounds are used as platform chemicals for polymer, food, agricultural and pharmaceutical sectors. Chemical synthesis of these compounds from petroleum derivatives is currently their major source of production. However, increasing environmental concerns have prompted the production of organic acids by microorganisms. The current trend is the exploitation of industrial biowastes to sustain microbial cell growth and valorize biomass conversion into organic acids. One of the major bottlenecks for the efficient and cost-effective bioproduction is the export of organic acids through the microbial plasma membrane. Membrane transporter proteins are crucial elements for the optimization of substrate import and final product export. Several transporters have been expressed in organic acid-producing species, resulting in increased final product titers in the extracellular medium and higher productivity levels. In this review, the state of the art of plasma membrane transport of organic acids is presented, along with the implications for industrial biotechnology.

Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae

One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.

Impact of Lachancea thermotolerans on chemical composition and sensory profiles of Merlot wines

Wines from warm(ing) climates often contain excessive ethanol but lack acidity. The yeast Lachancea thermotolerans can ameliorate such wines due to partial conversion of sugars to lactic acid during alcoholic fermentation. This study compared the performance of five L. thermotolerans strains in two inoculation modalities (sequential and co-inoculation) to Saccharomyces cerevisiae and un-inoculated treatments in high sugar/low acidity Merlot fermentations. The pH and ethanol levels in mixed-culture dry wines were either comparable, or significantly lower than in controls (decrease of up to 0.5 units and 0.90% v/v, respectively). The analysis of volatile compounds revealed marked differences in major flavour-active yeast metabolites, including up to a thirty-fold increase in ethyl lactate in certain L. thermotolerans modalities. The wines significantly differed in acidity perception, alongside 18 other sensory attributes. Together, these results highlight the potential of some L. thermotolerans strains to produce 'fresher' wines with lower ethanol content and improved flavour/balance.

Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer

Polylactic acid is a plastic polymer widely used in different applications from printing filaments for 3D printer to mulching films in agriculture, packaging materials, etc. Here, we report the production of poly-D-lactic acid (PDLA) in an engineered yeast strain of Yarrowia lipolytica. Firstly, the pathway for lactic acid consumption in this yeast was identified and interrupted. Then, the heterologous pathway for PDLA production, which contains a propionyl-CoA transferase (PCT) converting lactic acid into lactyl-CoA, and an evolved polyhydroxyalkanoic acid (PHA) synthase polymerizing lactyl-CoA, was introduced into the engineered strain. Among the different PCT proteins that were expressed in Y. lipolytica, the Clostridium propionicum PCT exhibited the highest efficiency in conversion of D-lactic acid to D-lactyl-CoA. We further evaluated the lactyl-CoA and PDLA productions by expressing this PCT and a variant of Pseudomonas aeruginosa PHA synthase at different subcellular localizations. The best PDLA production was obtained by expressing the PCT in the cytosol and the variant of PHA synthase in peroxisome. PDLA homopolymer accumulation in the cell reached 26 mg/g-DCW, and the molecular weights of the polymer (Mw = 50.5 × 103 g/mol and Mn = 12.5 × 103 g/mol) were among the highest reported for an in vivo production.

Domesticating a food spoilage yeast into an organic acid-tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailii

Lactic acid represents an important class of commodity chemicals, which can be produced by microbial cell factories. However, due to the toxicity of lactic acid at lower pH, microbial production requires the usage of neutralizing agents to maintain neutral pH. Zygosaccharomyces bailii, a food spoilage yeast, can grow under the presence of organic acids used as food preservatives. This unique trait of the yeast might be useful for producing lactic acid. With the goal of domesticating the organic acid-tolerant yeast as a metabolic engineering host, seven Z. bailii strains were screened in a minimal medium with 10 g/L of acetic, or 60 g/L of lactic acid at pH 3. The Z. bailii NRRL Y7239 strain was selected as the most robust strain to be engineered for lactic acid production. By applying a PAN-ARS-based CRISPR-Cas9 system consisting of a transfer RNA promoter and NAT selection, we demonstrated the targeted deletion of ADE2 and site-specific integration of Rhizopus oryzae ldhA coding for lactate dehydrogenase into the PDC1 locus. The resulting pdc1::ldhA strain produced 35 g/L of lactic acid without ethanol production. This study demonstrates the feasibility of the CRISPR-Cas9 system in Z. bailii, which can be applied for a fundamental study of the species.

