Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis

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.

Estamaran date vinegar: chemical and microbial dynamics during fermentation

Vinegar is a fermented food produced by alcoholic and then acetic acid microbial metabolism. Date palm fruit (Phoenix dactylifera L.) is a valuable source for the production of vinegar. Microbial identification has a major role in the improvement and bio-management of the fermentation process of vinegar. Estamaran and Kabkab two varieties of date palm fruit were selected to study the fermentation process. A culture-dependent approach was used to study bacterial dynamics. 16 S rRNA gene was amplified by Polymerase Chain Reaction (PCR), also restriction enzyme analysis with HinfI and TaqI, and sequencing was done. Assessment of microbial flora of date palm fruit during fermentation showed that Fructobacillus tropaeoli, Bacillus sp., Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, and Weissella paramesenteroides existed in the first phase of fermentation. With fermentation progress, microbial diversity decreased so only one species remained. Komagataeibacter xylinus as an acid acetic producer was present in the third phase of fermentation. Based on chemical analysis, the concentration of reducing sugars decreased during fermentation. With decreasing pH, a simultaneous increase in acidity and total phenolic compounds occurred. The trend of changes during Estamaran fermentation was more severe and a vinegar with desirable properties was produced. Therefore, this date variety is recommended for the production of date vinegar.

Genomic, probiotic, and metabolic potentials of Liquorilactobacillus nagelii AGA58, a novel bacteriocinogenic motile strain isolated from lactic acid-fermented shalgam

This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and probiotic features. AGA58 is gram-positive, motile, catalase-negative and appears as short rods under the light-microscope. The AGA58 chromosome comprises a single linear chromosome of 2,294,635 bp that is predicted to carry 2135 coding sequences, including 45 tRNA genes, 3 mRNA, and 3 rRNA operons. The genome has a G+C content of 36.9%, including 55 pseudogenes and a single intact prophage. AGA58 is micro-anaerobic due to achieving a shorter doubling time and faster growth rate than micro-aerophilic conditions. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior, which was confirmed with the in vitro motility test. AGA58 is an obligatory homofermentative lactobacillus that can ferment hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N-acetyl glucosamine, maltose, and trehalose to lactate through glycolysis. No acid production from pentoses implies that five-carbon sugars are being utilized for purine and pyrimidine synthesis. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin, and lactate forms from pyruvate. AGA58 is predicted to encode the LuxS gene and biosynthesis of class IIa and Blp family class-II bacteriocins suggesting this bacterium's antimicrobial potential, linked to antagonism tests that AGA58 can inhibit Escherichia coli ATCC 43895, Salmonellaenterica serovar Typhimurium ATCC 14028, and Klebsiellapneumonia ATCC 13883. Moreover, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions depicting the probiotic potential of the organism as the first report in literature within the same species.

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.

Backslopping Time, Rinsing of the Grains During Backslopping, and Incubation Temperature Influence the Water Kefir Fermentation Process

For eight backslopping steps, eight series of water kefir fermentation processes differing in backslopping time and rinsing of the grains during each backslopping step and eight series of fermentation processes differing in incubation temperature and backslopping time were followed. Short backslopping times resulted in high relative abundances of Liquorilactobacillus nagelii and Saccharomyces cerevisiae, intermediate backslopping times in high relative abundances of Leuconostoc pseudomesenteroides, and long backslopping times in high relative abundances of Oenococcus sicerae and Dekkera bruxellensis. When the grains were rinsed during each backslopping step, the relative abundances of Lentilactobacillus hilgardii and Leuc. pseudomesenteroides increased and those of D. bruxellensis and Liql. nagelii decreased. Furthermore, rinsing of the grains during each backslopping step resulted in a slightly higher water kefir grain growth and lower metabolite concentrations. The relative abundances of Liquorilactobacillus mali were highest at 17°C, those of Leuc. pseudomesenteroides at 21 and 25°C, and those of Liql. nagelii at 29°C. With a kinetic modeling approach, the impact of the temperature and rinsing of the grains during the backslopping step on the volumetric production rates of the metabolites was determined.

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.

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.

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.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

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.

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.

