Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae

Saccharomyces cerevisiae requirement for reduced sulfur to synthesize methionine and cysteine during alcoholic fermentation, is mainly fulfilled through the sulfur assimilation pathway. Saccharomyces cerevisiae reduces sulfate into sulfur dioxide (SO2) and sulfide (H2S), whose overproduction is a major issue in winemaking, due to its negative impact on wine aroma. The amount of H2S produced is highly strain-specific and also depends on SO2 concentration, often added to grape must. Applying a bulk segregant analysis to a 96-strain-progeny derived from two strains with different abilities to produce H2S, and comparing allelic frequencies along the genome of pools of segregants producing contrasting H2S quantities, we identified two causative regions involved in H2S production in the presence of SO2. A functional genetic analysis allowed the identification of variants in four genes able to impact H2S formation, viz; ZWF1, ZRT2, SNR2, and YLR125W, and involved in functions and pathways not associated with sulfur metabolism until now. These data point out that, in wine fermentation conditions, redox status, and zinc homeostasis are linked to H2S formation while providing new insights into the regulation of H2S production, and a new vision of the interplay between the sulfur assimilation pathway and cell metabolism.

The aromatic profile of wine distillates from Ugni blanc grape musts is influenced by the nitrogen nutrition (organic vs. inorganic) of Saccharomyces cerevisiae

Although the impact of nitrogen nutrition on the production of fermentative aromas in oenological fermentation is well known today, one may wonder whether the effects studied are the same when winemaking takes place at high turbidities, specifically for the production of wines intended for cognac distillation. To that effect, a fermentation robot was used to analyze 30 different fermentation conditions at two turbidity levels with several factors tested: (i) initial addition of nitrogen either organic (with a mixture of amino acids - MixAA) or inorganic with di-ammonium phosphate (DAP) at different concentrations, (ii) variation of the ratio of inorganic/organic nitrogen (MixAA and DAP) and (iii) addition of different single amino acids (alanine, arginine, aspartic acid and glutamic acid). A metabolomic analysis was carried out on all resulting wines to have a global vision of the impact of nitrogen on more than sixty aromatic molecules of various families. Then, at the end of the alcoholic fermentation, the wines were micro-distilled. A first interesting observation was that the aroma profiles of both wines and distillates were close, indicating that the concentration factor is rather similar for the different aromas studied. Secondly, the fermentation kinetics and aroma results have shown that the nitrogen concentration effect prevailed over the nature of nitrogen. Although the lipid concentration was in excess, an interaction between the assimilable nitrogen and lipid contents was still observed in wines or in micro-distillates. Alanine is involved in the synthesis of acetaldehyde, isobutanol, isoamyl alcohol and isoamyl acetate. Finally, it was demonstrated that modifying the ratio of assimilable nitrogen in musts is not an interesting technological response to improve the aromatic profile of wines and brandies. Indeed, unbalance the physiological ratio of the must by adding a single source of assimilable nitrogen (organic or inorganic) has been shown to deregulate the synthesis of most of the fermentation aromas produced by the yeast. Wine metabolomic analysis confirmed the results that had been observed in micro-distillates but also in the other aromatic families, especially on terpenes. The contribution of solid particles, but also yeast biosynthesis (via sterol management in must) to wine terpenes is discussed. Indeed, the synthesis of terpenes in this oenological context seems to be favored, especially since the concentration of assimilable nitrogen (in addition to the lipid content) favor their accumulation in the medium. A non-negligible vintage effect on the terpene profile was also demonstrated with variations in their distribution depending on the years. Thus, the present study focuses on the metabolism of wine yeasts under different environmental conditions (nitrogen and lipid content) and on the impact of distillation on the fate of flavor compounds. The results highlight once again the complexity of metabolic fluxes and of the impact of nitrogen source (nature and amount) and of lipids. Furthermore, this study demonstrates that beyond the varietal origin of terpenes, the part resulting from the de novo synthesis by the yeast during the fermentation cannot be neglected in the context of cognac winemaking with high levels of turbidity.

