Sequence-based analysis of the microbial composition of water kefir from multiple sources

Challenges in water kefir production and limitations in human consumption: A comprehensive review of current knowledge

Water kefir is a convenient dairy-free alternative to dairy-based fermented beverages. It is prepared by fermenting a sucrose solution with fresh and dried fruits using water kefir grains, and demineralized whey can be used in water kefir production. This review describes current knowledge on water kefir production and its health effects. The main aims of this paper are to focus on the microbial composition, potential health-promoting properties, limitations in human consumption, and challenges in the production of water kefir. Water kefir grains and substrates, including brown sugar, dried and fresh fruits, vegetables, and molasses, used in the production influence the fermentation characteristics and composition of water kefir. Lactic acid bacteria, acetic acid bacteria, and yeasts are the microorganisms involved in the fermentation process. Lactobacillus species are the most common microorganisms found in water kefir. Water kefir contains various bioactive compounds that have potential health benefits. Water kefir may inhibit the growth of certain pathogenic microorganisms and food spoilage bacteria, resulting in various health-promoting properties, including immunomodulatory, antihypertensive, anti-inflammatory, anti-ulcerogenic, antiobesity, hypolipidemic, and hepatoprotective activities.

Identification of the Microbiota in Coconut Water, Kefir, Coconut Water Kefir and Coconut Water Kefir-Fermented Sourdough Using Culture-Dependent Techniques and Illumina-MiSeq Sequencing

The principal objective of this study was to isolate and identify the microorganisms present in commercial kefir grains, a novel kefir-fermented coconut water (CWK) and a novel coconut water kefir-fermented sourdough using phenotypic identification and Sanger sequencing and examine the microbial diversity of CWK and CWK-fermented sourdough throughout the fermentation process using the MiSeq Illumina sequencing method. The phenotypic characterisation based on morphology identified ten isolates of LAB, five AAB and seven yeasts from kefir (K), CWK and CWK-fermented sourdough (CWKS). The results confirm the presence of the LAB species Limosilactobacillus fermentum, Lactobacillus. plantarum, L. fusant, L. reuteri and L. kunkeei; the AAB species Acetobacter aceti, A. lovaniensis and A. pasteurianus; and the yeast species Candida kefyr, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, C. guilliermondii and C. colliculosa. To the best of our knowledge, the identification of Rhodotorula from kefir is being reported for the first time. This study provides important insights into the relative abundances of the microorganisms in CWKS. A decrease in pH and an increase in the titratable acidity for CWK- and CWK-fermented sourdough corresponded to the increase in D- and L-lactic acid production after 96 h of fermentation. Significant reductions in the pHs of CWK and CWKS were observed between 48 and 96 h of fermentation, indicating that the kefir microorganisms were able to sustain highly acidic environments. There was also increased production of L-lactic acid with fermentation, which was almost twice that of D-lactic acid in CWK.

Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition

Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.

The potential use of Zymomonas mobilis for the food industry

Zymomonas mobilis is a gram-negative facultative anaerobic spore, which is generally recognized as a safe. As a promising ethanologenic organism for large-scale bio-ethanol production, Z. mobilis has also shown a good application prospect in food processing and food additive synthesis for its unique physiological characteristics and excellent industrial characteristics. It not only has obvious advantages in food processing and becomes the biorefinery chassis cell for food additives, but also has a certain healthcare effect on human health. Until to now, most of the research is still in theory and laboratory scale, and further research is also needed to achieve industrial production. This review summarized the physiological characteristics and advantages of Z. mobilis in food industry for the first time and further expounds its research status in food industry from three aspects of food additive synthesis, fermentation applications, and prebiotic efficacy, it will provide a theoretical basis for its development and applications in food industry. This review also discussed the shortcomings of its practical applications in the current food industry, and explored other ways to broaden the applications of Z. mobilis in the food industry, to promote its applications in food processing.

Chemical and Sensory Characteristics of Fruit Juice and Fruit Fermented Beverages and Their Consumer Acceptance

Recent social, economic, and technological evolutions have impacted consumption habits. The new consumer is more rational, more connected and demanding with products, more concerned with the management of the family budget, with the health, origin, and sustainability of food. The food industry over the last few years has shown remarkable technological and scientific evolution, with an impact on the development and innovation of new products using non-thermal processing. Non-thermal processing technologies involve methods by which fruit juices receive microbiological inactivation and enzymatic denaturation with or without the direct application of low heat, thereby lessening the adverse effects on the nutritional, bioactive, and flavor compounds of the treated fruit juices, extending their shelf-life. The recognition of the nutritional and protective values of fruit juices and fermented fruit beverages is evident and is attributed to the presence of different bioactive compounds, protecting against chronic and metabolic diseases. Fermentation maintains the fruit's safety, nutrition, and shelf life and the development of new products. This review aims to summarize the chemical and sensory characteristics of fruit juices and fermented fruit drinks, the fermentation process, its benefits, and its effects.

