Yogurt Produced by Novel Natural Starter Cultures Improves Gut Epithelial Barrier In Vitro

Geroprotective potential of microbiome modulators in the Caenorhabditis elegans model

Aging is associated with cellular and physiological changes, which significantly reduce the quality of life and increase the risk for disease. Geroprotectors improve lifespan and slow the progression of detrimental aging-related changes such as immune system senescence, mitochondrial dysfunction, and dysregulated nutrient sensing and metabolism. Emerging evidence suggests that gut microbiota dysbiosis is a hallmark of aging-related diseases and microbiome modulators, such as probiotics (live bacteria) or postbiotics (non-viable bacteria/bacterial byproducts) may be promising geroprotectors. However, because they are strain-specific, the geroprotective effects of probiotics and postbiotics remain poorly understood and understudied. Drosophila melanogaster, Caenorhabditis elegans, and rodents are well-validated preclinical models for studying lifespan and the role of probiotics and/or postbiotics, but each have their limitations, including cost and their translation to human aging biology. C. elegans is an excellent model for large-scale screening to determine the geroprotective potential of drugs or probiotics/postbiotics due to its short lifecycle, easy maintenance, low cost, and homology to humans. The purpose of this article is to review the geroprotective effects of microbiome modulators and their future scope, using C. elegans as a model. The proposed geroprotective mechanisms of these probiotics and postbiotics include delaying immune system senescence, preventing or reducing mitochondrial dysfunction, and regulating food intake (dietary restriction) and metabolism. More studies are warranted to understand the geroprotective potential of probiotics and postbiotics, as well as other microbiome modulators, like prebiotics and fermented foods, and use them to develop effective therapeutics to extend lifespan and reduce the risk of debilitating aging-related diseases.

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.

Assessment of stability and bioactive compounds in yogurt containing novel natural starter cultures with the ability to promote longevity in Caenorhabditis elegans

Yogurt represent one of the oldest fermented foods containing viable lactic acid bacteria and many bioactive compounds that could exhibit beneficial effects on human health and train our immune system to better respond to invading pathogens. Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus are commonly used for yogurt preparation under controlled temperature and environmental conditions. In this study, we investigated probiotic features of S. thermophilus BGKMJ1-36 and L. bulgaricus BGVLJ1-21 strains isolated from artisanal sour milk and yogurt by using Caenorhabditis elegans as an in vivo model system. Further, we evaluated content of total fat, saturated fatty acids, proteins, and lactose, as well as vitamins and AA of yogurt prepared from above-mentioned starter cultures during 21 d of storage at 4°C to get insights of final product stability. We showed that S. thermophilus BGKMJ1-36 and L. bulgaricus BGVLJ1-21 strains applied in combination upregulated the expression of autophagy-related genes in C. elegans. Beside autophagy, we observed activation of TIR-1-dependent transcription of lysozyme-like antimicrobial genes involved in the immune defense of C. elegans. Upregulation of these genes strongly correlates with an increase in the longevity of the worms fed with yogurt culture bacteria. Further, we showed that yogurt prepared with S. thermophilus BGKMJ1-36 and L. bulgaricus BGVLJ1-21, as a final product, is rich with vitamin B2 and dominant AA known by their prolongevity properties. Taken together, our study pointed to the beneficial features of the tested starter cultures and yogurt and highlighted their potential to be used as a fermented food with added-value properties.

Influences of Yogurt with Functional Ingredients from Various Sources That Help Treat Leaky Gut on Intestinal Barrier Dysfunction in Caco-2 Cells

