Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations

Addition of Saccharomyces eubayanus to SCOBY fermentations modulates the chemical and volatile compound profiles in kombucha

Kombucha is a fermented beverage derived from a sweetened tea fermentation inoculated with a bacteria-yeast consortium referred to as Symbiotic Culture of Bacteria and Yeast (SCOBY). Different SCOBY cultures can impact the beverage's quality and make the whole process highly variable. Adding Saccharomyces yeast cultures to the fermentation process can avoid stalled fermentations, providing a reproducible beverage. Here, we explored using different Saccharomyces eubayanus strains together with SCOBY in the context of kombucha fermentation. Our results show that yeast x SCOBY co-cultures exhibited a robust fermentation profile, providing ethanol and acetic acid levels ranging from 0,18-1,81 %v/v and 0,35-1,15 g/L, respectively. The kombucha volatile compound profile of co-cultures was unique, where compounds such as Isopentyl acetate where only found in yeast x SCOBY fermentations. Metabarcoding revealed that the SCOBY composition was also dependent on the S. eubayanus genotype, where besides Saccharomyces, amplicon sequence variants belonging to Brettanomyces and Starmerella were detected. These differences concomitated global changes in transcript levels in S. eubayanus related to the metabolism of organic molecules used in kombucha fermentation. This study highlights the potential for exploring different S. eubayanus strains for kombucha fermentation, and the significant yeast genotype effect in the profile differentiation in this process.

Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl₂ conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level.

IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

Strain diversity of plant-associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.

Application of mixed starter culture for table olive production

The fermentation of olives is usually carried out spontaneously by natural microbiota. Spontaneous fermentation has some disadvantages, such as the formation of defects in the end product due to the activities of undesirable microorganisms. The use of starter cultures could be a promising option to provide a more controlled fermentation environment and to reduce the risk of spoilage. Mixed starter culture use (generally selected Lactobacillus strains with or without yeasts) could reduce pH in a shorter time, producing a higher amount of lactic acid and enhancing microbial safety compared to fermentation with starter cultures containing single species or natural fermentation. Their use could also enhance the organoleptical properties of table olives. Particularly the use of yeast (such as strains of W. anomolus, S. cerevisiae) in the fermentation of olives, in combination or sequentially with lactic acid bacteria could result in an increase in volatile compounds and a more aromatic final product.

Inoculation with acetic acid bacteria improves the quality of natural green table olives

This study aims to develop a method for the preparation of natural table olives using locally selected microorganisms and without resorting to the usual techniques which employ lye treatment and acids. The effects of parameters, such as lye treatment, inoculation with yeasts, substitution of organic acids with vinegar and/or acetic acid bacteria, and finally alternating aeration have been assessed. Four different combinations were applied to the “Picholine marocaine” olive variety using indigenous strains, namely Lactobacillus plantarum S1, Saccharomyces cerevisiae LD01 and Acetobacter pasteurianus KU710511 (CV01) isolated respectively from olive brine, Bouslikhen dates and Cactus. Two control tests, referring to traditional and industrial processes, were used as references. Microbial and physicochemical tests showed that the L3V combination (inoculated with A. pasteurianus KU710511 and L. plantarum S1 under the optimal growth conditions of the Acetic Acid Bacteria (AAB) strain with 6% NaCl) was found to be favorable for the growth of the Lactic Acid Bacteria (LAB) strain which plays the key role in olive fermentation. This result was confirmed by sensory evaluation, placing L3V at the top of the evaluated samples, surpassing the industrial one where a chemical debittering treatment with lye was used. In addition, alternating aeration served to increase the microbial biomass of both AAB and LAB strains along with Saccharomyces cerevisiae LD01 strain, but also to use lower concentration of NaCl and to reduce the deterioration of olives compared to the anaerobic fermentation process. Finally, a mixed starter containing the three strains was prepared in a 10-L Lab-fermenter from the L3V sample in order to improve it in subsequent studies. The prepared starter mixture could be suitable for use as a parental strain to prepare table olives for artisan and industrial application in Morocco.

Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria

Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g^-1 to over 10^8.5 CFU g^-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.

Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health

Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.