Molecular Characterization and Enological Potential of A High Lactic Acid-Producing Lachancea thermotolerans Vineyard Strain

Lactic acid production is an important feature of the yeast Lachancea thermotolerans that has gained increasing interest in winemaking. In particular, in light of climate change, the biological acidification and ethanol reduction by the use of selected yeast strains may counteract the effect of global warming in wines. Here, the enological potential of a high lactate-producing L. thermotolerans strain (P-HO1) in mixed fermentations with S. cerevisiae was examined. Among the different inoculation schemes evaluated, the most successful implantation of L. thermotolerans was accomplished by sequential inoculation of S. cerevisiae, i.e., at 1% vol. ethanol. P-HO1produced the highest levels of lactic acid ever recorded in mixed fermentations (10.4 g/L), increasing thereby the acidity and reducing ethanol by 1.6% vol. L. thermotolerans was also associated with increases in ethyl isobutyrate (strawberry aroma), free SO₂, organoleptically perceived citric nuances and aftertaste. To start uncovering the molecular mechanisms of lactate biosynthesis in L. thermotolerans, the relative expressions of the three lactate dehydrogenase (LDH) paralogous genes, which encode the key enzyme for lactate biosynthesis, along with the alcohol dehydrogenase paralogs (ADHs) were determined. Present results point to the possible implication of LDH2, but not of other LDH or ADH genes, in the high production of lactic acid in certain strains at the expense of ethanol. Taken together, the important enological features of P-HO1 highlighted here, and potentially of other L. thermotolerans strains, indicate its great importance in modern winemaking, particularly in the light of the upcoming climate change and its consequences in the grape/wine system.

Lachancea fermentati Strains Isolated From Kombucha: Fundamental Insights, and Practical Application in Low Alcohol Beer Brewing

With a growing interest in non-alcoholic and low alcohol beer (NABLAB), researchers are looking into non-conventional yeasts to harness their special metabolic traits for their production. One of the investigated species is Lachancea fermentati, which possesses the uncommon ability to produce significant amounts of lactic acid during alcoholic fermentation, resulting in the accumulation of lactic acid while exhibiting reduced ethanol production. In this study, four Lachancea fermentati strains isolated from individual kombucha cultures were investigated. Whole genome sequencing was performed, and the strains were characterized for important brewing characteristics (e.g., sugar utilization) and sensitivities toward stress factors. A screening in wort extract was performed to elucidate strain-dependent differences, followed by fermentation optimization to enhance lactic acid production. Finally, a low alcohol beer was produced at 60 L pilot-scale. The genomes of the kombucha isolates were diverse and could be separated into two phylogenetic groups, which were related to their geographical origin. Compared to a Saccharomyces cerevisiae brewers' yeast, the strains' sensitivities to alcohol and acidic conditions were low, while their sensitivities toward osmotic stress were higher. In the screening, lactic acid production showed significant, strain-dependent differences. Fermentation optimization by means of response surface methodology (RSM) revealed an increased lactic acid production at a low pitching rate, high fermentation temperature, and high extract content. It was shown that a high initial glucose concentration led to the highest lactic acid production (max. 18.0 mM). The data indicated that simultaneous lactic acid production and ethanol production occurred as long as glucose was present. When glucose was depleted and/or lactic acid concentrations were high, the production shifted toward the ethanol pathway as the sole pathway. A low alcohol beer (<1.3% ABV) was produced at 60 L pilot-scale by means of stopped fermentation. The beer exhibited a balanced ratio of sweetness from residual sugars and acidity from the lactic acid produced (13.6 mM). However, due to the stopped fermentation, high levels of diacetyl were present, which could necessitate further process intervention to reduce concentrations to acceptable levels.