Potential Probiotic Strains From Milk and Water Kefir Grains in Singapore—Use for Defense Against Enteric Bacterial Pathogens

Kefir grains consist of complex symbiotic mixtures of bacteria and yeasts, and are reported to impart numerous health-boosting properties to milk and water kefir beverages. The objective of this work was to investigate the microbial communities in kefir grains, and explore the possibility of deriving useful probiotic strains from them. A total of 158 microbial strains, representing six fungal and 17 bacterial species, were isolated from milk and water kefir grains collected from a Singapore-based homebrewer. Based on 16S rRNA sequencing, isolated genera included Lactobacillus, Liquorilactobacillus, Lacticaseibacillus, Lentilactobacillus, Leuconostoc, Lactococcus, Acetobacter, Gluconobacter, Oenococcus, Clostridium, Zymomonas, Saccharomyces, Kluyveromyces, Pichia, Lachancea, Candida, and Brettanomyces. To characterize these isolates, a funnel approach, involving numerous phenotypic and genomic screening assays, was applied to identify kefir-derived microbial strains with the highest probiotic potential. Particular focus was placed on examining the pathogen inhibitory properties of kefir isolates toward enteric pathogens which pose a considerable global health burden. Enteric pathogens tested include species of Bacillus, Salmonella, Vibrio, Clostridium, Klebsiella, Escherichia, and Staphylococcus. Well diffusion assays were conducted to determine the propensity of kefir isolates to inhibit growth of enteric pathogens, and a competitive adhesion/exclusion assay was used to determine the ability of kefir isolates to out-compete or exclude attachment of enteric pathogens to Caco-2 cells. Seven bacterial strains of Lentilactobacillus hilgardii, Lacticaseibacillus paracasei, Liquorilactobacillus satsumensis, Lactobacillus helveticus, and Lentilactobacillus kefiri, were ultimately identified as potential probiotics, and combined to form a “kefir probiotics blend.” Desirable probiotic characteristics, including good survival in acid and bile environments, bile salt hydrolase activity, antioxidant activity, non-cytotoxicity and high adhesion to Caco-2 cells, and a lack of virulence or antimicrobial resistance genes. In addition, vitamin and γ-aminobutyric acid (GABA) synthesis genes, were identified in these kefir isolates. Overall, probiotic candidates derived in this study are well-characterized strains with a good safety profile which can serve as novel agents to combat enteric diseases. These kefir-derived probiotics also add diversity to the existing repertoire of probiotic strains, and may provide consumers with alternative product formats to attain the health benefits of kefir.

Water Kefir Grains vs. Milk Kefir Grains: Physical, Microbial and Chemical Comparison

AIMS

Even though kefir has been known for centuries, there is confusion between the two types of kefir grains, e.g., milk kefir grain and water kefir grain. This study aimed to unravel the differences and similarities between water kefir grain and milk kefir grain.

METHODS AND RESULTS

Microbiological analyses, identification of grains microbiota and enumeration of microbiological content of the grains as well as Scanning Electron Microscope (SEM) imaging, dry matter, protein, ash, and mineral content, and color analyses were carried out for the two types of grains. As a result, significant differences were found in microbiological content, chemical properties, and colors (p<0.05). Additionally, SEM images revealed the different intrinsic structures for the microbiota and the structure of the two types of grains.

CONCLUSIONS

MK grain has more nutritional content compared to WK grain. Despite not as widely known and used as MK grain, WK grain is a good source for minerals and health-friendly microorganisms like lactic acid bacteria (LAB) and yeasts. WK grain is possibly suitable for vegans and allergic individuals to fulfill nutritional requirements. Moreover, in this study, the variety of WK grain microbial consortia was wider than that of MK grains, and this significantly affected the resultant WK products.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study that comprehensively compares two different kefir grains in microbial, chemical, and physical properties.

Microorganisms in Whole Botanical Fermented Foods Survive Processing and Simulated Digestion to Affect Gut Microbiota Composition

Botanical fermented foods have been shown to improve human health, based on the activity of potentially beneficial lactic acid bacteria (LAB) and yeasts and their metabolic outputs. However, few studies have explored the effects of prolonged storage and functional spices on microbial viability of whole fermented foods from fermentation to digestion. Even fewer have assessed their impact on the gut microbiota. Our study investigated the effects of production processes on LAB and yeast microbial viability and gut microbiota composition. We achieved this by using physicochemical assessments and an in vitro gastrointestinal and a porcine gut microbiota model. In low-salt sauerkraut, we assessed the effects of salt concentration, starter cultures, and prolonged storage, and in tibicos, prolonged storage and the addition of spices cayenne, ginger, and turmeric. In both food matrices, LAB counts significantly increased (p<0.05), reaching a peak of 7–8 log cfu/g, declining to 6–6.5 log cfu/g by day 96. Yeast viability remained at 5–6 log cfu/g in tibicos. Ginger tibicos had significantly increased LAB and yeast viability during fermentation and storage (p<0.05). For maximum microbial consumption, tibicos should be consumed within 28days, and sauerkraut, 7weeks. Simulated upper GI digestion of both products resulted in high microbial survival rates of 70–80%. The 82% microbial survival rate of cayenne tibicos was significantly higher than other treatments (p<0.05). 16S rRNA sequencing of simulated porcine colonic microbiota showed that both spontaneously fermented sauerkraut and tibicos increase the relative abundance of Megasphaera 85-fold. These findings will inform researchers, producers, and consumers about the factors that affect the microbial content of fermented foods, and their potential effects on the gut.

