Isolation and Genome-Resolved Characterisation of Selected Indigenous Lactic Acid Bacteria from Traditional Fermented Dairy Products of Kazakhstan

Traditional fermented dairy products of Kazakhstan represent potential sources of indigenous lactic acid bacteria (LAB). However, the cultivable LAB associated with these products remain insufficiently characterised. This study aimed to isolate and taxonomically characterise cultivable LAB recovered from traditional dairy products of Kazakhstan using a culture-dependent workflow combined with MALDI-TOF MS, 16S rRNA gene sequencing, phylogenetic analysis, and whole-genome sequencing (WGS) of selected isolates. A total of 102 samples, including kumis, shubat, raw mare’s milk, raw camel’s milk, and freshly prepared soft camel milk cheese, were analysed. Samples were cultured on MRS agar under aerobic conditions at 30 °C for 48 h, and colonies were collected from randomly selected sectors of the plates and purified for further analysis, irrespective of their morphology. In total, 315 bacterial isolates were recovered, of which 79 were confirmed as LAB and retained for further taxonomic analysis. Eight LAB species belonging to four genera were identified, with Leuconostoc mesenteroides being predominant among the recovered LAB isolates (48/79, 60.8%), followed by Lactococcus lactis (19/79, 24.1%). Lentilactobacillus hilgardii, Lentilactobacillus kefiri, and Lentilactobacillus diolivorans were detected only among isolates recovered from fermented products, whereas Lacticaseibacillus paracasei was detected at low frequency. Five representative isolates, including both frequently and less frequently recovered species, were selected for WGS. WGS supported the taxonomic assignments and yielded draft genome assemblies ranging from 1.68 to 2.69 Mb, with GC contents of 34.8–43.1%. OrthoANI analysis further supported their species-level assignments and enabled subspecies-level resolution for selected isolates. Overall, the study establishes a culture-based collection of indigenous LAB recovered from traditional dairy products of Kazakhstan, representing the genera Leuconostoc, Lactococcus, Lentilactobacillus, and Lacticaseibacillus. The observed LAB species composition reflects the cultivable fraction recovered under the applied cultivation and colony-selection conditions and should not be interpreted as a comprehensive representation of LAB diversity in the investigated products. The resulting strain collection and genome sequences provide a basis for subsequent comparative genomic, physiological, and technological studies of selected indigenous LAB.