Comparison of bacterial and fungal biodiversity of Turkish kefir grains with high-throughput metagenomic analysis

Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil

The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.

The composition of Tibetan kefir grain TKG-Y and the antibacterial potential and milk fermentation ability of S. warneri KYS-164 screened from TKG-Y

This study utilized high-throughput sequencing and SEM observation to elucidate the microbial composition of a Tibetan herder's homemade kefir grain named TKG-Y. Subsequently, S. warneri KYS-164 was isolated from TKG-Y, which can produce mixed protein substances with antibacterial activity, namely bacteriocin-like inhibitory substances (BLIS). BLIS can significantly reduce the growth rate of Escherichia coli 366-a, Staphylococcus aureus CICC 10384 and mixed strains at low concentrations (1 × MIC). The presence of the warnericin-centered gene cluster in KYS-164 may explain the antibacterial properties of the BLIS. Pepsin and an acidic environment can reduce the number of colonies of KYS-164 by 2.5 Log10 CFU mL-1 within 1 h, and reduce the antibacterial activity of BLIS by 21.48%. S. warneri KYS-164 showed no antibiotic resistance and biological toxicity after 80 subcultures, while BLIS produced by 40 generations of the strain retained their inhibitory efficacy against pathogenic bacteria. After 48-hour fermentation of milk with KYS-164, volatile compounds such as aldehydes, phenols, esters, and alcohols, giving it a floral, fruity, milky, oily, and nutty aroma, were released, enriching the sensory characteristics of dairy products. This study not only revealed the bacterial colony composition information of home-made kefir grain TKG-Y but also discovered and proved that S. warneri KYS-164 has the potential to inhibit bacteria and ferment dairy products. This will provide a basis for subsequent applied research on KYS-164.

Bifidobacteria in Fermented Dairy Foods: A Health Beneficial Outlook

Bifidobacteria, frequently present in the human gastrointestinal tract, play a crucial role in preserving gut health and are mostly recognized as beneficial probiotic microorganisms. They are associated with fermenting complex carbohydrates, resulting in the production of short-chain fatty acids, bioactive peptides, exopolysaccharides, and vitamins, which provide energy and contribute to gut homeostasis. In light of these findings, research in food processing technologies has harnessed probiotic bacteria such as lactobacilli and bifidobacteria for the formulation of a wide range of fermented dairy products, ensuring their maximum survival and contributing to the development of distinctive quality characteristics and therapeutic benefits. Despite the increased interest in probiotic dairy products, introducing bifidobacteria into the dairy food chain has proved to be complicated. However, survival of Bifidobacterium species is conditioned by strain of bacteria used, metabolic interactions with lactic acid bacteria (LAB), fermentation parameters, and the temperature of storage and preservation of the dairy products. Furthermore, fortification of dairy foods and whey beverages with bifidobacteria have ability to change physicochemical and rheological properties beyond economic value of dairy products. In summary, this review underscores the significance of bifidobacteria as probiotics in diverse fermented dairy foods and accentuates their positive impact on human health. By enhancing our comprehension of the beneficial repercussions associated with the consumption of bifidobacteria-rich products, we aim to encourage individuals to embrace these probiotics as a means of promoting holistic health.

A robust nanoLC high-resolution mass spectrometry methodology for the comprehensive profiling of lactic acid bacteria in milk kefir

Consumer attention to functional foods containing probiotics is growing because of their positive effects on human health. Kefir is a fermented milk beverage produced by bacteria and yeasts. Given the emerging kefir market, there is an increasing demand for new methodologies to certify product claims such as colony-forming units/g and bacterial taxa. MALDI-TOF MS proved to be useful for the detection/identification of bacteria in clinical diagnostics and agri-food applications. Recently, LC-MS/MS approaches have also been applied to the identification of proteins and proteotypic peptides of lactic acid bacteria in fermented food matrices. Here, we developed an innovative nanoLC-ESI-MS/MS-based methodology for profiling lactic acid bacteria in commercial and artisanal milk kefir products as well as in kefir grains at the genus, species and subspecies level. The proposed workflow enables the authentication of kefir label claims declaring the presence of probiotic starters. An overview of the composition of lactic acid bacteria was also obtained for unlabelled kefir highlighting, for the first time, the great potential of LC-MS/MS as a sensitive tool to assess the authenticity of fermented foods.