Water kefir: Factors affecting grain growth and health-promoting properties of the fermented beverage

Nowadays, the interest in the consumption of healthy foods has increased as well as the homemade preparation of artisanal fermented product. Water kefir is an ancient drink of uncertain origin, which has been passed down from generation to generation and is currently consumed practically all over the world. Considering the recent and extensive updates published on sugary kefir, this work aims to shed light on the scientific works that have been published so far in relation to this complex ecosystem. We focused our review evaluating the factors that affect the beverage microbial and chemical composition that are responsible for the health attribute of water kefir as well as the grain growth. The microbial ecosystem that constitutes the grains and the fermented consumed beverage can vary according to the fermentation conditions (time and temperature) and especially with the use of different substrates (source of sugars, additives as fruits and molasses). In this sense, the populations of microorganisms in the beverage as well as the metabolites that they produce varies and in consequence their health properties. Otherwise, the knowledge of the variables affecting grain growth are also discussed for its relevance in maintenance of the starter biomass as well as the use of dextran for technological application.

Water Kefir and Derived Pasteurized Beverages Modulate Gut Microbiota, Intestinal Permeability and Cytokine Production In Vitro

Fermentation is an ancient food preservation process, and fermented products have been traditionally consumed in different cultures worldwide over the years. The interplay between human gut microbiota, diet and host health is widely recognized. Diet is one of the main factors modulating gut microbiota potentially with beneficial effects on human health. Fermented dairy products have received much attention, but other sources of probiotic delivery through food received far less attention. In this research, a combination of in vitro tools mimicking colonic fermentation and the intestinal epithelium have been applied to study the effect of different pasteurized and non-pasteurized water kefir products on gut microbiota, epithelial barrier function and immunomodulation. Water kefir increased beneficial short-chain fatty acid production at the microbial level, reduced detrimental proteolytic fermentation compounds and increased Bifidobacterium genus abundance. The observed benefits are enhanced by pasteurization. Pasteurized products also had a significant effect at the host level, improving inflammation-induced intestinal epithelial barrier disruption and increasing IL-10 and IL-1β compared to the control condition. Our data support the potential health benefits of water kefir and demonstrate that pasteurization, performed to prolong shelf life and stability of the product, also enhanced these benefits.

Effect of freeze-dried kombucha culture on microbial composition and assessment of metabolic dynamics during fermentation

Kombucha is a traditional fermented beverage gaining popularity around the world. So far, few studies have investigated its microbiome using next-generation DNA sequencing, whereas the correlation between the microbial community and metabolites evolution along fermentation is still unclear. In this study, we explore this correlation in a traditionally produced kombucha by evaluating its microbial community and the main metabolites produced. We also investigated the effects of starter cultures processed in three different ways (control, starter culture without liquid suspension (CSC), and a freeze-dried starter culture (FDSC)) to evaluate changes in kombucha composition, such as antioxidant activity and sensory analysis. We identified seven genera of bacteria, including Komagataeibacter, Gluconacetobacter, Gluconobacter, Acetobacter, Liquorilactobacillus, Ligilactobacillus, and Zymomonas, and three genera of yeasts, Dekkera/Brettanomyces, Hanseniaspora, and Saccharomyces. Although there were no statistically significant differences in the acceptance test in sensory analysis, different starter cultures resulted in products showing different microbial and biochemical compositions. FDSC decreased Zymomonas and Acetobacter populations, allowing for Gluconobacter predominance, whereas in the control and CSC kombuchas the first two were the predominant genera. Results suggest that the freeze-drying cultures could be implemented to standardize the process and, despite it changes the microbial community, a lower alcohol content could be obtained.

Health-Promoting Properties of Lacticaseibacillus paracasei: A Focus on Kefir Isolates and Exopolysaccharide-Producing Strains

Among artisanal fermented beverages, kefir (fermented milk drink) and water kefir (fermented nondairy beverage) are of special interest because their grains can be considered natural reservoirs of safe and potentially probiotic strains. In the last years, several reports on Lacticaseibacillus paracasei (formerly Lactobacillus paracasei) isolated from both artisanal fermented beverages were published focusing on their health-promoting properties. Although this is not the predominant species in kefir or water kefir, it may contribute to the health benefits associated to the consumption of the fermented beverage. Since the classification of L. paracasei has been a difficult task, the selection of an adequate method for identification, which is essential to avoid mislabeling in products, publications, and some publicly available DNA sequences, is discussed in the present work. The last findings in health promoting properties of L. paracasei and the bioactive compounds are described and compared to strains isolated from kefir, providing a special focus on exopolysaccharides as effector molecules. The knowledge of the state of the art of Lacticaseibacillus paracasei from kefir and water kefir can help to understand the contribution of these microorganisms to the health benefits of artisanal beverages as well as to discover new probiotic strains for applications in food industry.