Genomic and physiological insights into the lifestyle of Bifidobacterium species from water kefir

Water kefir is a fermented beverage employing a natural microbial consortium, which harbours bifidobacteria, namely Bifidobacterium aquikefiri and Bifidobacterium tibiigranuli. However, little information is available on their metabolic properties or role in the consortium. In this study, we combined genomic and physiologic investigations to predict and characterize the properties of these organisms and their possible role in the consortium. When comparing the genomes of these psychrotrophic organisms with that of the three selected mesophilic probiotic Bifidobacterium strains, we could find 143 genes shared by the 3 known isolates of bifidobacteria from water kefir that do not occur in the probiotic strains. These include genes involved in acid and oxygen tolerance. In addition, their genomically predicted carbohydrate usage and transport suggest adaptation to sucrose and other plant-related sugars. Furthermore, they proved prototrophic for all amino acids in vitro, which enables them to cope with the strong amino acid limitation in water kefir.

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.

Identification and probiotic properties of lactobacilli isolated from two different fermented beverages

Purpose

Scientific information regarding the microbial content and functional aspects of fermented beverages traditionally produced in certain parts of Europe are scarce. However, such products are believed to have some health benefits and might contain functional bacterial strains, such as probiotics. The aim of the study was to identify such lactic acid bacteria strains isolated from water kefir and, for the first time, from braga, a Romanian fermented beverage made of cereals.

Methods

Lactic acid bacteria (LAB) were identified to species level based on (GTG)5-PCR fingerprinting and 16S rRNA gene sequencing. Selected strains were screened for their antibacterial activity and probiotic potential.

Results

Eight isolates belonging to seven Lactobacillus species were recovered from the two drinks. The identification of LAB involved in the fermentation of braga (Lactobacillus plantarum, Lactobacillus fermentum, and Lactobacillus delbrueckii) is firstly reported here. Five of the Lactobacillus isolates showed antibacterial activity against pathogenic bacteria, including Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, and Salmonella enterica. Moreover, most of them showed a good resistance to pH 2.5 and some survived at high concentrations of bile salts (up to 2%). Two L. plantarum isolates were able to inhibit all the indicator strains, and showed the best viability (about 70%) after a sequential treatment simulating the passage through the gastrointestinal tract.

Conclusion

Based on the results, the most promising candidates for designing new probiotic products are: L. plantarum BR9 from braga and L. plantarum CR1 from water kefir.

AFLP protocol comparison for microbial diversity fingerprinting

Over the last decade, several methods based on genomic DNA have been developed for the identification and genotyping of prokaryotic and eukaryotic organisms. These genomic methods differ regarding taxonomic range, discriminatory power, reproducibility, and ease of interpretation and standardization. The amplified fragment length polymorphism (AFLP) technique is a very powerful DNA fingerprinting technique for DNA of any source or complexity, varying in both size and base composition. In addition, this method shows high discriminatory power and good reproducibility allowing it to be efficient in discriminating at both the species and strain levels. The development and application of AFLP have allowed significant progress in the study of biodiversity and taxonomy of microorganisms. In the last years, the Applied Biosystems AFLP Microbial Fingerprinting Kit, now out of production, was widely used in various studies to perform AFLP characterization of selected bacteria strains (described by Vos et al. (Nucleic Acids Res 23(21):4407-4414, 1995)). Its replacement gives the possibility for laboratories to continue the use of the previous AFLP data as a reference for bacteria genetic fingerprinting analysis in biodiversity studies. To overcome this issue a result comparison, by using an improved AFLP protocol and the AFLP commercial kit, was performed. In particular, previous results on different species (Listeria monocytogenes, Lactobacillus plantarum, and Streptococcus thermophilus) obtained with the commercial kit were compared with the improved AFLP procedure to validate the protocol. When compared with the AFLP Microbial Fingerprinting Kit, the improved protocol shows high reproducibility, resolution, and overall, is a faster method with lower costs.

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.

Prediction of in situ metabolism of photobacteria in modified atmosphere packaged poultry meat using metatranscriptomic data

Modified atmosphere packaging (MAP) is widely used in food industry to extend the microbiological shelf life of meat. Common CO₂-containing gas atmospheres for poultry meat packaging are either nearly O₂-free or high O₂ MAPs. In this work, we compared spoilage microbiota of skinless chicken breast in CO₂/O₂ (30/70%) and CO₂/N₂ (30/70%) MAP, which are culturable with conventional methods and identified isolates by MALDI-TOF MS. These data were compared to metatranscriptome sequencing enabling a culture-independent overview on the composition of microbiota at species level. While typical MAP meat spoilers were confirmed in the transcriptomic approach, we also found high numbers of transcripts mapping to Photobacterium spp. sequences in these samples. As photobacteria were recently shown to occur in different MAP and vacuum packaged meats, we used the respective part of the metatranscriptomic data for prediction of Photobacterium spp. major metabolic routes in situ, upon growth in MAP poultry meat. It is predicted that they employ similar metabolism in both atmospheres: In the lack of carbohydrates upon meat spoilage, the pyruvate pool is filled via glycerol originating from lipolysis and amino acid conversions. From the pyruvate pool, gluconeogenesis is fed enabling cell wall biosynthesis and growth as well as catabolism to lactate and other metabolites, or anaplerosis towards the citric acid cycle. Production is predicted of several biogenic amines including tyramine and cadaverine, enabling generation of proton motive force. Taken together, photobacteria express metabolic pathways upon growth on meat, which should lead to compounds overlapping with those of known potent meat spoilers.