Downscaling screening cultures in a multifunctional bioreactor array-on-a-chip for speeding up optimization of yeast-based lactic acid bioproduction

A key challenge for bioprocess engineering is the identification of the optimum process conditions for the production of biochemical and biopharmaceutical compounds using prokaryotic as well as eukaryotic cell factories. Shake flasks and bench-scale bioreactor systems are still the golden standard in the early stage of bioprocess development, though they are known to be expensive, time-consuming, and labor-intensive as well as lacking the throughput for efficient production optimizations. To bridge the technological gap between bioprocess optimization and upscaling, we have developed a microfluidic bioreactor array to reduce time and costs, and to increase throughput compared with traditional lab-scale culture strategies. We present a multifunctional microfluidic device containing 12 individual bioreactors (V_t  = 15 µl) in a 26 mm × 76 mm area with in-line biosensing of dissolved oxygen and biomass concentration. Following initial device characterization, the bioreactor lab-on-a-chip was used in a proof-of-principle study to identify the most productive cell line for lactic acid production out of two engineered yeast strains, evaluating whether it could reduce the time needed for collecting meaningful data compared with shake flasks cultures. Results of the study showed significant difference in the strains' productivity within 3 hr of operation exhibiting a 4- to 6-fold higher lactic acid production, thus pointing at the potential of microfluidic technology as effective screening tool for fast and parallelizable industrial bioprocess development.

Multi-Product Lactic Acid Bacteria Fermentations: A Review

Industrial biotechnology is a continuously expanding field focused on the application of microorganisms to produce chemicals using renewable sources as substrates. Currently, an increasing interest in new versatile processes, able to utilize a variety of substrates to obtain diverse products, can be observed. A robust microbial strain is critical in the creation of such processes. Lactic acid bacteria (LAB) are used to produce a wide variety of chemicals with high commercial interest. Lactic acid (LA) is the most predominant industrial product obtained from LAB fermentations, and its production is forecasted to rise as the result of the increasing demand of polylactic acid. Hence, the creation of new ways to revalorize LA production processes is of high interest and could further enhance its economic value. Therefore, this review explores some co-products of LA fermentations, derived from LAB, with special focus on bacteriocins, lipoteichoic acid, and probiotics. Finally, a multi-product process involving LA and the other compounds of interest is proposed.

Efficient production of d-lactate from methane in a lactate-tolerant strain of Methylomonas sp. DH-1 generated by adaptive laboratory evolution

BACKGROUND

Methane, a main component of natural gas and biogas, has gained much attention as an abundant and low-cost carbon source. Methanotrophs, which can use methane as a sole carbon and energy source, are promising hosts to produce value-added chemicals from methane, but their metabolic engineering is still challenging. In previous attempts to produce lactic acid (LA) from methane, LA production levels were limited in part due to LA toxicity. We solved this problem by generating an LA-tolerant strain, which also contributes to understanding novel LA tolerance mechanisms.

RESULTS

In this study, we engineered a methanotroph strain Methylomonas sp. DH-1 to produce d-lactic acid (d-LA) from methane. LA toxicity is one of the limiting factors for high-level production of LA. Therefore, we first performed adaptive laboratory evolution of Methylomonas sp. DH-1, generating an LA-tolerant strain JHM80. Genome sequencing of JHM80 revealed the causal gene watR, encoding a LysR-type transcription factor, whose overexpression due to a 2-bp (TT) deletion in the promoter region is partly responsible for the LA tolerance of JHM80. Overexpression of the watR gene in wild-type strain also led to an increase in LA tolerance. When d form-specific lactate dehydrogenase gene from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 was introduced into the genome while deleting the glgA gene encoding glycogen synthase, JHM80 produced about 7.5-fold higher level of d-LA from methane than wild type, suggesting that LA tolerance is a critical limiting factor for LA production in this host. d-LA production was further enhanced by optimization of the medium, resulting in a titer of 1.19 g/L and a yield of 0.245 g/g CH4.