The impact of yogurts made with starter culture bacteria (L. bulgaricus and S. thermophilus) and supplemented with ingredients (maitake mushrooms, quercetin, L-glutamine, slippery elm bark, licorice root, N-acetyl-D-glucosamine, zinc orotate, and marshmallow root) that can help treat leaky gut were investigated using the Caco-2 cell monolayer as a measure of intestinal barrier dysfunction. Milk from the same source was equally dispersed into nine pails, and the eight ingredients were randomly allocated to the eight pails. The control had no ingredients. The Caco-2 cells were treated with isoflavone genistein (negative control) and growth media (positive control). Inflammation was stimulated using an inflammatory cocktail of cytokines (interferon-γ, tumor necrosis factor-α, and interleukin-1β) and lipopolysaccharide. The yogurt without ingredients (control yogurt) was compared to the yogurt treatments (yogurts with ingredients) that help treat leaky gut. Transepithelial electrical resistance (TEER) and paracellular permeability were measured to evaluate the integrity of the Caco-2 monolayer. Transmission electron microscopy (TEM), immunofluorescence microscopy (IM), and real-time quantitative polymerase chain reaction (RTQPCR) were applied to measure the integrity of tight junction proteins. The yogurts were subjected to gastric and intestinal digestion, and TEER was recorded. Ferrous ion chelating activity, ferric reducing potential, and DPPH radical scavenging were also examined to determine the yogurts' antioxidant capacity. Yogurt with quercetin and marshmallow root improved the antioxidant activity and TEER and had the lowest permeability in fluorescein isothiocyanate (FITC)-dextran and Lucifer yellow flux among the yogurt samples. TEM, IM, and RTQPCR revealed that yogurt enhanced tight junction proteins' localization and gene expression. Intestinal digestion of the yogurt negatively impacted inflammation-induced Caco-2 barrier dysfunction, while yogurt with quercetin, marshmallow root, maitake mushroom, and licorice root had the highest TEER values compared to the control yogurt. Yogurt fortification with quercetin, marshmallow root, maitake mushroom, and licorice root may improve functionality when dealing with intestinal barrier dysfunction.

Targeted Application of Functional Foods as Immune Fitness Boosters in the Defense against Viral Infection

In recent times, the emergence of viral infections, including the SARS-CoV-2 virus, the monkeypox virus, and, most recently, the Langya virus, has highlighted the devastating effects of viral infection on human life. There has been significant progress in the development of efficacious vaccines for the prevention and control of viruses; however, the high rates of viral mutation and transmission necessitate the need for novel methods of control, management, and prevention. In recent years, there has been a shift in public awareness on health and wellbeing, with consumers making significant dietary changes to improve their immunity and overall health. This rising health awareness is driving a global increase in the consumption of functional foods. This review delves into the benefits of functional foods as potential natural means to modulate the host immune system to enhance defense against viral infections. We provide an overview of the functional food market in Europe and discuss the benefits of enhancing immune fitness in high-risk groups, including the elderly, those with obesity, and people with underlying chronic conditions. We also discuss the immunomodulatory mechanisms of key functional foods, including dairy proteins and hydrolysates, plant-based functional foods, fermentates, and foods enriched with vitamin D, zinc, and selenium. Our findings reveal four key immunity boosting mechanisms by functional foods, including inhibition of viral proliferation and binding to host cells, modulation of the innate immune response in macrophages and dendritic cells, enhancement of specific immune responses in T cells and B cells, and promotion of the intestinal barrier function. Overall, this review demonstrates that diet-derived nutrients and functional foods show immense potential to boost viral immunity in high-risk individuals and can be an important approach to improving overall immune health.

Diarrhea Caused by High-Fat and High-Protein Diet Was Associated With Intestinal Lactase-Producing Bacteria

BACKGROUND/AIMS

This study aimed to investigate the effect of diarrhea induced by a high-fat and high-protein diet on lactase-producing bacteria in the intestinal contents of mice from the perspective of diarrhea-related genes.

MATERIALS AND METHODS

Ten specific pathogen-free Kunming male mice were chosen and randomly divided into the normal group and model group. The mice in the normal group were fed with high-fat and high-protein diet plus gavage of vegetable oil, while those in the model group were fed with general diet plus gavage of distilled water. After successful modeling, the distribution and diversity of lactase-producing bacteria in the intestinal contents were characterized by metagenomic sequencing technology.

RESULTS

After high-fat and high-protein diet intervention, Chao1, observed species index, and operational taxonomic units number decreased in the model group (P > .05), while the Shannon, Simpson, Pielou's evenness, and Goods coverage indices increased (P > .05). The principal coordinate analysis showed that the composition of lactase-producing bacteria differed between the normal group and model group (P < .05). The lactase-producing bacterial source in the intestinal contents of mice was Actinobacteria, Firmicutes, and Proteobacteria, of which Actinobacteria was the most abundant phylum. At the genus level, both groups had their unique genera, respectively. Compared to the normal group, the abundance of Bifidobacterium, Rhizobium, and Sphingobium increased, while Lachnoclostridium, Lactobacillus, Saccharopolyspora, and Sinorhizobium decreased in the model group.