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.

Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics

In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.

Biotechnological potential of microbial consortia and future perspectives

Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.

Development of a novel fermented pumpkin-based beverage inoculated with water kefir grains: a response surface methodology approach

Pumpkin (Cucurbita pepo) is well known for its health and nutritional benefits and is recommended for daily consumption. This is the first report on optimization and development of fermented pumpkin-based water kefir beverage. Optimum pumpkin puree and brown sugar concentrations were found at 22.28 and 9.07% w/v, respectively, were made into a pumpkin-based beverage and fermented with water kefir grains for 24 h at 32 °C. The optimized fermented pumpkin-based water kefir beverage was found to be non-alcoholic, achieved good overall acceptability and high Lactobacillus, acetic acid bacteria and yeast cell viability of approximately 1012, 109 and 109 CFU mL-1, respectively. Overall, the optimized product attained superb technological characteristics and has the potential for industrial exploitation as a refreshing water kefir drink.

Structural characterization of the exopolysaccharides from water kefir

Water kefir is a beverage which is produced by initiating fermentation of a fruit extract/sucrose solution with insoluble kefir grains. Exopolysaccharides that are formed from sucrose play a major role in the kefir grain formation, but the exopolysaccharides in the kefir beverage and the detailed structural composition of the whole kefir grains have not been studied yet. Therefore, kefir grains and the corresponding kefir beverage were analyzed for exopolysaccharides by multiple chromatographic approaches and two-dimensional NMR spectroscopy. Furthermore, different fractionation techniques were applied to obtain further information about the exopolysaccharides. The exopolysaccharide-fraction of the investigated kefir beverage was predominantly composed of O3- and O2-branched dextrans as well as lower amounts of levans. The insoluble dextrans from the kefir grains were mostly O3-branched and contained an elevated portion of 1,3-linked glucose units compared to the soluble dextrans. The structurally different exopolysaccharides in water kefir suggest the involvement of multiple bacteria.

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.

LAMP, PCR, and real-time PCR detection of Acetobacter aceti in yogurt

Acetic acid bacteria (AAB) can spoil food. Acetobacter aceti as a core subgroup of AAB is usually isolated from yogurt. A. aceti should be timely and effectively detected to prevent yogurt contamination. The present study focused on A. aceti to establish an assay that can be performed to detect AAB in yogurt. LAMP, PCR, and real-time PCR were applied and compared for detecting A. aceti from pure culture and artificially contaminated yogurt samples. In pure culture, LAMP showed the highest detection sensitivity with 10-1 CFU/mL. For yogurt samples, the sensitivity limit of LAMP was 102 CFU/mL, which was lower than that of real-time PCR (101 CFU/mL). The results indicated that these methods could be quickly and efficiently applied to detect A. aceti. As LAMP technology has low cost and high detection efficiency, it can potentially be applied for detecting A. aceti in production and quality control programs of yogurt.

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.

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.

Bifidobacterium aquikefiri sp. nov., isolated from water kefir

A novel Bifidobacterium, strain LMG 28769^T, was isolated from a household water kefir fermentation process. Cells were Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, oxidase-negative and facultatively anaerobic short rods. Analysis of its 16S rRNA gene sequence revealed Bifidobacterium crudilactis and Bifidobacterium psychraerophilum (97.4 and 97.1 % similarity towards the respective type strain sequences) as nearest phylogenetic neighbours. Its assignment to the genus Bifidobacterium was confirmed by the presence of fructose 6-phosphate phosphoketolase activity. Analysis of the hsp60 gene sequence revealed very low similarity with nucleotide sequences in the NCBI nucleotide database. The genotypic and phenotypic analyses allowed the differentiation of strain LMG 28769^T from all recognized Bifidobacterium species. Strain LMG 28769^T ( = CCUG 67145^T = R 54638^T) therefore represents a novel species, for which the name Bifidobacterium aquikefiri sp. nov. is proposed.