CONCLUSIONS

JHM80, an LA-tolerant strain of Methylomonas sp. DH-1, generated by adaptive laboratory evolution was effective in LA production from methane. Characterization of the mutated genes in JHM80 revealed that overexpression of the watR gene, encoding a LysR-type transcription factor, is responsible for LA tolerance. By introducing a heterologous lactate dehydrogenase gene into the genome of JHM80 strain while deleting the glgA gene, high d-LA production titer and yield were achieved from methane.

Effect of Co-Inoculation with Saccharomyces cerevisiae and Lactic Acid Bacteria on the Content of Propan-2-ol, Acetaldehyde and Weak Acids in Fermented Distillery Mashes

The qualitative and quantitative composition of volatile compounds in fermented distillery mash determines the quality of the obtained distillate of agricultural origin (i.e., raw spirit) and the effectiveness of further purification steps. Propan-2-ol (syn. isopropyl alcohol), due to its low boiling point, is difficult to remove by rectification. Therefore, its synthesis needs to be limited during fermentation by Saccharomyces cerevisiae yeast, while at the same time controlling the levels of acetaldehyde and acetic acid, which are likewise known to determine the quality of raw spirit. Lactic acid bacteria (LAB) are a common but undesirable contaminant in distillery mashes. They are responsible for the production of undesirable compounds, which can affect synthesis of propan-2-ol. Some bacteria strains are able to synthesize isopropyl alcohol. This study therefore set out to investigate whether LAB with S. cerevisiae yeast are responsible for conversion of acetone to propan-2-ol, as well as the effects of the amount of LAB inoculum and fermentation parameters (pH and temperature) on the content of isopropyl alcohol, acetaldehyde, lactic acid and acetic acid in fermented mashes. The results of NMR and comprehensive two-dimensional gas chromatography coupled with time of flight mass spectrometry (GC × GC-TOF MS) analysis confirmed the ability of the yeast and LAB strains to metabolize acetone via its reduction to isopropyl alcohol. Efficient fermentation of distillery mashes was observed in all tested mashes with an initial LAB count of 3.34–6.34 log cfu/mL, which had no significant effect on the ethanol content. However, changes were observed in the contents of by-products. Lowering the initial pH of the mashes to 4.5, without and with LAB (3.34–4.34 log cfu/mL), resulted in a decrease in propan-2-ol and a concomitant increase in acetaldehyde content, while a higher pH (5.0 and 5.5) increased the content of propan-2-ol and decreased acetaldehyde content. Higher temperature (35 °C) promoted propan-2-ol synthesis and also resulted in increased acetic acid content in the fermented mashes compared to the controls. Moreover, the acetic acid content rose with increases in the initial pH and the initial LAB count.

Efficient l-lactic acid production from corncob residue using metabolically engineered thermo-tolerant yeast

Lactic acid is an important industrial product and the production from inexpensive and renewable lignocellulose can reduce the cost and environmental pollution. In this study, a Kluyveromyces marxianus strain which produced lactic acid efficiently from corncob was constructed. Firstly, two of six different lactate dehydrogenases, which from Plasmodium falciparum and Bacillus subtilis, respectively, were proved to be effective for l-lactic acid production. Then, five single genetic modifications were conducted. The overexpression of Saccharomyces cerevisiae proton-coupled monocarboxylate transporter, K. marxianus 6-phosphofructokinase, or disruption of K. marxianus putative d-lactate dehydrogenase enhanced the l-lactic acid accumulation. Finally, the strain YKX071, obtained via combination of above effective genetic engineering, produced 103.00 g/L l-lactic acid at 42 °C with optical purity of 99.5% from corncob residue via simultaneous saccharification and co-fermentation. This study first developed an effective platform for high optical purity l-lactic acid production from lignocellulose using yeast with inexpensive nitrogen sources.