Metagenomic and phytochemical analyses of kefir water and its subchronic toxicity study in BALB/c mice

BACKGROUND

In recent years, researchers are interested in the discovery of active compounds from traditional remedies and natural sources, as they reveal higher therapeutic efficacies and improved toxicological profiles. Among the various traditional treatments that have been widely studied and explored for their potential therapeutic benefits, kefir, a fermented beverage, demonstrates a broad spectrum of pharmacological properties, including antioxidant, anti-inflammation, and healing activities. These health-promoting properties of kefir vary among the kefir cultures found at the different part of the world as different media and culture conditions are used for kefir maintenance and fermentation.

METHODS

This study investigated the microbial composition and readily found bioactive compounds in water kefir fermented in Malaysia using 16S rRNA microbiome and UHPLC sequencing approaches. The toxicity effects of the kefir water administration in BALB/c mice were analysed based on the mice survival, body weight index, biochemistry profile, and histopathological changes. The antioxidant activities were evaluated using SOD, FRAP, and NO assays.

RESULTS

The 16S rRNA amplicon sequencing revealed the most abundant species found in the water kefir was Lactobacillus hilgardii followed by Lactobacillus harbinensis, Acetobacter lovaniensis, Lactobacillus satsumensis, Acetobacter tropicalis, Lactobacillus zeae, and Oenococcus oeni. The UHPLC screening showed flavonoid and phenolic acid derivatives as the most important bioactive compounds present in kefir water which has been responsible for its antioxidant activities. Subchronic toxicity study showed no toxicological signs, behavioural changes, or adverse effects by administrating 10 mL/kg/day and 2.5 mL/kg/day kefir water to the mice. Antioxidants assays demonstrated enhanced SOD and FRAP activities and reduced NO level, especially in the brain and kidney samples.

CONCLUSIONS

This study will help to intensify the knowledge on the water kefir microbial composition, available phytochemicals and its toxicological and antioxidant effects on BALB/c mice since there are very limited studies on the water kefir grain fermented in Malaysia.

Changes in Microbiota During Multiple Fermentation of Kefir in Different Sugar Solutions Revealed by High-Throughput Sequencing

Kefir is a fermented beverage produced through the activity of its grains, which is constituted by lactic acid and acetic acid bacteria and yeasts. We studied the bacterial succession during multiple fermentation of Argentinian kefir in brown sugar, purified molasses or high-test molasses, using 16S high-throughput sequencing. Firmicutes was dominant (up to 98% of total population) in grains and beverages made from various sugar substrates, except in high-test molasses beverage, which was dominated by Proteobacteria (up to 78% of total population). Major bacterial species in Firmicutes were Liquorilactobacillus nagelii, Lentilactobacillus hilgardii/diolivorans and Lacticaseibacillus casei/paracasei, which are active in lactic acid fermentation. Proteobacteria comprised Acetobacter lovaniensis and Gluconobacter oxydans/roseus as major species, which are presumably responsible for the acetic acid formation in sugary kefir beverages. Bacteria differ in abundance depending on the sugar type, as revealed by the competitive dominances between L. nagelii and A. loveniensis. Purified molasses led to scarce acetic acid bacteria during fermentation, indicating that it is not a suitable substrate for their growth. Our results suggest that acetic acid (and/or ethanol) in sugary kefir modulates the succession and dominance of specific lactic acid bacteria. This study will provide valuable information for designing more sophisticated non-dairy fermented beverages with stable microbial properties.

An update on water kefir: Microbiology, composition and production

Water kefir is a sparkling, slightly acidic fermented beverage produced by fermenting a solution of sucrose, to which dried fruits have been added, with water kefir grains. These gelatinous grains are a symbiotic culture of bacteria and yeast embedded in a polysaccharide matrix. Lactic acid bacteria, yeast and acetic acid bacteria are the primary microbial members of the sugary kefir grain. Amongst other contributions, species of lactic acid bacteria produce the exopolysaccharide matrix from which the kefir grain is formed, while yeast assists the bacteria by a nitrogen source that can be assimilated. Exactly which species predominate within the grain microbiota, however, appears to be dependent on the geographical origin of the grains and the fermentation substrate and conditions. These factors ultimately affect the characteristics of the beverage produced in terms of aroma, flavour, and acidity, for example, but can also be controlled and exploited in the production of a beverage of desired characteristics. The production of water kefir has traditionally occurred on a small scale and the use of defined starter cultures is not commonly practiced. However, as water kefir increases in popularity as a beverage - in part because of consumer lifestyle trends and in part due to water kefir being viewed as a health drink with its purported health benefits - the need for a thorough understanding of the biology and dynamics of water kefir, and for defined and controlled production processes, will ultimately increase. The aim of this review is to provide an update into the current knowledge of water kefir.