CONCLUSION

High-fat and high-protein diet altered the structure of lactase-producing bacteria in the intestinal contents, elevating the abundance of dominant lactase-producing bacteria, while decreasing the richness of lactase-producing bacteria, which may further induce the occurrence of diarrhea.

Special Issue 'Food Fermentations: Microorganisms in Food Production and Preservation': Editorial

For centuries, microorganisms have been exploited for the production and preservation of substates intended for human consumption [...].

Baohe pill decoction for diarrhea induced by high-fat and high-protein diet is associated with the structure of lactase-producing bacterial community

Background

This study investigated the effects of Baohe pill decoction on the diversity and community composition of lactase-producing bacteria in the intestinal contents of mice with diarrhea induced by high-fat and high-protein diet, which provided an experimental basis for the study on the therapeutic mechanism of Baohe pill decoction.

Materials and methods

The Traditional Chinese Medicine Systems Pharmacology (TCMSP), DisGeNET, UniProt, National Center for Biotechnology Information (NCBI), and GeneCards databases were used to collect the potential targets with active ingredients of Baohe pill decoction, diarrhea, and lactase, and then construct correlation networks. Fifteen Kunming mice were randomly divided into the control group (CN), natural recovery group (NR), and Baohe pill decoction treatment group (BHP), with five mice in each group. After constructing a mouse diarrhea model by HFHPD induction, BHP was gavaged with Baohe pill decoction, and the other groups were gavaged with distilled water of equal. The intestinal contents were collected from ileal to jejunal and analyzed using metagenomic sequencing to characterize the intestinal content of lactase-producing bacteria in mice.

Results

The core active ingredients related to diarrhea in Baohe pill decoction were quercetin, luteolin, kaempferol, forsythin, and wogonin. And there was no intersection between the potential targets with the active ingredient of Baohe pill, lactase, and diarrhea. After the intervention of Baohe pill decoction, the Observed species, Chao1 index, and Operational Taxonomic Units (OTU) number increased in BHP (P > 0.05), while the Pielous evenness and Shannon index decreased (P > 0.05). In Beta diversity, the community structure of the NR was significantly different from CN and BHP (P < 0.05), and the community structure of the CN was not significant difference from BHP (P > 0.05). Compared to NR, the relative abundance of Bifidobacterium and Amycolatopsis increased, while the relative abundance of Lachnoclostridium, Sinorhizobium, Cedecea, and Escherichia decreased in BHP, but none of the significant differences (P > 0.05).

Conclusion

The therapeutic effect of Baohe pill decoction on diarrhea induced by HFHPD does not appear to involve the body’s lactase gene targets directly, but is associated with the change of the construction of lactase-producing bacterial communities.

Polysorbate 80 improves the adhesion and survival of yogurt starters with cholesterol uptake abilities

The goal of this study is to improve the adhesion and survival of yogurt bacteria with probiotic traits by using polysorbate 80, a food additive emulsifier commonly found in milk derivative products. Polysorbate 80 was used at 1% (w/v), and its effects on yogurt bacteria's survival under simulated digestive conditions, cholesterol uptake activities, bile salt hydrolase (BSH) activity, and adhesion to HT-29 culture were studied. In the presence of 1% polysorbate 80, both starters demonstrated better cholesterol uptake and BSH activities, as well as higher bacterial survival at pH 2.5, particularly in associated cultures. In the presence of 0.3 % bile or cholic acid, polysorbate 80 reduced the drop in L. bulgaricus's survival load. However, the carbon source had a greater impact on S. thermophilus bile tolerance than the food additive emulsifier. Oleic acid was incorporated into both bacterial membranes when grown in the presence of bile and polysorbate 80, resulting in a higher unsaturated/saturated fatty acid ratio. In the presence of polysorbate 80, S. thermophilus adhered to HT-29 cells 2.3-fold better, while L. bulgaricus's adhesion remained unchanged. We suggest that polysorbate 80 may have a protective effect on cell survival under simulated digestive stress as well as a role in yogurt bacteria adhesion to the intestines, giving these bacteria more opportunities to exert their purported cholesterol-removal activities.

A food-grade vector for Streptococcus thermophilus based on the α-complementation of β-galactosidase

Streptococcus thermophilus is a common yogurt starter that consumes lactose as its primary carbon source. The enzyme β-galactosidase is essential for the lactose metabolism and the growth of this species. Streptococcus thermophilus appears to be a promising cell factory. Food-grade vectors have advantages in heterologous protein expression. This study aimed to determine whether the β-galactosidase of S. thermophilus has the α-complementary characteristic and to develop a novel food-grade vector based on this phenomenon. The N-terminal 7 to 36 AA residues of the β-galactosidase in S. thermophilus were deleted. The obtained mutant S. thermophilus Δα lost β-galactosidase activity and growth ability in the lactose medium. Subsequently, plasmids expressing α-fragments with different lengths of 1 to 36 (Sα1), 1 to 53 (Sα2), and 1 to 88 (Sα3) AA were constructed and transformed into S. thermophilus Δα. Recombinant S. thermophilus Δα expressing Sα2 or Sα3 recovered the ability to grow in the lactose medium, and their β-galactosidase activity accounted for 24.5% or 11.5% of the wild strain, respectively. These results indicated that the α-complementation system of β-galactosidase existed in S. thermophilus. Based on the characteristic, a food-grade vector pSEα was constructed. Except for Sα2, vector pSEα expressed the α-donor derived from E. coli β-galactosidase. This facilitated the construction of recombinant plasmids in E. coli DH5α and thus improved the transformation efficiency of S. thermophilus. Green fluorescent protein as a reporter protein could be highly expressed in S. thermophilus using this vector. As a result, pSEα is an efficient and safe vector for S. thermophilus with potential food applications.

Lactobacillus brevis BGZLS10-17 and Lb. plantarum BGPKM22 Exhibit Anti-Inflammatory Effect by Attenuation of NF-κB and MAPK Signaling in Human Bronchial Epithelial Cells

Bronchial epithelial cells are exposed to environmental influences, microbiota, and pathogens and also serve as a powerful effector that initiate and propagate inflammation by the release of pro-inflammatory mediators. Recent studies suggested that lung microbiota differ between inflammatory lung diseases and healthy lungs implicating their contribution in the modulation of lung immunity. Lactic acid bacteria (LAB) are natural inhabitants of healthy human lungs and also possess immunomodulatory effects, but so far, there are no studies investigating their anti-inflammatory potential in respiratory cells. In this study, we investigated immunomodulatory features of 21 natural LAB strains in lipopolysaccharide (LPS)-stimulated human bronchial epithelial cells (BEAS-2B). Our results show that several LAB strains reduced the expression of pro-inflammatory cytokine and chemokine genes. We also demonstrated that two LAB strains, Lactobacillus brevis BGZLS10-17 and Lb. plantarum BGPKM22, effectively attenuated LPS-induced nuclear factor-κB (NF-κB) nuclear translocation. Moreover, BGZLS10-17 and BGPKM22 reduced the activation of p38, extracellular signal-related kinase (ERK), and c-Jun amino-terminal kinase (JNK) signaling cascade resulting in a reduction of pro-inflammatory mediator expressions in BEAS-2B cells. Collectively, the LAB strains BGZLS10-17 and BGPKM22 exhibited anti-inflammatory effects in BEAS-2B cells and could be employed to balance immune response in lungs and replenish diminished lung microbiota in chronic lung diseases.

A Lactic Acid Bacteria Consortium Impacted the Content of Casein-Derived Biopeptides in Dried Fresh Cheese

This study aimed to define a consortium of lactic acid bacteria (LAB) that will bring added value to dried fresh cheese through specific probiotic properties and the synthesis of bioactive peptides (biopeptides). The designed LAB consortium consisted of three Lactobacillus strains: S-layer carrying Levilactobacillus brevis D6, exopolysaccharides producing Limosilactobacillus fermentum D12 and plantaricin expressing Lactiplantibacillus plantarum D13, and one Enterococcus strain, Enterococcus faecium ZGZA7-10. Chosen autochthonous LAB strains exhibited efficient adherence to the Caco-2 cell line and impacted faecal microbiota biodiversity. The cheese produced by the LAB consortium showed better physicochemical, textural and sensory properties than the cheese produced by a commercial starter culture. Liquid chromatography coupled with matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry (LC-MALDI-TOF/TOF) showed the presence of 18 specific biopeptides in dried fresh cheeses. Their identification and relative quantification was confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using multiple reaction monitoring (MRM). The results also showed that their synthesis resulted mainly from β-casein and also α-S1 casein degradation by proteolytic activities of the LAB consortium. The designed LAB consortium enhanced the functional value of the final product through impact on biopeptide concentrations and specific probiotic properties.

