Isolation and molecular identification of yeasts in Greek kefir

Growth and survival of Listeria monocytogenes during the manufacture and storage of artisanal kefir

This study aimed to evaluate the behavior of Listeria monocytogenes during the manufacture and storage of artisanal kefir. A five-strain cocktail of L. monocytogenes was introduced (at ca. 3.0 log10 CFU/mL) into UHT milk as a pre-fermentation contaminant. The growth of L. monocytogenes, lactic acid bacteria and yeasts was monitored during the 24-h fermentation period of milk with two types of kefir grains at 20 °C and the subsequent storage of kefir under adequate (4 °C) and inadequate (10 °C) refrigerated-storage conditions. L. monocytogenes grew into much higher cell densities (5.3-5.8 log10 CFU/mL) by the end of the fermentation period, but the final (24-h) counts were substantially lower than those obtained in the corresponding control trials with unfermented milk (7.2 log10 CFU/mL). The growth rate of L. monocytogenes during fermentation differed depending on the type of kefir grain used. During the subsequent 11-day storage of the kefir filtrates at 4 °C or 10 °C, the behavior of L. monocytogenes varied from no growth to further population increases (of up to 1.1 log10 CFU/mL), depending on the storage temperature, but also depending on the type of kefir grain and the grain surface-to-weight ratio that had been used to ferment the milk. This study highlights the need for strict adherence to good hygiene practices during artisanal kefir making and shows that L. monocytogenes can sustain considerable growth during milk fermentation and further grow during the subsequent cold storage of kefir, particularly under inadequate refrigerated storage conditions.

Influence of Substrate on the Fermentation Characteristics and Culture-Dependent Microbial Composition of Water Kefir

Water kefir is a sparkling fermented beverage produced by fermenting water kefir grains in a sucrose solution containing dried fruits or fruit extracts. The objective of this study was to investigate the influence of substrate composition on the fermentation kinetics and culture-dependent microbial composition of water kefir. First, the impact of different fruit substrates and nitrogen limitation was examined. Fermentation of different fruit-based media with a single water kefir culture demonstrated that the substrate mainly influenced the type and ratio of the organic acids produced. These organic acid profiles could be linked to the culture-dependent microbial composition. In addition, the microbial composition and the associated dominant microorganisms observed were influenced by the water kefir fermentation conditions. Investigation of the effect of nitrogen limitation on the fermentation kinetics of several water kefir cultures showed that under such conditions, the fermentative capacity of the cultures declined. However, this decline was not immediate, and specific water kefir microorganisms may have enabled some cultures to maintain a higher fermentative capacity for longer. Thus, the water kefir fermentation kinetics and characteristics could be linked to the substrate composition, microorganisms present, and the process conditions under which the fermentations were performed.

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.

Yeasts from Iranian traditional milk kefir samples: isolation, molecular identification and their potential probiotic properties

Milk kefir is a fermented dairy product with numerous attributed health benefits due to the presence of a complex eukaryotic and prokaryotic microbiota. In this study, a total number of 26 yeast isolates were obtained from eight kefir samples from three different cities of Iran. The isolates belonged to Kluyveromyces marxianus, Saccharomyces cerevisiae, Pichia fermentans and P. kudriavzevii. The potential probiotic characteristics of the isolates were evaluated based on their ability to tolerate the stimulated condition of the gastrointestinal tract. In addition, hemolytic activity, adherence to different solvents, auto-aggregation, adhesion to the epithelial intestine-derived cells and antimicrobial activity of the selected isolates were evaluated. Overall, four yeast strains (three strains of S. cerevisiae and one strain of P. fermentans) showed resistance and survival ability against the gastrointestinal physiological conditions including acidic pH, presence of bile salt and digestive enzymes. They were able to grow at 37 °C and had the capacity to adhere to epithelial intestine-derived cells. These results suggest that the selected strains can be proper candidates as probiotic yeast strains for the development of novel functional foods.