Gene co-expression network analysis reveals the positive impact of endocytosis and mitochondria-related genes over nitrogen metabolism in Saccharomyces cerevisiae

Nitrogen metabolism is essential for most cellular activities. Therefore, a deep understanding of its regulatory mechanisms is necessary for the efficient utilization of nitrogen sources for Saccharomyces cerevisiae. In this study, a gene co-expression network was constructed for S. cerevisiae S288C with different nitrogen sources. From this, a key gene co-expression module related to nitrogen source preference utilization was obtained, and 10 hub genes centrally located in the co-expression network were identified. Functional studies verified that the endocytosis-related genes CAP1 and END3 significantly increased the utilization of multiple non-preferred amino acids and reduced the accumulation of the harmful nitrogen metabolite precursor urea by regulating amino acid transporters and TOR pathway. The mitochondria-related gene ATP12, MRPL22, MRP1 and NAM9 significantly increased the utilization of multiple non-preferred amino acids and reduced accumulation of the urea by coordinately regulating nitrogen catabolism repression, Ssy1p-Ptr3p-Ssy5p signaling sensor system, amino acid transporters, TOR pathway and urea metabolism-related pathways. Furthermore, these data revealed the potential positive effects of endocytosis and mitochondrial ribosomes protein translation on nitrogen source preference. This study provides new analytical perspectives for complex regulatory networks involving nitrogen metabolism in S. cerevisiae.

The Timing of Nitrogen Addition Impacts Yeast Genes Expression and the Production of Aroma Compounds During Wine Fermentation

Among the different compounds present in the must, nitrogen is an essential nutrient for the management of fermentation kinetics but also plays an important role in the synthesis of fermentative aromas. To address the problems related to nitrogen deficiencies, nitrogen additions during alcoholic fermentation have been implemented. The consequences of such additions on the main reaction are well known. However, their impact on aromas synthesis is still poorly understood. So, the main objective of this study was to determine the impact of nitrogen addition during the stationary phase on both the fermentation kinetics and aroma synthesis. To reach this goal, we used a transdisciplinary approach combining statistical modeling (Box-Behnken design and response surface modeling) and gene expression study (transcriptomic analysis). Our results indicated that nitrogen metabolism, central carbon metabolism (CCM), fermentation kinetics and aroma production were significantly impacted by nitrogen addition. The most remarkable point was the different regulation of the bioconversion of higher alcohols into acetate esters on one hand and of fatty acids into ethyl esters on the other hand. We highlighted that the conversion of higher alcohols into acetate esters was maximum when nitrogen was added at the beginning of the stationary phase. Conversely, the highest conversion of acids into ethyl esters was reached when nitrogen was added close to the end of the stationary phase. Moreover, even if the key element in the production of these two ester families appeared to be the enzymatic activity responsible for their production, rather than the availability of the corresponding precursors, these enzymatic activities were differently regulated. For acetate esters, the regulation occurred at gene level: the ATF2 gene was overexpressed following nitrogen addition during the stationary phase. On the opposite, no induction of gene expression was noted for ethyl esters; it seemed that there was an allosteric regulation.

Characterization and Role of Sterols in Saccharomyces cerevisiae during White Wine Alcoholic Fermentation

Responsible for plasma membrane structure maintenance in eukaryotic organisms, sterols are essential for yeast development. The role of two sterol sources in Saccharomyces cerevisiae during wine fermentation is highlighted in this review: ergosterol (yeast sterol produced by yeast cells under aerobic conditions) and phytosterols (plant sterols imported by yeast cells from grape musts in the absence of oxygen). These compounds are responsible for the maintenance of yeast cell viability during white wine fermentation under stress conditions, such as ethanol stress and sterol starvation, to avoid sluggish and stuck fermentations.

The Impact of Must Nutrients and Yeast Strain on the Aromatic Quality of Wines for Cognac Distillation

In order to understand the influence of nitrogen and lipid nutrition on the aromatic quality of wines for cognac distillation, we developed a transdisciplinary approach that combined statistical modeling (experimental central composite design and response surface modeling) with metabolomic analysis. Three Saccharomyces cerevisiae strains that met the requirements of cognac appellation were tested at a laboratory scale (1 L) and a statistical analysis of covariance was performed to highlight the organoleptic profile (fermentative aromas, terpenes, alcohols and aldehydes) of each strain. The results showed that nitrogen and lipid nutrients had an impact on the aromatic quality of cognac wines: high lipid concentrations favored the production of organic acids, 1-octen-3-ol and terpenes and inhibited the synthesis of esters. Beyond this trend, each yeast strain displayed its own organoleptic characteristics but had identical responses to different nutritional conditions.

Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts

BACKGROUND

Metabolomics coupled with genome-scale metabolic modeling approaches have been employed recently to quantitatively analyze the physiological states of various organisms, including Saccharomyces cerevisiae. Although yeast physiology in laboratory strains is well-studied, the metabolic states under industrially relevant scenarios such as winemaking are still not sufficiently understood, especially as there is considerable variation in metabolism between commercial strains. To study the potential causes of strain-dependent variation in the production of volatile compounds during enological conditions, random flux sampling and statistical methods were used, along with experimental extracellular metabolite flux data to characterize the differences in predicted intracellular metabolic states between strains.

RESULTS

It was observed that four selected commercial wine yeast strains (Elixir, Opale, R2, and Uvaferm) produced variable amounts of key volatile organic compounds (VOCs). Principal component analysis was performed on extracellular metabolite data from the strains at three time points of cell cultivation (24, 58, and 144 h). Separation of the strains was observed at all three time points. Furthermore, Uvaferm at 24 h, for instance, was most associated with propanol and ethyl hexanoate. R2 was found to be associated with ethyl acetate and Opale could be associated with isobutanol while Elixir was most associated with phenylethanol and phenylethyl acetate. Constraint-based modeling (CBM) was employed using the latest genome-scale metabolic model of yeast (Yeast8) and random flux sampling was performed with experimentally derived fluxes at various stages of growth as constraints for the model. The flux sampling simulations allowed us to characterize intracellular metabolic flux states and illustrate the key parts of metabolism that likely determine the observed strain differences. Flux sampling determined that Uvaferm and Elixir are similar while R2 and Opale exhibited the highest degree of differences in the Ehrlich pathway and carbon metabolism, thereby causing strain-specific variation in VOC production. The model predictions also established the top 20 fluxes that relate to phenotypic strain variation (e.g. at 24 h). These fluxes indicated that Opale had a higher median flux for pyruvate decarboxylase reactions compared with the other strains. Conversely, R2 which was lower in all VOCs, had higher median fluxes going toward central metabolism. For Elixir and Uvaferm, the differences in metabolism were most evident in fluxes pertaining to transaminase and hexokinase associated reactions. The applied analysis of metabolic divergence unveiled strain-specific differences in yeast metabolism linked to fusel alcohol and ester production.

CONCLUSIONS

Overall, this approach proved useful in elucidating key reactions in amino acid, carbon, and glycerophospholipid metabolism which suggest genetic divergence in activity in metabolic subsystems among these wine strains related to the observed differences in VOC formation. The findings in this study could steer more focused research endeavors in developing or selecting optimal aroma-producing yeast stains for winemaking and other types of alcoholic fermentations.

Impact of high lipid contents on the production of fermentative aromas during white wine fermentation

In Cognac, the musts are rich in grape solids and fermentations are usually run with turbidities ranging between 500 and 1500 NTU (nephelometric turbidity unit). These conditions, considered favourable for generating the desired organoleptic profiles of the final Eaux-de-vies, are unusual in winemaking, and, consequently, their impact on yeast metabolism is poorly understood. This study aims to better describe and understand the synthesis of fermentative aromas in such lipid-excess conditions, while integrating the effect of two other very important parameters: the initial concentration of assimilable nitrogen and the temperature of fermentation. To reach this objective, a Box-Behnken design was implemented to describe and model the simple effects of these factors as well as their interactions. Although the lipid concentration was very high, impacts on the production of fermentative aromas were observed. Indeed, high lipid levels promoted the synthesis of higher alcohols. Observing this effect was surprising because there is no metabolic connection between the anabolic pathways of production of these alcohols and the lipid pathway. This effect may be partly explained by impairment in the activity of alcohol acetyl transferases in the presence of lipids, which catalyse the conversion of higher alcohols into the corresponding esters. Therefore, in this study, the negative impact of turbidity was very significant on acetate esters related to the production of acetyl-CoA, which was the main molecule disturbed by the strong presence of lipids. Finally, and more surprisingly, lipid intake did not impact the synthesis of ethyl esters, which depended on the concentration of exogenous lipids. KEY POINTS: • Innovative work on the fermentation of white wine musts with very high lipid contents. • Precise fermentation management and monitoring in Cognac-making conditions. • Experimental design to study the impact of lipids, assimilable nitrogen and temperature on fermentative aroma synthesis.