Dairy Lactic Acid Bacteria and Their Potential Function in Dietetics: The Food-Gut-Health Axis

Fermented dairy products are the good source of different species of live lactic acid bacteria (LAB), which are beneficial microbes well characterized for their health-promoting potential. Traditionally, dietary intake of fermented dairy foods has been related to different health-promoting benefits including antimicrobial activity and modulation of the immune system, among others. In recent years, emerging evidence suggests a contribution of dairy LAB in the prophylaxis and therapy of non-communicable diseases. Live bacterial cells or their metabolites can directly impact physiological responses and/or act as signalling molecules mediating more complex communications. This review provides up-to-date knowledge on the interactions between LAB isolated from dairy products (dairy LAB) and human health by discussing the concept of the food–gut-health axis. In particular, some bioactivities and probiotic potentials of dairy LAB have been provided on their involvement in the gut–brain axis and non-communicable diseases mainly focusing on their potential in the treatment of obesity, cardiovascular diseases, diabetes mellitus, inflammatory bowel diseases, and cancer.

Exopolysaccharides from Bifidobacterium animalis Ameliorate Escherichia coli-Induced IPEC-J2 Cell Damage via Inhibiting Apoptosis and Restoring Autophagy

Enteropathogenic Escherichia coli (EPEC) is a common zoonotic pathogen that causes acute infectious diarrhea. Probiotics like Bifidobacterium are known to help prevent pathogen infections. The protective effects of Bifidobacterium are closely associated with its secretory products exopolysaccharides (EPS). We explored the effects of the EPS from Bifidobacterium animalis subsp. lactis (B. lactis) on ameliorating the damage of an intestinal porcine epithelial cell line (IPEC-J2) during EPEC infection. Pretreatment with EPS alleviated EPEC-induced apoptosis through the restoration of cell morphology and the downregulation of protein expressions of cleaved-caspase 8, cleaved-caspase 3, and cleaved-PARP. EPS-mediated remission of apoptosis significantly improved cell viability during EPEC infection. EPEC infection also resulted in impaired autophagy, as demonstrated by decreased expressions of autophagy-related proteins Beclin 1, ATG5, and microtubule-binding protein light chain-3B (LC3B) and the increased expression of p62 through western blot analysis. However, EPS reversed these effects which indicated that EPS promoted autophagosome formation. Furthermore, EPS prevented the lysosome damage induced by EPEC as it enhanced lysosomal acidification and raised lysosome-associated protein levels, thus promoted autophagosome degradation. Our findings suggest that the amelioration of EPEC-induced cell damages by EPS is associated with the limitation of detrimental apoptosis and the promotion of autophagy flux.

Protective Effect of an Exopolysaccharide Produced by Lactiplantibacillus plantarum BGAN8 Against Cadmium-Induced Toxicity in Caco-2 Cells

Cadmium (Cd) ranks seventh on the list of most significant potential threats to human health based on its suspected toxicity and the possibility of exposure to it. It has been reported that some bacterial exopolysaccharides (EPSs) have the ability to bind heavy metal ions. We therefore investigated the capacity of eight EPS-producing lactobacilli to adsorb Cd in the present study, and Lactiplantibacillus plantarum BGAN8 was chosen as the best candidate. In addition, we demonstrate that an EPS derived from BGAN8 (EPS-AN8) exhibits a high Cd-binding capacity and prevents Cd-mediated toxicity in intestinal epithelial Caco-2 cells. Simultaneous use of EPS-AN8 with Cd treatment prevents inflammation, disruption of tight-junction proteins, and oxidative stress. Our results indicate that the EPS in question has a strong potential to be used as a postbiotic in combatting the adverse effects of Cd. Moreover, we show that higher concentrations of EPS-AN8 can alleviate Cd-induced cell damage.

