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Cocoa fermentation plays a key role in defining chocolate’s flavor, with yeasts being central to this process. This study aimed to explore intraspecific genetic diversity of major indigenous yeasts (i.e., Saccharomyces cerevisiae and Pichia kudriavzevii), and their potential interaction in the cocoa pulp environment. Their metabolic intraspecific diversity was characterized in synthetic cocoa pulp medium. Then, Saccharomyces cerevisiae, Pichia kudriavzevii, and other strains were introduced to each other to evaluate their potential negative interaction. Interesting strain associations were selected to further explore their interaction in synthetic cocoa pulp medium as well as real fresh cocoa pulp. From a fermentation campaign in Ivory Coast, a set of Saccharomyces (S.) cerevisiae and Pichia (P.) kudriavzevii strains were isolated from batches classified according to their chocolate quality (i.e., standard, intermediate, or premium chocolate). Less abundant species (i.e., Torulaspora franciscae, Kluyveromyces marxianus) were also isolated and tested for their potential negative interactions with S. cerevisiae and P. kudriavzevii. A set of strains were selected and cultured in single and in co-culture in a minimal cocoa pulp synthetic medium and in fresh cocoa pulp to highlight potential positive and/or negative interactions regarding fermentative aroma profile (i.e., higher alcohols, acetate esters, medium-chain fatty acids, and ethyl esters). The results highlighted the dominance of S. cerevisiae in fermentation kinetics and medium- to long-chain ester production, contrasted with P. kudriavzevii’s efficiency in short-chain ester synthesis. Intraspecific aroma profile variations can be pointed out. The co-cultures of P. kudriavzevii and S. cerevisiae strains isolated from the premium chocolate batch had a positive impact on the fermented pulp aroma profile. Negative interactions were observed with Torulaspora franciscae, which eliminated P. kudriavzevii’s aroma expression. Finally, the comparison of the data obtained for the minimal cocoa pulp synthetic medium compared to the cocoa pulp allowed us to draw conclusions about the use of synthetic media for studying cocoa fermentation. These findings emphasize the complex microbial interactions in cocoa fermentation that could shape future cocoa bean aroma.

Ochratoxin A (OTA) is a mycotoxin mainly produced by Aspergillus section Circumdati and section Nigri across the coffee chain. OTA is nephrotoxic and is a threat to human health. This review summarizes current knowledge on how to reduce OTA concentration in coffee from farm to cup. After a brief introduction to the OTA occurrence in coffee, current good management practices are introduced. The core of this review focuses on biocontrol and microbial decontamination by lactic acid bacteria, yeasts and fungi, and their associated enzymes currently reported in the literature. Special attention is given to publications closest to in vivo applications of biocontrol agents and microbial OTA adsorption or degradation agents. Finally, this review provides an opinion on which future techniques to promote within the coffee supply chain.

Patulin is a secondary metabolite primarily synthesized by the fungus Penicillium expansum, which is responsible for blue mold disease on apples. The latter are highly susceptible to fungal infection in the postharvest stages. Apples destined to produce compotes are processed throughout the year, which implies that long periods of storage are required under controlled atmospheres. P. expansum is capable of infecting apples throughout the whole process, and patulin can be detected in the end-product. In the present study, 455 apples (organically and conventionally grown), destined to produce compotes, of the variety “Golden Delicious” were sampled at multiple postharvest steps. The apple samples were analyzed for their patulin content and P. expansum was quantified using real-time PCR. The patulin results showed no significant differences between the two cultivation techniques; however, two critical control points were identified: the long-term storage and the deck storage of apples at ambient temperature before transport. Additionally, alterations in the epiphytic microbiota of both fungi and bacteria throughout various steps were investigated through the application of a metabarcoding approach. The alpha and beta diversity analysis highlighted the effect of long-term storage, causing an increase in the bacterial and fungal diversity on apples, and showed significant differences in the microbial communities during the different postharvest steps. The different network analyses demonstrated intra-species relationships. Multiple pairs of fungal and bacterial competitive relationships were observed. Positive interactions were also observed between P. expansum and multiple fungal and bacterial species. These network analyses provide a basis for further fungal and bacterial interaction analyses for fruit disease biocontrol.

Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.

Qymyz is a traditional acidic and ethanolic beverage in central Asian countries made from mare milk fermentation with lactic acid bacteria (LAB) and yeasts. Modeling the growth of microorganisms during fermentation is one of the methods used to control the quality of fermented products. The objective of the study was, firstly, to model the growth kinetics of Kazachstania unispora found in qymyz, and, secondly, to understand their interaction with Lacticaseibacillus casei and Lactobacillus kefiri during the fermentation of mare milk. The K. unispora optimum values of pH and temperature were 4.81 ± 0.22 and 30.16 ± 0.53 °C, respectively, with an optimal growth rate (µopt) of 0.56 ± 0.02 h−1. K. unispora had an ethanol production rate of 6.1 × 10−8 mg·CFU−1. Growth, in terms of limiting substrates showed a lower Ks value for galactose at 0.13 ± 0.04 mg·mL−1 with µopt of 0.45 ± 0.01 h−1, while, for glucose, the Ks was 0.24 ± 0.03 mg·mL−1 with the same µopt. Cocultures of K. unispora were conducted with L. casei and L. kefiri in a synthetic medium and mare milk. The results showed that K. unispora growth was limited and, thus, its ethanol production capacity was inhibited. VOC analysis of mare milk fermented with the studied strains and their cocultures resulted in 37 major volatile compounds. Statistical analysis of the VOC profiles showed that K. unispora modulates the aroma production in coculture with LAB.

The growth characteristics of two strains of lactic acid bacteria (LAB), Lacticaseibacillus casei and Lactobacillus kefiri, isolated from qymyz, a traditional fermented mare milk beverage, were studied and modeled, including the effect of different carbohydrates, pH, and temperature. Along with population, substrates, and metabolites, lactic acid and ethanol were monitored by HPLC. Growth parameters were obtained from mono- and biphasic logistic growth models that fit the population evolution of L. casei and L. kefiri, respectively. The effect of temperature and pH on the growth rate was represented with the gamma concept model, while the effect of the limiting substrate was evaluated according to the Monod equation. Lastly, a simplified Luedeking and Piret equation was used to represent metabolite production. The optimum values of pH and temperature were 6.69 ± 0.20, 38.63 ± 0.32 °C, 5.93 ± 0.08, and 33.15 ± 0.53 °C, with growth rate values of 0.66 ± 0.01 h−1 and 0.29 ± 0.01 h−1 for L. casei and L. kefiri, respectively. L. casei had a homofermentative pathway, while L. kefiri was heterofermentative, with an ethanol production rate of 2.90 × 10−9 mg·CFU−1. The Monod model showed that L. casei had the lowest Ks value for lactose, while for L. kefiri, it was the highest among milk carbohydrates. These results show that the population of the two LAB strains and therefore the concentrations of acid and ethanol can be controlled by the fermentation conditions and that our model can help to significantly improve the production of qymyz.