Study of Oenological Fermentation: Which Strategy and Which Tools?

Wine fermentation is a specific and complex research subject and its control is essential to ensure full process completion while improving wine quality. It displays several specificities, in particular, (i) musts with a very high sugar content, low pH, and some limiting nutrients, as well as a great variability in must composition according to the year, grape variety, and so on; (ii) atypical fermentation conditions with non-isothermal temperature profiles, a quasi-anaerobiosis and legal constraints with a limited and predefined list of authorized operations. New challenges have emerged, related to the increasing diversity of commercially available yeast strains; the fluctuating composition of musts, particularly owing to climate change; and sustainability, which has become a key issue. This paper synthesizes approaches implemented to address all these issues. It details the example of our laboratory that, for many years, has been developing an integrated approach to study yeast diversity, understand their metabolism, and develop new fermentation control strategies. This approach requires the development of specific fermentation devices to study yeast metabolism in a controlled environment that mimics practical conditions and to develop original fermentation control strategies. All these tools are described here, together with their role in the overall scientific strategy and complementary approaches in the literature.

The metabolism of lipids in yeasts and applications in oenology

Lipids are valuable compounds present in all living organisms, which display an array of functions related to compartmentalization, energy storage and enzyme activation. Furthermore, these compounds are an integral part of the plasma membrane which is responsible for maintaining structure, facilitating the transport of solutes in and out of the cell and cellular signalling necessary for cell survival. The lipid composition of the yeast Saccharomyces cerevisiae has been extensively investigated and the impact of lipids on S. cerevisiae cellular functions during wine alcoholic fermentation is well documented. Although other yeast species are currently used in various industries and are receiving increasing attention in winemaking, little is known about their lipid metabolism. This review article provides an extensive and critical evaluation of our knowledge on the biosynthesis, accumulation, metabolism and regulation of fatty acids and sterols in yeasts. The implications of the yeast lipid content on stress resistance as well as performance during alcoholic fermentation are discussed and a particular emphasis is given on non-Saccharomyces yeasts. Understanding lipid requirements and metabolism in non-Saccharomyces yeasts may lead to a better management of these yeast to enhance their contributions to wine properties.

Effect of Unsaturated Fatty Acids on Intra-Metabolites and Aroma Compounds of Saccharomyces cerevisiae in Wine Fermentation

The small changes in concentration of unsaturated fatty acids (UFAs) cause a significant influence on the aromatic component of wines. In this work, the effect of UFAs mixture (including linoleic, oleic, and α-linolenic acids) addition on intra-metabolites and aromatic compounds of two Saccharomyces cerevisiae strain EC1118 and BDX were investigated in red wine fermentation, respectively. The results showed that the pre-fermentative addition of UFAs significantly modified the physiological and energetic state of cells, and affected the levels of intra-metabolites in glycolysis pathway and TCA cycle, redox balance, ATP pool, fatty acids, and amino acids metabolism, which consequently altered the chemical and volatile composition of the wines. Different with the control wine, the wines produced by UFAs addition were characterized with higher amounts of glycerol, C6-alcohols and higher alcohols, and lower levels of acetic acid, medium-chain fatty acids, and acetate esters. Interestingly, the production of ethyl esters showed opposite profiles in different strains due to the distinct expression of EEB1, indicating that the effect of UFAs on ethyl esters syntheses is strain-specificity. Our results highlighted the effectiveness of modulating UFAs content in shaping aroma characteristics, and verified that fine adjusting the content of UFAs combined with inoculating proper yeast is a promising strategy to modulate the aromatic quality of wine, which probably provides an alternative approach to meet the expectations of wine consumers for diverse aromatic qualities.

Comparative Lipidomics of Different Yeast Species Associated to Drosophila suzukii

Yeasts constitute a dietary source for the spotted wing drosophila (SWD) and produce compounds that attract these flies. The study of the chemical composition of the yeast communities associated with SWD should therefore help to understand the relationship between the biology of the insect and the yeast's metabolism. In the present study, the lipidome of five yeast species isolated from grapes infested by SWD (three Hanseniaspora uvarum strains, Candida sp., Issatchenkia terricola, Metschnikowia pulcherrima and Saccharomycopsis vini) and a laboratory strain of Saccharomyces cerevisiae was explored using an untargeted approach. Additionally, the lipid profile of two species, S. cerevisiae and H. uvarum, which were reported to elicit different responses on SWD flies based on feeding and behavioral trials, was compared with a chemical enrichment approach. Overall, 171 lipids were annotated. The yeast species could be distinguished from each other based on their lipid profile, except for the three strains of H. uvarum, which were very similar to each other. The chemical enrichment analysis emphasized diversities between S. cerevisiae and H. uvarum, that could not be detected based on their global lipid profile. The information concerning differences between species in their lipidome may be of interest to future entomological studies concerning the yeast-insect interaction and could help to explain the responses of SWD to diverse yeast species.

Nitrogen Sources Added to Must: Effect on the Fermentations and on the Tempranillo Red Wine Quality

Nitrogen supplementation in musts or during the alcoholic fermentation is a common practice to promote fermentations. In this study, the impact of the supplementation of two different sources of nitrogen during Tempranillo red wine elaboration was studied. Mineral and organic nitrogen was added after the exponential yeast growth phase and during winemaking, examining its impact on the alcoholic and malolactic fermentation development, on the aromatic wine composition and on the nitrogenous wine composition. The nitrogen supplementation did not provide neither significant advantages in kinetics and fermentations time, nor differences in the chemical wine composition. The aromatic composition of the wines improved with the addition of inorganic nitrogen, although its organoleptic evaluation was not favored. Moreover, the concentration of amino acids in wines increased slightly after the malolactic fermentation and significantly during the stabilization time, especially with organic nitrogen addition. However, the synthesis of biogenic amines did not increase in wines neither after the malolactic fermentation, nor after the storage period.

Transcriptional Comparison Investigating the Influence of the Addition of Unsaturated Fatty Acids on Aroma Compounds During Alcoholic Fermentation

The levels of unsaturated fatty acids (UFAs) in grape must significantly influence yeast metabolism and the production of aroma compounds. In this work, cDNA microarray technology was applied to analyze the transcriptional discrepancies of wine yeast (commercial wine yeast Lalvin EC1118) fermenting in synthetic grape must supplemented with different concentrations of a mixture of UFAs (including linoleic acid, oleic acid, and α-linolenic acid). The results showed that the initial addition of a high level of UFAs can significantly enrich the intracellular UFAs when compared to a low addition of UFAs and further increase the cell population and most volatiles, including higher alcohols and esters, except for several fatty acids. Microarray analyses identified that 63 genes were upregulated, and 91 genes were downregulated during the different fermentation stages. The up-regulated genes were involved in yeast growth and proliferation, stress responses and amino acid transportation, while the repressed genes were associated with lipid and sterol biosynthesis, amino acid metabolism, TCA cycle regulation, mitochondrial respiration, and stress responses. Unexpectedly, the genes directly related to the biosynthesis of volatile compounds did not vary substantially between the fermentations with the high and low UFA additions. The beneficial aromatic function of the UFAs was ascribed to the increased biomass and amino acid transportation, considering that the incorporation of the additional UFAs in yeast cells maintains high membrane fluidity and increases the ability of the cells to resist deleterious conditions. Our results highlighted the importance of UFAs in the regulation of aroma biosynthesis during wine fermentation and suggested that the improvement of the resistance of yeast to extreme stresses during alcoholic fermentation is essential to effectively modulate and improve the production of aroma compounds. A potential way to achieve this goal could be the rational increase of the UFA contents in grape must.

Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome

Sequential fermentation of grape must inoculated with L. thermotolerans and then S. cerevisiae 24 h later (typical wine-making practice) was conducted with or without cell-cell contact between the two yeast species. We monitored cell viability of the two species throughout fermentation by flow cytometry. The cell viability of S. cerevisiae decreased under both conditions, but the decrease was greater if there was cell-cell contact. An investigation of the nature of the interactions showed competition between the two species for nitrogen compounds, oxygen, and must sterols. Volatile-compound analysis showed differences between sequential and pure fermentation and that cell-cell contact modifies yeast metabolism, as the volatile-compound profile was significantly different from that of sequential fermentation without cell-cell contact. We further confirmed that cell-cell contact modifies yeast metabolism by analyzing the exo-metabolome of all fermentations by FT-ICR-MS analysis. These analyses show specific metabolite production and quantitative metabolite changes associated with each fermentation condition. This study shows that cell-cell contact not only affects cell viability, as already reported, but markedly affects yeast metabolism.

Influence of nitrogen status in wine alcoholic fermentation

Nitrogen is an essential nutrient for yeast during alcoholic fermentation. Nitrogen is involved in the biosynthesis of protein, amino acids, nucleotides, and other metabolites, including volatile compounds. However, recent studies have called several mechanisms that regulate its role in biosynthesis into question. An initial focus on S. cerevisiae has highlighted that the concept of "preferred" versus "non-preferred" nitrogen sources is extremely variable and strain-dependent. Then, the direct involvement of amino acids consumed in the formation of proteins and volatile compounds has recently been reevaluated. Indeed, studies have highlighted the key role of lipids in nitrogen regulation in S. cerevisiae and their involvement in the mechanism of cell death. New winemaking strategies using non-Saccharomyces yeast strains in co- or sequential fermentation improve nitrogen management. Indeed, recent studies show that non-Saccharomyces yeasts have significant and specific needs for nitrogen. Moreover, sluggish fermentation can occur when they are associated with S. cerevisiae, necessitating nitrogen addition. In this context, we will present the consequences of nitrogen addition, discussing the sources, time of addition, transcriptome changes, and effect on volatile compound composition.

Enhanced Wort Fermentation with De Novo Lager Hybrids Adapted to High-Ethanol Environments

Interspecific hybridization is a valuable tool for developing and improving brewing yeast in a number of industry-relevant aspects. However, the genomes of newly formed hybrids can be unstable. Here, we exploited this trait by adapting four brewing yeast strains, three of which were de novo interspecific lager hybrids with different ploidy levels, to high ethanol concentrations in an attempt to generate variant strains with improved fermentation performance in high-gravity wort. Through a batch fermentation-based adaptation process and selection based on a two-step screening process, we obtained eight variant strains which we compared to the wild-type strains in 2-liter-scale wort fermentations replicating industrial conditions. The results revealed that the adapted variants outperformed the strains from which they were derived, and the majority also possessed several desirable brewing-relevant traits, such as increased ester formation and ethanol tolerance, as well as decreased diacetyl formation. The variants obtained from the polyploid hybrids appeared to show greater improvements in fermentation performance than those derived from diploid strains. Interestingly, it was not only the hybrid strains, but also the Saccharomyces cerevisiae parent strain, that appeared to adapt and showed considerable changes in genome size. Genome sequencing and ploidy analysis revealed that changes had occurred at both the chromosome and single nucleotide levels in all variants. Our study demonstrates the possibility of improving de novo lager yeast hybrids through adaptive evolution by generating stable and superior variants that possess traits relevant to industrial lager beer fermentation.IMPORTANCE Recent studies have shown that hybridization is a valuable tool for creating new and diverse strains of lager yeast. Adaptive evolution is another strain development tool that can be applied in order to improve upon desirable traits. Here, we apply adaptive evolution to newly created lager yeast hybrids by subjecting them to environments containing high ethanol levels. We isolated and characterized a number of adapted variants which possess improved fermentation properties and ethanol tolerance. Genome analysis revealed substantial changes in the variants compared to the original strains. These improved variant strains were produced without any genetic modification and are suitable for industrial lager beer fermentations.

mixOmics: An R package for 'omics feature selection and multiple data integration

The advent of high throughput technologies has led to a wealth of publicly available 'omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to the discovery of important biological insights, provided that relevant information can be extracted in a holistic manner. Current statistical approaches have been focusing on identifying small subsets of molecules (a 'molecular signature') to explain or predict biological conditions, but mainly for a single type of 'omics. In addition, commonly used methods are univariate and consider each biological feature independently. We introduce mixOmics, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation. By adopting a systems biology approach, the toolkit provides a wide range of methods that statistically integrate several data sets at once to probe relationships between heterogeneous 'omics data sets. Our recent methods extend Projection to Latent Structure (PLS) models for discriminant analysis, for data integration across multiple 'omics data or across independent studies, and for the identification of molecular signatures. We illustrate our latest mixOmics integrative frameworks for the multivariate analyses of 'omics data available from the package.