Production of biofuels and chemicals from xylose using native and engineered yeast strains

Numerous metabolic engineering strategies have allowed yeasts to efficiently assimilate xylose, the second most abundant sugar component of lignocellulosic biomass. During the investigation of xylose utilization by yeasts, a global rewiring of metabolic networks upon xylose cultivation has been captured, as opposed to a pattern of glucose repression. A clear understanding of the xylose-induced metabolic reprogramming in yeast would shed light on the optimization of yeast-based bioprocesses to produce biofuels and chemicals using xylose. In this review, we delved into the characteristics of yeast xylose metabolism, and potential benefits of using xylose as a carbon source to produce various biochemicals with examples. Transcriptomic and metabolomic patterns of xylose-grown yeast cells were distinct from those on glucose-a conventional sugar of industrial biotechnology-and the gap might lead to opportunities to produce biochemicals efficiently. Indeed, limited glycolytic metabolic fluxes during xylose utilization could result in enhanced production of metabolites whose biosynthetic pathways compete for precursors with ethanol fermentation. Also, alleviation of glucose repression on cytosolic acetyl coenzyme A (acetyl-CoA) synthesis, and respiratory energy metabolism during xylose utilization enhanced production of acetyl-CoA derivatives. Consideration of singular properties of xylose metabolism, such as redox cofactor imbalance between xylose reductase and xylitol dehydrogenase, is necessary to maximize these positive xylose effects. This review argues the importance and benefits of xylose utilization as not only a way of expanding a substrate range, but also an effective environmental perturbation for the efficient production of advanced biofuels and chemicals in yeasts.

Oenological traits of Lachancea thermotolerans show signs of domestication and allopatric differentiation

The yeast Lachancea thermotolerans (previously Kluyveromyces thermotolerans) is a species of large, yet underexplored, oenological potential. This study delivers comprehensive oenological phenomes of 94 L. thermotolerans strains obtained from diverse ecological niches worldwide, classified in nine genetic groups based on their pre-determined microsatellite genotypes. The strains and the genetic groups were compared for their alcoholic fermentation performance, production of primary and secondary metabolites and pH modulation in Chardonnay grape juice fermentations. The common oenological features of L. thermotolerans strains were their glucophilic character, relatively extensive fermentation ability, low production of acetic acid and the formation of lactic acid, which significantly affected the pH of the wines. An untargeted analysis of volatile compounds, used for the first time in a population-scale phenotyping of a non-Saccharomyces yeast, revealed that 58 out of 90 volatiles were affected at an L. thermotolerans strain level. Besides the remarkable extent of intra-specific diversity, our results confirmed the distinct phenotypic performance of L. thermotolerans genetic groups. Together, these observations provide further support for the occurrence of domestication events and allopatric differentiation in L. thermotolerans population.

L-Lactic acid production from glucose and xylose with engineered strains of Saccharomyces cerevisiae: aeration and carbon source influence yields and productivities

BACKGROUND

Saccharomyces cerevisiae, engineered for L-lactic acid production from glucose and xylose, is a promising production host for lignocellulose-to-lactic acid processes. However, the two principal engineering strategies-pyruvate-to-lactic acid conversion with and without disruption of the competing pyruvate-to-ethanol pathway-have not yet resulted in strains that combine high lactic acid yields (Y_LA) and productivities (Q_LA) on both sugar substrates. Limitations seemingly arise from a dependency on the carbon source and the aeration conditions, but the underlying effects are poorly understood. We have recently presented two xylose-to-lactic acid converting strains, IBB14LA1 and IBB14LA1_5, which have the L-lactic acid dehydrogenase from Plasmodium falciparum (pfLDH) integrated at the pdc1 (pyruvate decarboxylase) locus. IBB14LA1_5 additionally has its pdc5 gene knocked out. In this study, the influence of carbon source and oxygen on Y_LA and Q_LA in IBB14LA1 and IBB14LA1_5 was investigated.