The Type and Concentration of Inoculum and Substrate as Well as the Presence of Oxygen Impact the Water Kefir Fermentation Process

Eleven series of water kefir fermentation processes differing in the presence of oxygen and the type and concentration of inoculum and substrate, were followed as a function of time to quantify the impact of these parameters on the kinetics of this process via a modeling approach. Increasing concentrations of the water kefir grain inoculum increased the water kefir fermentation rate, so that the metabolic activity during water kefir fermentation was mainly associated with the grains. Water kefir liquor could also be used as an alternative means of inoculation, but the resulting fermentation process progressed slower than the one inoculated with water kefir grains, and the production of water kefir grain mass was absent. Substitution of sucrose with glucose and/or fructose reduced the water kefir grain growth, whereby glucose was fermented faster than fructose. Lacticaseibacillus paracasei (formerly known as Lactobacillus paracasei), Lentilactobacillus hilgardii (formerly known as Lactobacillus hilgardii), Liquorilactobacillus nagelii (formerly known as Lactobacillus nagelii), Saccharomyces cerevisiae, and Dekkera bruxellensis were the main microorganisms present. Acetic acid bacteria were present in low abundances under anaerobic conditions and only proliferated under aerobic conditions. Visualization of the water kefir grains through scanning electron microscopy revealed that the majority of the microorganisms was attached onto their surface. Lactic acid bacteria and yeasts were predominantly associated with the grains, whereas acetic acid bacteria were predominantly associated with the liquor.

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

A review of nondairy kefir products: their characteristics and potential human health benefits

Functional foods are foods that, in addition to having nutrients, contain in their composition ingredients that act specifically on body functions associated with the control and reduction of the risk of developing some diseases. In this sense, kefir, a group of microorganisms in symbiosis, mainly yeasts and lactic acid bacteria, stands out. The trend of ingesting kefir has been focused on the development of products that serve specific consumers, such as those who are lactose-intolerant, vegans and vegetarians, and consumers in general who seek to combine the consumption of functional products with the improvement of their health and lifestyle. This overview provides an insight into kefir, presenting the technological process to produce a nondairy beverage and evidence of the benefits of its use to reduce the risk of disease. We also discuss regulatory aspects of products fermented using kefir. Until now, the use of kefir (isolated microorganism, kefiran, or fermented product) has demonstrated the potential to promote an increase in the number of bifidobacteria in the colon and an increase in the glycemic control while reducing the blood cholesterol and balancing the intestinal microbiota, which helps in reducing constipation and diarrhea, improving intestinal permeability, and stimulating and balancing the immune system. However, the literature still has gaps that need to be clarified, such as the consumption dose of kefir or its products to cause some health benefit.

Bacterial Populations in International Artisanal Kefirs

Artisanal kefir is a traditional fermented dairy product made using kefir grains. Kefir has documented natural antimicrobial activity and health benefits. A typical kefir microbial community includes lactic acid bacteria (LAB), acetic acid bacteria, and yeast among other species in a symbiotic matrix. In the presented work, the 16S rRNA gene sequencing was used to reveal bacterial populations and elucidate the diversity and abundance of LAB species in international artisanal kefirs from Fusion Tea, Britain, the Caucuses region, Ireland, Lithuania, and South Korea. Bacterial species found in high abundance in most artisanal kefirs included Lactobacillus kefiranofaciens, Lentilactobacillus kefiri,Lactobacillus ultunensis, Lactobacillus apis, Lactobacillus gigeriorum, Gluconobacter morbifer, Acetobacter orleanensis, Acetobacter pasteurianus, Acidocella aluminiidurans, and Lactobacillus helveticus. Some of these bacterial species are LAB that have been reported for their bacteriocin production capabilities and/or health promoting properties.

Study of kefir drinks produced by backslopping method using kefir grains from Bosnia and Herzegovina: Microbial dynamics and volatilome profile

Kefir is a well-known health-promoting beverage that can be produced by using kefir grains (traditional method) or by using natural starter cultures from kefir (backslopping method). The aim of this study was to elucidate the microbial dynamics and volatilome profile occurring during kefir production through traditional and backslopping methods by using five kefir grains that were collected in Bosnia and Herzegovina. The results from conventional pour plating techniques and amplicon-based sequencing were combined. The kefir drinks have also been characterized in terms of their physico-chemical and colorimetric parameters. A bacterial shift from Lactobacillus kefiranofaciens to Acetobacter syzygii, Lactococcus lactis and Leuconostoc pseudomesenteroides from kefir grains in traditional kefir to backslopped kefir was generally observed. Despite some differences within samples, the dominant mycobiota of backslopped kefir samples remained quite similar to that of the kefir grain samples. However, unlike the lactic acid and acetic acid bacteria, the yeast counts decreased progressively from the grains to the backslopped kefir. The backslopped kefir samples showed higher protein, lactose and ash content and lower ethanol content compared to traditional kefir samples, coupled with optimal pH values that contribute to a pleasant sensory profile. Concerning the volatilome, backslopped kefir samples were correlated with cheesy, buttery, floral and fermented odors, whereas the traditional kefir samples were correlated with alcoholic, fruity, fatty and acid odors. Overall, the data obtained in the present study provided evidence that different kefir production methods (traditional vs backslopping) affect the quality characteristics of the final product. Hence, the functional traits of backslopped kefir should be further investigated in order to verify the suitability of a potential scale-up methodology for backslopping.

Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir

Two Bifidobacterium strains, TMW 2.2057^T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium, with Bifidobacterium subtile DSM 20096^T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA-DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096^T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057^T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057^T (=DSM 108414^T=LMG 31086^T) is the type strain.