Microbial community diversity associated with Tibetan kefir grains and its detoxification of Ochratoxin A during fermentation

Tibetan kefir grains (TKG) are multi-functional starter cultures used in foods and have been applied in various fermentation systems. This study aimed to investigate the microbial community composition of TKG, the detoxification abilities of TKG and their isolates towards common mycotoxins, and the potential for applying TKG and their associated microbial populations to avoid mycotoxin contamination in dairy products. Cultivation-independent high-throughput sequencing of bacterial and fungal rDNA genes indicated that Lactobacillus kefiranofaciens and Kazachstania turicensis were the most abundant bacterial and fungal taxa, respectively. In addition, 27 total isolates were obtained using cultivation methods. TKG removed more than 90% of the Ochratoxin A (OTA) after 24 h, while the isolate Kazachstania unisporus AC-2 exhibited the highest removal capacity (~46.1%). Further, the isolate exhibited good resistance to acid and bile salts environment. Analysis of the OTA detoxification mechanism revealed that both adsorption and degradation activities were exhibited by TKG, with adsorption playing a major detoxification role. Furthermore, the addition of OTA did not affect the microbial community structure of TKG. These results indicate that TKG-fermented products can naturally remove mycotoxin contamination of milk and could potentially be practically applied as probiotics in fermentation products.

Functional Properties of Kefiran in Medical field and food industry

Kefir is produced through the fermentation of milk using kefir grain as a starter culture. Kefir grains include heterogeneous microorganisms embedded in a polysaccharide matrix called kefiran which is considered a biofilm, it also has many uses due to its therapeutic values. Kefiran is a microbial exopolysaccharide (EPS) obtained from the flora (acid- lactic bacteria and yeasts) of kefir grains and glucose units, in almost the same proportion. Kefiran has prebiotic nature agitating the growth of probiotics in the gastrointestinal tract of the human entity. It extends certain therapeutic benefits through balancing the microbiota in the intestine. This review presents the most recent advances regarding kefir and kefiran, their cultural condition, biological activities, and potential applications in the health and food industries.

Zooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses

Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL^–1 or g^–1, and 2.49 to 7.80 log CFU mL^–1 or g^–1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples. On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.

Quantification of Major Bacteria and Yeast Species in Kefir Consortia by Multiplex TaqMan qPCR

Kefir grains are complex microbial systems of several groups of microorganisms. The identification and quantification of the microbial composition of milk kefirs was described in several studies, which provided an insight into the microbial consortia in this complex ecosystem. Nevertheless, the current methods for identification and quantification are not appropriate for deeper studies on kefir consortia, e.g., population dynamics and microbial interactions in kefir grains. This requires another sensitive and reliable quantitative method. Therefore, this study aims to develop multiplexed qPCR assays to specifically detect and quantify, as an example, several microorganisms of the milk kefir microbial community. Primer-probe sets, which target species-specific genes in six bacteria and five yeasts, were designed, and their sensitivity and specificity to the target species was analyzed in simplex as well as four multiplex qPCR assays. The self-designed multiplex assays were applied for the detection of target bacteria and yeast species in milk kefirs, in both, grain and beverage fractions. Detection of all target microorganisms in simplex and multiplex qPCR was achieved by good linearity, efficiency, repeatability and reproducibility in all assays. When the designed assays were applied on six kefirs, all target microorganisms were detected in different samples, but not all in one kefir sample. The two ubiquitous lactobacilli Lactobacillus kefiranofaciens and Lb. kefiri were present in all six kefirs studied, but were associated with different other yeasts and bacteria. Especially on the yeast community a significant diversity was observed. In general, multiplex TaqMan qPCR as developed here was proven to have high potential for specific identification of target microorganisms in kefir samples and for the first time, eleven target bacteria and yeasts of kefir microbiota were rapidly detected and quantified. This study, thus, provides a fast and reliable protocol for future studies on kefir and other similar microbial ecosystems.

Fermented Foods as a Dietary Source of Live Organisms

The popularity of fermented foods and beverages is due to their enhanced shelf-life, safety, functionality, sensory, and nutritional properties. The latter includes the presence of bioactive molecules, vitamins, and other constituents with increased availability due to the process of fermentation. Many fermented foods also contain live microorganisms that may improve gastrointestinal health and provide other health benefits, including lowering the risk of type two diabetes and cardiovascular diseases. The number of organisms in fermented foods can vary significantly, depending on how products were manufactured and processed, as well as conditions and duration of storage. In this review, we surveyed published studies in which lactic acid and other relevant bacteria were enumerated from the most commonly consumed fermented foods, including cultured dairy products, cheese, fermented sausage, fermented vegetables, soy-fermented foods, and fermented cereal products. Most of the reported data were based on retail food samples, rather than experimentally produced products made on a laboratory scale. Results indicated that many of these fermented foods contained 105-7 lactic acid bacteria per mL or gram, although there was considerable variation based on geographical region and sampling time. In general, cultured dairy products consistently contained higher levels, up to 109/mL or g. Although few specific recommendations and claim legislations for what constitutes a relevant dose exist, the findings from this survey revealed that many fermented foods are a good source of live lactic acid bacteria, including species that reportedly provide human health benefits.