RESULTS

In anaerobic fermentation IBB14LA1 showed a higher Y_LA on xylose (0.27 g g _Xyl^-1 ) than on glucose (0.18 g g _Glc^-1 ). The ethanol yields (Y_EtOH, 0.15 g g _Xyl^-1 and 0.32 g g _Glc^-1 ) followed an opposite trend. In IBB14LA1_5, the effect of the carbon source on Y_LA was less pronounced (~ 0.80 g g _Xyl^-1 , and 0.67 g g _Glc^-1 ). Supply of oxygen accelerated glucose conversions significantly in IBB14LA1 (Q_LA from 0.38 to 0.81 g L^-1 h^-1) and IBB14LA1_5 (Q_LA from 0.05 to 1.77 g L^-1 h^-1) at constant Y_LA (IBB14LA1 ~ 0.18 g g _Glc^-1 ; IBB14LA1_5 ~ 0.68 g g _Glc^-1 ). In aerobic xylose conversions, however, lactic acid production ceased completely in IBB14LA1 and decreased drastically in IBB14LA1_5 (Y_LA aerobic ≤ 0.25 g g _Xyl^-1 and anaerobic ~ 0.80 g g _Xyl^-1 ) at similar Q_LA (~ 0.04 g L^-1 h^-1). Switching from aerobic to microaerophilic conditions (pO₂ ~ 2%) prevented lactic acid metabolization, observed for fully aerobic conditions, and increased Q_LA and Y_LA up to 0.11 g L^-1 h^-1 and 0.38 g g _Xyl^-1 , respectively. The pfLDH and PDC activities in IBB14LA1 were measured and shown to change drastically dependent on carbon source and oxygen.

CONCLUSION

Evidence from conversion time courses together with results of activity measurements for pfLDH and PDC show that in IBB14LA1 the distribution of fluxes at the pyruvate branching point is carbon source and oxygen dependent. Comparison of the performance of strain IBB14LA1 and IBB14LA1_5 in conversions under different aeration conditions (aerobic, anaerobic, and microaerophilic) further suggest that xylose, unlike glucose, does not repress the respiratory response in both strains. This study proposes new genetic engineering targets for rendering genetically engineering S. cerevisiae better suited for lactic acid biorefineries.

Effect of Pyruvate Decarboxylase Knockout on Product Distribution Using Pichia pastoris (Komagataella phaffii) Engineered for Lactic Acid Production

Lactic acid is the monomer unit of the bioplastic poly-lactic acid (PLA). One candidate organism for lactic acid production is Pichia pastoris, a yeast widely used for heterologous protein production. Nevertheless, this yeast has a poor fermentative capability that can be modulated by controlling oxygen levels. In a previous study, lactate dehydrogenase (LDH) activity was introduced into P. pastoris, enabling this yeast to produce lactic acid. The present study aimed to increase the flow of pyruvate towards the production of lactic acid in P. pastoris. To this end, a strain designated GLp was constructed by inserting the bovine lactic acid dehydrogenase gene (LDHb) concomitantly with the interruption of the gene encoding pyruvate decarboxylase (PDC). Aerobic fermentation, followed by micro-aerophilic culture two-phase fermentations, showed that the GLp strain achieved a lactic acid yield of 0.65 g/g. The distribution of fermentation products demonstrated that the acetate titer was reduced by 20% in the GLp strain with a concomitant increase in arabitol production: arabitol increased from 0.025 g/g to 0.174 g/g when compared to the GS115 strain. Taken together, the results show a significant potential for P. pastoris in producing lactic acid. Moreover, for the first time, physiological data regarding co-product formation have indicated the redox balance limitations of this yeast.

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production.

IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains.