Virulence related traits in yeast species associated with food; Debaryomyces hansenii, Kluyveromyces marxianus, and Wickerhamomyces anomalus

Deep learning enabled rapid classification of yeast species in food by imaging of yeast microcolonies

Diverse species of yeasts are commonly associated with food and food production environments. The contamination of food products by spoilage yeasts poses significant challenges, leading to quality degradation and food loss. Similarly, the introduction of undesirable strains during fermentation can cause considerable challenges with the quality and progress of the fermentation process. Conventional detection methods require the isolation of visible yeast colonies for genetic or biochemical characterization, which takes 5-7 days and demands significant labor. This study presents a deep learning-based yeast classification approach that combines conventional cultivation methods, white light optical microscopy of microcolony, and deep learning techniques for rapidly detecting and classifying yeasts. Utilizing deep convolutional neural networks, the model accurately discriminates 7 different yeasts within 6 h, achieving a mPrecision of 96.0 % and a mRecall of 96.3 %. Synthetic image dataset generated by generative adversarial networks (GAN) model further improved the model performance for Debaryomyces hansenii and Wickerhamomyces anomalus, yeast species with lower initial classification performance. With the addition of synthetic images in the training process, Precision for W. anomalus and Recall for D. hansenii increased by 7.7 % and 5.6 %, respectively. The yeast classification model was validated in the presence of microscopic food debris using tomato and tomato juice as representative examples of fresh produce and processed juice. The model maintained high classification accuracy in the presence of food debris (mPrecision and mRecall >93.9 %). Overall, this methodology significantly accelerates the detection and classification of yeast species using conventional cultivation and simple white light microscopy in combination with deep learning. The simplicity, including low cost of the experimental approaches and the robustness of the deep learning model make it a highly applicable approach for routine yeast monitoring and yeast spoilage control in the food industry.

The Potential of Co-Fermentation with Pichia kluyveri and Saccharomyces cerevisiae for the Production of Low-Alcohol Craft Beer

The potential health impacts of moderate alcohol consumption have long been debated. The COVID-19 pandemic has heightened public awareness of health concerns, creating a clear market opportunity for low-alcohol craft beer development. This study investigated the possibility of low-alcohol craft beer by co-fermentation with different ratios of Pichia kluyveri (P. kluyveri) and Saccharomyces cerevisiae (SC) according to the established quality indexes. Specifically, this study was conducted to identify the low-alcohol craft beer quality by fermentation kinetics, growth kinetics, apparent attenuation (AA), real attenuation (RA), residual sugar content, alcohol by volume (ABV), and volatile organic compounds. This study demonstrated that the co-fermentation of SC and P. kluyveri in a 1:10 ratio produced an ABV of 2.98% (v/v). In addition, high concentrations of isoamyl acetate and phenyl ethyl acetate revealed banana, rose, apple, and honey flavors, respectively. Overall, this study revealed that the fermentation of P. kluyveri and SC by co-fermentation and the fermentation process by adjusting the yeast composition developed a craft beer with low alcohol content and rich aroma while establishing the quality indicators.

Probiotic Properties and Safety Evaluation in the Invertebrate Model Host Galleria mellonella of the Pichia kudriavzevii YGM091 Strain Isolated from Fermented Goat Milk

Potential probiotic yeast strains isolated from fermented food need to meet safe and beneficial conditions for the host's health. The Pichia kudriavzevii YGM091 strain isolated from fermented goat milk has outstanding probiotic characteristics, including: the high survival percentage in digestive system conditions (reaching up 247.13 ± 0.12 and 145.03 ± 0.06% at pH 3.0 and bile salt 0.5%, respectively); good tolerance to temperature, salt, phenol, ethanol; good surface properties such as high hydrophobicity percentage (> 60%), the high auto-aggregation percentage rate (66.56 ± 1.45% after 45 min of incubation) and the high co-aggregation percentage rate with pathogenic bacteria in a short time (> 40% after 2 h of incubation); biofilm forming after 24 h of incubation on abiotic surfaces; antioxidant activity reached excellent level after only 24 h of incubation (The percentage free radical scavenging and the Trolox equivalent reaching up 79.86 ± 0.70% and 92.09 ± 0.75 µg/mL after 72 h of incubation); extracellular enzymes production protease and cellulase with high activity, amylase and pectinase with moderate activity and non-lipase activity. Simultaneously, the YGM091 strain is the in vitro safety yeast: insensitive to antibiotics and fluconazole, negative for gelatinase, phospholipase, coagulase, and non-hemolysis activities. Furthermore, this strain is in vivo safety yeast with the dosages below 106 CFU/larva in the Galleria mellonella model with over 90% survival larvae and the yeast density reduced to just 102-103 CFU/larva after 72 h post-injection. Research results have demonstrated that the Pichia kudriavzevii YGM091 strain is a safe potential probiotic yeast and could become a candidate probiotic food to be used in the future.