Yeasts and Bacterial Consortia from Kefir Grains Are Effective Biocontrol Agents of Postharvest Diseases of Fruits

Fungal pathogens in fruits and vegetables cause significant losses during handling, transportation, and storage. Biological control with microbial antagonists replacing the use of chemical fungicides is a major approach in postharvest disease control, and several products based on single antagonists have been developed but have limitations related to reduced and inconsistent performance under commercial conditions. One possible approach to enhance the biocontrol efficacy is to broaden the spectrum of the antagonistic action by employing compatible microbial consortia. Here, we explore commercial kefir grains, a natural probiotic microbial consortium, by culture-dependent and metagenomic approaches and observed a rich diversity of co-existing yeasts and bacterial population. We report effective inhibition of the postharvest pathogen Penicillium expansum on apple by using the grains in its fresh commercial and milk-activated forms. We observed few candidate bacteria and yeasts from the kefir grains that grew together over successive enrichment cycles, and these mixed fermentation cultures showed enhanced biocontrol activities as compared to the fresh commercial or milk-activated grains. We also report several individual species of bacteria and yeasts with biocontrol activities against Penicillium rots on apple and grapefruit. These species with antagonistic properties could be further exploited to develop a synthetic consortium to achieve enhanced antagonistic effects against a wide range of postharvest pathogens.

Lactic Fermented Fruit or Vegetable Juices: Past, Present and Future

Numerous traditional low-alcohol fermented beverages produced from fruit or vegetables are described around the world. Fruit and vegetables and lactic fermented products both present nutritional benefits, which give reasons for the recent expansion of non-dairy lactic fermented juices on the market. In addition, fruit and vegetable juices are new carriers for probiotic bacteria. Specific phenotypic traits of lactic acid bacteria (LAB) are required so that LAB can effectively grow in fruit or vegetable juices, increase their safety and improve their sensory and nutritional quality. From the diversity of microbiota of spontaneous fermentations, autochthonous starters can be selected, and their higher performance than allochthonous LAB was demonstrated. Achieving long-term storage and constant high quality of these beverages requires additional processing steps, such as heat treatment. Alternatives to conventional treatments are investigated as they can better preserve nutritional properties, extract bioactive compounds and promote the growth and metabolism of LAB. Specific processing approaches were shown to increase probiotic viability of fruit and vegetable juices. More knowledge on the metabolic activity of lactic acid bacterium consortium in fruit or vegetable juices has become a bottleneck for the understanding and the prediction of changes in bioactive compounds for functional beverages development. Hopefully, the recent developments of metabolomics and methods to describe enzymatic machinery can result in the reconstruction of fermentative pathways.

The Buffer Capacity and Calcium Concentration of Water Influence the Microbial Species Diversity, Grain Growth, and Metabolite Production During Water Kefir Fermentation

Eight water kefir fermentation series differing in buffer capacity and calcium concentration of the water used for fermentation were studied during eight backslopping steps. High buffer capacities resulted in high pH values and high calcium concentrations resulted in low pH values at the end of each backslopping step. When the water buffer capacity and/or calcium concentration were below certain minima, the water kefir grain growth decreased gradually over multiple backsloppings. High water buffer capacities resulted in high concentrations of residual total carbohydrate concentrations and low metabolite concentrations. Further, high water buffer capacities resulted in high ratios of lactic acid bacteria to yeasts, which was reflected in high molar ratios of the concentrations of lactic acid to ethanol and acetic acid to ethanol. The most prevalent microorganisms of the water kefir grain inoculum and grains of all fermentation series at the end of the eighth backslopping step were Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei, Bifidobacterium aquikefiri, Saccharomyces cerevisiae, and Dekkera bruxellensis. These microbial communities were influenced by the water buffer capacity and had an impact on the substrate consumption and metabolite production during water kefir fermentation.

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

Water kefir is a fruity, sour, slightly alcoholic and carbonated beverage, which is made by fermentation of an aqueous sucrose solution in the presence of dried figs and water kefir grains. These polysaccharide grains contain lactic acid bacteria (LAB), yeasts, and sometimes bifidobacteria and/or acetic acid bacteria, which consume sucrose to produce exopolysaccharides, lactic acid, acetic acid, ethanol, and carbon dioxide. Shotgun metagenomic sequencing was used to examine the microbial species diversity present at two time points during water kefir fermentation in detail, both in the water kefir liquor and on the water kefir grains, hence representing four samples. Lactobacillus harbinensis, Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei, and a Lactobacillus species similar to Lactobacillus hordei/mali were present in the water kefir examined, along with Bifidobacterium aquikefiri and two yeast species, namely Saccharomyces cerevisiae and Dekkera bruxellensis. In addition, evidence for a novel Oenococcus species related to Oenococcus oeni and Oenococcus kitaharae was found. Its genome was derived from the metagenome and made available under the name of Candidatus Oenococcus aquikefiri. Through functional analysis of the four metagenomic data sets, it was possible to link the production of lactic acid, acetic acid, ethanol, and carbon dioxide to subgroups of the microbial species found. In particular, the production of mannitol from fructose was linked to L. hilgardii, Candidatus O. aquikefiri, and B. aquikefiri, whereas glycerol production was associated with S. cerevisiae. Also, there were indications of cross-feeding, for instance in the case of amino acid supply. Few bacterial species could synthesize a limited number of cofactors, making them reliant on the figs or S. cerevisiae. The LAB species in turn were found to be capable of contributing to water kefir grain growth, as dextransucrase-encoding genes were attributed to L. hilgardii, L. hordei/mali, and Candidatus O. aquikefiri.