Probiotic-mediated p38 MAPK immune signaling prolongs the survival of Caenorhabditis elegans exposed to pathogenic bacteria

The host-microbiota cross-talk represents an important factor contributing to innate immune response and host resistance during infection. It has been shown that probiotic lactobacilli exhibit the ability to modulate innate immunity and enhance pathogen elimination. Here we showed that heat-inactivated probiotic strain Lactobacillus curvatus BGMK2-41 stimulates immune response and resistance of the Caenorhabditis elegans against Staphylococcus aureus and Pseudomonas aeruginosa. By employing qRT-PCR and western blot analysis we showed that heat-inactivated BGMK2-41 activated PMK-1/p38 MAPK immunity pathway which prolongs the survival of C. elegans exposed to pathogenic bacteria in nematode killing assays. The C. elegans pmk-1 mutant was used to demonstrate a mechanistic basis for the antimicrobial potential of BGMK2-41, showing that BGMK2-41 upregulated PMK-1/p38 MAPK dependent transcription of C-type lectins, lysozymes and tight junction protein CLC-1. Overall, this study suggests that PMK-1/p38 MAPK-dependent immune regulation by BGMK2-41 is essential for probiotic-mediated C. elegans protection against gram-positive and gram-negative bacteria and could be further explored for development of probiotics with the potential to increase resistance of the host towards pathogens.

Traditional Bulgarian Dairy Products: Ethnic Foods with Health Benefits

The reported health effects of fermented dairy foods, which are traditionally manufactured in Bulgaria, are connected with their microbial biodiversity. The screening and development of probiotic starters for dairy products with unique properties are based exclusively on the isolation and characterization of lactic acid bacterial (LAB) strains. This study aims to systematically describe the LAB microbial content of artisanal products such as Bulgarian-type yoghurt, white brined cheese, kashkaval, koumiss, kefir, katak, and the Rhodope's brano mliako. The original technologies for their preparation preserve the valuable microbial content and improve their nutritional and probiotic qualities. This review emphasises the features of LAB starters and the autochthonous microflora, the biochemistry of dairy food production, and the approaches for achieving the fortification of the foods with prebiotics, bioactive peptides (ACE2-inhibitors, bacteriocins, cyclic peptides with antimicrobial activity), immunomodulatory exopolysaccharides, and other metabolites (indol-3-propionic acid, free amino acids, antioxidants, prebiotics) with reported beneficial effects on human health. The link between the microbial content of dairy foods and the healthy human microbiome is highlighted.

Bioactive Compounds Produced by the Accompanying Microflora in Bulgarian Yoghurt

Bulgarian yoghurt is associated with health benefits and longevity of consumers. The specific microflora producing bioactive metabolites is responsible for this effect. The present study examines the biodiversity in four homemade yoghurts from regions containing endemic microflora. Metagenome sequencing indicated Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus were predominant in all samples. In addition, yoghurts contained accompanying lactic acid bacteria (LAB) including Lacticaseibacillus paracasei, Lb. helveticus, Limosilactobacillus fermentum, Lb. rhamnosus, Lactococcus lactis, Pediococcus acidilactici, Leuconostoc mesenteroides, and Leuc. pseudomesenteroides. A negligible amount of pollutant strains was found. Twenty-four LAB strains were isolated from the yoghurts and identified. Lb. delbrueckii subsp. bulgaricus strains were genotyped by randomly amplified polymorphic DNA–PCR (RAPD), multi-locus sequence typing (MLST), and pulse field gel electrophoresis (PFGE), which demonstrated their uniqueness and non-commercial origin. To estimate the bioactive metabolites produced by the accompanying microflora, yoghurts fermented by single LAB strains were analyzed using liquid chromatography and mass spectrometry (LC-MS). The fermented samples contained large amounts of free essential amino acids (arginine, citrulline, tryptophan, lysine, and histidine), the neuroprotector indole-3-propionic acid (IPA), and significant quantities of the cyclic antimicrobial peptides cyclo(phenylalanyl-prolyl) and cyclo(leucyloprolyl). The disclosure of these special qualities draws attention to the accompanying microflora as a source of potential probiotic strains that can fortify the yoghurts’ content with bioactive compounds.