Microbiome composition of kombucha tea from Türkiye using high-throughput sequencing

Kombucha is a fermented tea with a combination of yeast and bacteria. Kombucha teas may have a variable microbiota based on geographic origin and cultural conditions. The microbial flora of kombucha has been studied with culture-dependent methods. But, the improvement of the metataxonomic approach has broadened our perspective on fermented foods. In this study, a kombucha mother was procured from an artisanal supplier in Türkiye. High-throughput new-generation sequencing (16S rRNA and Internal Transcribed Spacer (ITS)) was carried out to investigate the microbial communities of kombucha after 7 days of fermentation in both liquid tea (L) and pellicle (P). Microbial counts, pH (4.42 ± 0.01 and 3.50 ± 0.02), and TA% (0.26 ± 0.02 and 0.60 ± 0.04) were also detected on the first and 7th days of fermentation. According to metataxonomic results, the dominant bacteria were Komagataeibacter obediens (%21.13), an acetic acid-producing bacteria, and the dominant fungal genus was Pichia kudriavzevii (64.35%) in L while Romboutsia sp. CE17 was the dominant bacteria (7%) and Pichia kudriavzevii was also the dominant yeast in P. This study also revealed different species which were not common in kombucha including propionic acid and butyric acid-producing bacteria such as Anaerotignum propionicum and Butyrivibrio fibrisolvens, a butyrivibriocin producing bacteria. Accordingly, different yeast species were detected such as Tetrapisispora phaffii and Ogataea polimorpha.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05725-z.

Bacterial Profile and Fatty Acid Composition of Anatolian Bee Bread Samples by Metataxonomic and Metabolomic Approach

This study investigated the bacterial and postbiotic potential of three Anatolian bee bread samples obtained from different regions of Turkey (Marmara, Aegean, and Mediterranean) and offered for human consumption. The families most commonly found in Anatolian bee bread were Lactobacillaceae, Oscillospiraceae, Bacteroidaceae, Prevotellaceae, and Lachnospiraceae. Lactobacillus delbruckeii was highly abundant, but also other beneficial bacteria, known to be next-generation probiotics, were revealed in bee bread, such as Prevotalla copri, Faecalibacterium prausnitzii, and Akkermansia muciniphila. Apart from these beneficial bacteria, bee bread samples also harbored undesired bacteria such as Phocaeicola vulgatus, Phocaeicola dorei, and Clostridium perfringens. Fatty acid composition showed that bee bread samples had butyric acid, a short-chain fatty acid, as a postbiotic. Additionally, polyunsaturated fatty acids were also found such as alfa-linolenic acid and eicosadienoic acid. The fatty acids with the highest amounts were palmitic acid (~ 30%), stearic acid (~ 17%), and alpha-linolenic acid (~ 12%). One of the samples exhibited antimicrobial activity against Staphylococcus aureus.

Microbial Communities in Home-Made and Commercial Kefir and Their Hypoglycemic Properties

Kefir is a popular traditional fermented dairy product in many countries. It has a complex and symbiotic culture made up of species of the genera Leuconostoc, Lactococcus, and Acetobacter, as well as Lactobacilluskefiranofaciens and Lentilactobacillus kefiri. Though kefir has been commercialized in some countries, people are still traditionally preparing kefir at the household level. Kefir is known to have many nutritious values, where its consistent microbiota has been identified as the main valuable components of the product. Type 2 diabetes mellitus (T2DM) is a common diet-related disease and has been one of the main concerns in the world’s growing population. Kefir has been shown to have promising activities in T2DM, mostly via hypoglycemic properties. This review aims to explain the microbial composition of commercial and home-made kefir and its possible effects on T2DM. Some studies on animal models and human clinical trials have been reviewed to validate the hypoglycemic properties of kefir. Based on animal and human studies, it has been shown that consumption of kefir reduces blood glucose, improves insulin signaling, controls oxidative stress, and decreases progression of diabetic nephropathy. Moreover, probiotic bacteria such as lactic-acid bacteria and Bifidobacterium spp. and their end-metabolites in turn directly or indirectly help in controlling many gut disorders, which are also the main biomarkers in the T2DM condition and its possible treatment.