Assessment of the microbial diversity of Chinese Tianshan tibicos by single molecule, real-time sequencing technology

Chinese Tianshan tibico grains were collected from the rural area of Tianshan in Xinjiang province, China. Typical tibico grains are known to consist of polysaccharide matrix that embeds a variety of bacteria and yeasts. These grains are widely used in some rural regions to produce a beneficial sugary beverage that is slightly acidic and contains low level of alcohol. This work aimed to characterize the microbiota composition of Chinese Tianshan tibicos using the single molecule, real-time sequencing technology, which is advantageous in generating long reads. Our results revealed that the microbiota mainly comprised of the bacterial species of Lactobacillus hilgardii, Lactococcus raffinolactis, Leuconostoc mesenteroides, Zymomonas mobilis, together with a Guehomyces pullulans-dominating fungal community. The data generated in this work helps identify beneficial microbes in Chinese Tianshan tibico grains.

Proteomic Analysis of Lactobacillus nagelii in the Presence of Saccharomyces cerevisiae Isolated From Water Kefir and Comparison With Lactobacillus hordei

Water kefir is a slightly alcoholic and traditionally fermented beverage, which is prepared from sucrose, water, kefir grains, and dried or fresh fruits (e.g., figs). Lactobacillus (L.) nagelii, L. hordei, and Saccharomyces (S.) cerevisiae are predominant and stable lactic acid bacteria and yeasts, respectively, isolated from water kefir consortia. The growth of L. nagelii and L. hordei are improved in the presence of S. cerevisiae. In this work we demonstrate that quantitative comparative proteomics enables the investigation of interactions between LAB and yeast to predict real-time metabolic exchange in water kefir. It revealed 73 differentially expressed (DE) in L. nagelii TMW 1.1827 in the presence of S. cerevisiae. The presence of the yeast induced changes in the changes in the carbohydrate metabolism of L. nagelii and affected reactions involved in NAD⁺/NADH homeostasis. Furthermore, the DE enzymes involved in amino acid biosynthesis or catabolism predict that S. cerevisiae releases glutamine, histidine, methionine, and arginine, which are subsequently used by L. nagelii to ensure its survival in the water kefir consortium. In co-culture with S. cerevisiae, L. nagelii profits from riboflavin, most likely secreted by the yeast. The reaction of L. nagelii to the presence of S. cerevisiae differs from that one of the previously studied L. hordei, which displays 233 differentially expressed proteins, changes in citrate metabolism and an antidromic strategy for NAD⁺/NADH homeostasis. So far, aggregation promotion factors, i.e., formation of a specific glucan and bifunctional enzymes were only detected in L. hordei.

Lactobacillus hordei dextrans induce Saccharomyces cerevisiae aggregation and network formation on hydrophilic surfaces

Water kefir granules are supposed to mainly consist of dextrans produced by Lactobacillus (L.) hilgardii. Still, other microorganisms such as L. hordei, L. nagelii, Leuconostoc (Lc.) citreum and Saccharomyces (S.) cerevisiae are commonly isolated from water kefir granules, while their contribution to the granule formation remains unknown. We studied putative functions of these microbes in granule formation, upon development of a simplified model system containing hydrophilic object slides, which mimics the hydrophilic surface of a growing kefir granule. We found that all tested lactic acid bacteria produced glucans, while solely those isolated from the four different L. hordei strains induced yeast aggregation on the hydrophilic slides. Therefore, structural differences between these glucans were investigated with respect to their size distributions and their linkage types. Beyond the finding that all glucans were identified as dextrans, those of the four L. hordei strains were highly similar among each other regarding portions of linkage types and size distributions. Thus, our study suggests the specific size and structural organization of the dextran produced by L. hordei as the main cause for inducing S. cerevisiae aggregation and network formation on hydrophilic surfaces and thus as crucial initiation of the stepwise water kefir granule growth.

The water kefir grain inoculum determines the characteristics of the resulting water kefir fermentation process

AIMS

To investigate the influence of the water kefir grain inoculum on the characteristics of the water kefir fermentation process.

METHODS AND RESULTS

Three water kefir fermentation processes were started with different water kefir grain inocula and followed as a function of time regarding microbial species diversity, community dynamics, substrate consumption profile and metabolite production course. The inoculum determined the water kefir grain growth, the viable counts on the grains, the time until total carbohydrate exhaustion, the final metabolite concentrations and the microbial species diversity. There were always 2-10 lactic acid bacterial cells for every yeast cell and the majority of these micro-organisms was always present on the grains. Lactobacillus paracasei, Lactobacillus hilgardii, Lactobacillus nagelii and Saccharomyces cerevisiae were always present and may be the key micro-organisms during water kefir fermentation. Low water kefir grain growth was associated with small grains with high viable counts of micro-organisms, fast fermentation and low pH values, and was not caused by the absence of exopolysaccharide-producing lactic acid bacteria.

