Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties.

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32–35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel’s milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

Chukotka is an arctic region located in the continuous permafrost zone, but thermal springs are abundant there. In this study, for the first time, the microbial communities of the Chukotka hot springs (CHS) biofilms and sediments with temperatures 54–94 °C were investigated and analyzed by NGS sequencing of 16S rRNA gene amplicons. In microbial mats (54–75 °C), phototrophic bacteria of genus Chloroflexus dominated (up to 89% of all prokaryotes), while Aquificae were the most numerous at higher temperatures in Fe-rich sediments and filamentous “streamers” (up to 92%). The electron donors typical for Aquificae, such as H₂S and H₂, are absent or present only in trace amounts, and the prevalence of Aquificae might be connected with their ability to oxidize the ferrous iron present in CHS sediments. Armatimonadetes, Proteobacteria, Deinococcus-Thermus, Dictyoglomi, and Thermotogae, as well as uncultured bacteria (candidate divisions Oct-Spa1-106, GAL15, and OPB56), were numerous, and Cyanobacteria were present in low numbers. Archaea (less than 8% of the total community of each tested spring) belonged to Bathyarchaeota, Aigarchaeota, and Thaumarchaeota. The geographical location and the predominantly autotrophic microbial community, built on mechanisms other than the sulfur cycle-based ones, make CHS a special and unique terrestrial geothermal ecosystem.

In this study, we used culture-independent analysis based on 16S rRNA gene amplicons and metagenomics to explore in depth the microbial communities and their metabolic capabilities of artisanal brine cheeses made in the North Caucasus. Additionally, analysis of organic acid profiles was carried out for cheese characterization. Twelve cheese samples (designated as 05SR–16SR) from various artisanal producers were taken from five different villages located in Northern Ossetia–Alania (Russia). These cheeses were made using methods based on cultural traditions inherited from previous generations and prepared using a relatively uncontrolled fermentation process. The microbial diversity of Caucasus artisanal cheeses was studied for the first time. The results showed a diverse composition in all cheeses, with Bacillota (synonym Firmicutes) (9.1–99.3%) or Pseudomonadota (synonym Proteobacteria) (0.2–89.2%) prevalence. The microbial communities of the majority of the studied cheeses were dominated by lactic acid bacteria (LAB) genera, like Lactococcus (10.3–77.1% in 07SR, 09SR, 10SR, 11SR, 13SR, 15SR, 16SR), Lactobacillus (54.6% in 09SR), Streptococcus (13.9–93.9% in 11SR, 13SR, 14SR, 15SR), Lactiplantibacillus (13.4–30.6% in 16SR and 07SR) and Lentilactobacillus (5.9–14.2% in 09SR, 10SR and 13SR). Halophilic lactic acid bacteria belonging to the Tetragenococcus genus accounted for 7.9–18.6% in 05SR and 06SR microbiomes. A distinctive feature of Ossetia cheese microbiomes was the large variety of halophilic proteobacteria, and in some cheeses they prevailed, e.g., Chromohalobacter (63–76.5% in 05SR and 06SR), Psychrobacter (10–47.1% in 08SR, 11SR, 12SR), Halomonas (2.9–33.5% in 06SR, 08SR, 11SR and 12SR), Marinobacter (41.9% in 12SR) or Idiomarina (2.9–14.4% in 06SR, 08SR and 11SR samples). Analysis of the genomes assembled from metagenomes of three cheeses with different bacterial composition revealed the presence of genes encoding a variety of enzymes, involved in milk sugar, proteins and lipid metabolism in genomes affiliated with LAB, as well as genes responsible for beneficial bioamine and bacteriocin synthesis. Also, most of the LAB did not contain antibiotic resistance genes, which makes them potential probiotics, so highly demanded nowadays. Analysis of the genomes related to halophilic proteobacteria revealed that they are not involved in milk fermentation; however, the search for “useful” genes responsible for the synthesis of beneficial products/metabolites was partially positive. In addition, it has been shown that some halophiles may be involved in the synthesis of inappropriate bioactive components. The results obtained by culture-independent analyses confirm the importance of using such techniques both to clarify the quality and health-promoting properties of the product, and to look for probiotic strains with specified unique properties. This study has shown that traditional dairy foods may be a source of such beneficial strains.