Microbial diversity and functional genes of red vinasse acid based on metagenome analysis

Red vinasse acid has a distinct flavor and a vivid red color that are directly tied to the intricate metabolic activities of microorganisms that produce it. In this study, metagenomic technology was used to mine its functional genes and examine the microbial diversity of red vinasse acid. The findings revealed the identification of 2,609 species, 782 genera, and 63 phyla of microorganisms, and the dominant genus was Lactobacillus. Amino acid metabolism and carbohydrate metabolism were significant activities among the 16,093 and 49,652 genes that were annotated in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. In gluconeogenesis, red vinasse acid encodes 194 genes controlling the transporter protein systems of different sugars and has key enzyme genes that catalyze the conversion of intracellular sugars into glycolytic intermediates. In amino acid flavor formation, red vinasse acid contains 32 control genes for branched-chain aminotransferase (BCAT), 27 control genes for aromatic-amino-acid transaminase (ArAT), 60 control genes for keto acid invertase, 123 control genes for alcohol/aldehyde dehydrogenase, and 27 control genes for acetyl esterase, which have the basis for the formation of strong flavor substances from amino acids.

Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure

The addition of anthocyanin to kefir for the production of more functional and bio-diversified kefir beverages has the potential to increase kefir's healthful activities. In the present study, anthocyanin extracts, obtained from black carrots, were added into kefir mixture during the fermentation process in different concentrations (1% and 5%, w/v). These kefir samples were then analyzed in terms of their microbiological qualities by metagenomic analysis. The results of the analyses show that the addition of anthocyanin has significant impacts on the community structure of kefir microbiome which in turn directly affects the expected health impacts of the beverage. Kefir with no anthocyanin included predominantly probiotic bacteria such as Lactococcus lactis (34%) and Lactobacillus kefiri (34%). On the other hand, kefir with 1% anthocyanin demonstrated a more balanced distribution of probiotic species like Lb. kefiri (17%), Leuconostoc mesenteroides (9%), and Lc. lactis (5%) at similar abundance rates. 5% anthocyanin kefir demonstrated the highest polarity in the community with a strong dominance of probiotic Lb. kefiri (72%), and distinctly less abundant bacteria such as Streptococcus salivarius subsp. thermophilus (3%). These findings provide that fortification with anthocyanins can be utilized to enhance the quality, composition, and beneficial functions of kefir.

The effect of young blood plasma administration on gut microbiota in middle-aged rats

Numerous in-depth studies continue to reveal the many benefits of gut microbiota and young blood plasma administration. Dysbiosis, which occurs in the intestinal microbiota, especially in the aging process, is associated with many metabolic and cognitive disorders. Therefore, many studies aim to reverse the dysbiosis that occurs. There are also studies showing that young blood plasma application reverses the effects of aging at the level of many tissues and organs. Today, while research continues to reveal all the benefits of young blood plasma application in terms of health, blood plasma centers are also being established. In this study, we aimed to reveal the impact of young blood plasma, administered for 1 month, on the intestinal microbiota of middle-aged rats. After detailed metagenome analysis, alpha diversity indices demonstrated greater bacterial richness in the microbiota of plasma-administered rats compared with control rats. In addition, the Firmicutes/Bacteroidetes ratio was significantly diminished in plasma group microbiota, confirming possible rejuvenation properties of young plasma. Furthermore, increased counts of Bifidobacterium longum, Coprococcus catus, and Romboutsia ilealis species were measured in plasma-administered rats. The study revealed many fluctuations in different bacterial taxonomic units of the microbiota that could be valuable in future research on blood-based anti-aging treatments.

Metataxonomic sequencing to assess microbial safety of Turkish white cheeses

High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.

Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.

The Microbial Diversity and Biofilm-Forming Characteristic of Two Traditional Tibetan Kefir Grains

In this study, a high-throughput sequencing technique was used to analyze bacterial and fungal diversity of two traditional Tibetan kefir grains from Linzhi (K1) and Naqu (K2) regions. Comparative bioinformatic analyses indicated that Lactobacillus kefiranofaciens, L. kefiri and Kluyveromyces marxianus were the main dominant strains in K1 and K2. In order to research the relationship of the growth of kefir grains, the biofilm and the extracellular polysaccharides (EPS) produced by microorganisms, the proliferation rate of kefir grains, the yield and chemical structure of EPS and the optimal days for biofilm formation were determined. The results showed that the growth rate, the yield of EPS and the biofilm formation ability of K1 were higher than K2, and the optimal day of their biofilm formation was the same in 10th day. Additionally, the live cells, dead cells and EPS in biofilm formation of K1 and K2 were observed by fluorescence microscope to clarify the formation process of kefir grains. To determine the influence of microbial interactions on biofilm and the formation of kefir grains, the essential role of microbial quorum sensing needs further attention.