CONCLUSIONS

The water kefir grain inoculum influences the microbial species diversity and characteristics of the fermentation process. A select group of key micro-organisms was always present during fermentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study allows a rational selection of a water kefir grain inoculum.

Traditional low-alcoholic and non-alcoholic fermented beverages consumed in European countries: a neglected food group

Fermented beverages hold a long tradition and contribution to the nutrition of many societies and cultures worldwide. Traditional fermentation has been empirically developed in ancient times as a process of raw food preservation and at the same time production of new foods with different sensorial characteristics, such as texture, flavour and aroma, as well as nutritional value. Low-alcoholic fermented beverages (LAFB) and non-alcoholic fermented beverages (NAFB) represent a subgroup of fermented beverages that have received rather little attention by consumers and scientists alike, especially with regard to their types and traditional uses in European societies. A literature review was undertaken and research articles, review papers and textbooks were searched in order to retrieve data regarding the dietary role, nutrient composition, health benefits and other relevant aspects of diverse ethnic LAFB and NAFB consumed by European populations. A variety of traditional LAFB and NAFB consumed in European regions, such as kefir, kvass, kombucha and hardaliye, are presented. Milk-based LAFB and NAFB are also available on the market, often characterised as 'functional' foods on the basis of their probiotic culture content. Future research should focus on elucidating the dietary role and nutritional value of traditional and 'functional' LAFB and NAFB, their potential health benefits and consumption trends in European countries. Such data will allow for LAFB and NAFB to be included in national food composition tables.

Investigation of the instability and low water kefir grain growth during an industrial water kefir fermentation process

A poorly performing industrial water kefir production process consisting of a first fermentation process, a rest period at low temperature, and a second fermentation process was characterized to elucidate the causes of its low water kefir grain growth and instability. The frozen-stored water kefir grain inoculum was thawed and reactivated during three consecutive prefermentations before the water kefir production process was started. Freezing and thawing damaged the water kefir grains irreversibly, as their structure did not restore during the prefermentations nor the production process. The viable counts of the lactic acid bacteria and yeasts on the water kefir grains and in the liquors were as expected, whereas those of the acetic acid bacteria were high, due to the aerobic fermentation conditions. Nevertheless, the fermentations progressed slowly, which was caused by excessive substrate concentrations resulting in a high osmotic stress. Lactobacillus nagelii, Lactobacillus paracasei, Lactobacillus hilgardii, Leuconostoc mesenteroides, Bifidobacterium aquikefiri, Gluconobacter roseus/oxydans, Gluconobacter cerinus, Saccharomyces cerevisiae, and Zygotorulaspora florentina were the most prevalent microorganisms. Lb. hilgardii, the microorganism thought to be responsible for water kefir grain growth, was not found culture-dependently, which could explain the low water kefir grain growth of this industrial process.

Selected Lactobacillus strains isolated from sugary and milk kefir reduce Salmonella infection of epithelial cells in vitro

The isolation of potentially probiotic strains and the subsequent study of their properties are very important steps to gain insight in the health benefits ascribed to sugary and milk kefir. The aim of the present study was to characterise fifteen Lactobacillus strains isolated from these beverages by determining some surface properties and their ability to antagonise enterocyte cell damage after Salmonella infection in vitro. Lactobacillus surface properties were determined by hydrophobicity, autoaggregation, and coaggregation assays with Salmonella. In addition, lactobacilli adhesion to Caco-2/TC-7 cells and the effect on Salmonella invasion were evaluated. Finally, the disassembly of F-actin cytoskeleton on intestinal epithelial cells was assayed in vitro when Salmonella infection was performed in the presence of selected Lactobacillus strains. Ten out of the 15 strains showed a high adhesion capacity to Caco-2/TC-7 cells. Most of the strains were hydrophilic and non-autoaggregating. Strains isolated from sugary kefir were non-coaggregating with Salmonella, while strains Lactobacillus paracasei CIDCA 83120, 83121, 83123, 83124, 8339, 83102 isolated from milk kefir were able to coaggregate after 1 h. L. paracasei CIDCA 8339 and Lactobacillus kefiri CIDCA 83102 were able to diminish Salmonella invasion to the enterocytes. An antagonistic effect on cytoskeleton disruption elicited by the pathogen was also demonstrated. Our results suggest that both strains isolated from milk kefir could be considered as appropriate probiotic candidates.

The ecology of Zymomonas: a review

Zymomonas mobilis is a Gram-negative bacterium studied primarily as a spoilage organism and ethanol producer. As with many bacteria, much remains to be learned about its ecology. It can serve as a model organism for examining microbial interactions, as well as interactions between plants and bacteria. Better understanding of its ecology can help with biotechnological applications, such as process improvement, new uses of the bacterium, and the search for new strains.