Comparative genomics of infective Saccharomyces cerevisiae strains reveals their food origin

Fungal infections are less studied than viral or bacterial infections and often more difficult to treat. Saccharomyces cerevisiae is usually identified as an innocuous human-friendly yeast; however, this yeast can be responsible for infections mainly in immunosuppressed individuals. S. cerevisiae is a relevant organism widely used in the food industry. Therefore, the study of food yeasts as the source of clinical infection is becoming a pivotal question for food safety. In this study, we demonstrate that S. cerevisiae strains cause infections to spread mostly from food environments. Phylogenetic analysis, genome structure analysis, and phenotypic characterization showed that the key sources of the infective strains are food products, such as bread and probiotic supplements. We observed that the adaptation to host infection can drive important phenotypic and genomic changes in these strains that could be good markers to determine the source of infection. These conclusions add pivotal evidence to reinforce the need for surveillance of food-related S. cerevisiae strains as potential opportunistic pathogens.

Raw milk kefir: microbiota, bioactive peptides, and immune modulation

This study aims to characterize the microbiota and peptidomic composition of raw milk kefir, and to address the potential anti-allergic effects of raw milk kefir using validated research models for food allergy. Raw milk kefir was produced after incubation with a defined freeze-dried starter culture. Kefir was sampled during fermentation at seven time intervals. For comparison, kefir was also prepared from heat-treated milk. Peptide compositions were determined for the raw and heated milk, and kefir end products made from these milks. In a murine food allergy model, the two kefir end products were investigated for their allergy modulating effects. In both kefirs, we identified amplicon sequence variants identical to those in the starter culture, matching the bacteria Lactococcus lactis, Streptococcus thermophilus, Leuconostoc and the yeast Debaryomyces. In raw milk kefir, additional sequence variants of Lactococcus lactis and the yeasts Pichia and Galactomyces could be identified, which were absent in heated milk kefir. Analysis of peptide compositions in both kefirs indicated that the number and intensity of peptides drastically increased after fermentation. Heating of the milk negatively affected the diversity of the peptide composition in kefir. Only raw milk kefir suppressed the acute allergic skin response to the food allergen ovalbumin in sensitised mice. These effects coincided with differences in the T-cell compartment, with lower percentages of activated Th1 cells and IFNg production after treatment with kefir made from heated milk. The results of this study indicate specific properties of raw milk kefir that may contribute to its additional health benefits.

Characterization of kefir yeasts with antifungal capacity against Aspergillus species

Kefir is a fermented probiotic drink obtained by placing kefir granules in a suitable substrate. The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. The aim of this research was the isolation and identification of yeasts from kefir of different origin, the evaluation of their antifungal capacity against Aspergillus spp., and the characterization of virulence related traits. Using RFLP of ITS1/ITS4 region, D1/D2 region sequencing, and RAPD techniques, 20 kefir isolates were identified as Geotrichum candidum, Pichia kudriavzevii, Pichia membranifaciens, Saccharomyces cerevisiae, and Candida ethanolica. Their antifungal capacity was evaluated by their conidia germination reduction, which allowed the selection of eight isolates with high to moderate conidia germination reduction against Aspergillus flavus and Aspergillus parasiticus. Furthermore, these selected isolates showed growth inhibition on contact in the dual culture assay for both Aspergillus species and 3 of them-belonging to S. cerevisiae and P. kudriavzevii species-generated volatile organic compounds which significantly affected the growth of both fungi. For the evaluation of virulence-related traits, growth at high temperatures, enzymatic activities, and the adhesion to Caco-2 cells were analyzed. The isolates did not present more than one positive virulence-related trait simultaneously. In particular, it is important to highlight that the adhesion capacity to the model of intestinal barrier was extremely low for all of them. According to the results obtained, further studies would be of interest for the possible use of these promising yeasts as biocontrol agents against fungi in food.