Isolation and molecular characterization of lactobacilli from traditional fermented Dahi produced at different altitudes in Nepal

Dairy products are an important part of daily food in the Himalayan country of Nepal. A wide variety of traditional fermented milk products are obtained in relation to different geo-climatic conditions of the country and different ethnic groups. Locally called Dahi is the most popular product, but little data are available on the autochthonous lactic acid bacteria (LAB) characterizing this yogurt-like product. Thirty-two replicate samples of indigenous Dahi were collected from four districts of Nepal at different altitude. In total of 193 isolates were obtained. Of these, the 120 rod-shaped isolates representing the dominant LAB population (62%) were further identified at the species level by using internal transcribed spacers (ITS) amplification, 16S rRNA gene sequence determination, and species-specific PCR. A further characterization at the strain level was carried out by combining analysis of repetitive elements and randomly amplified polymorphic DNA (RAPD) typing. Based on these analyses, the isolates were grouped in ten different species, among which Lactobacillus delbrueckii subsp. bulgaricus, L. paracasei, and L. rhamnosus represented the dominant species. A high degree of intraspecies diversity was also observed for all Lactobacillus species, except for L. rhamnosus isolates, which proved to give a single typing profile. Bacterial isolates represent a source of novel potential probiotics and starter cultures. The strain collection obtained from this study is a first step in the preservation of the natural biodiversity of bacterial population of the traditional Nepalese fermented Dahi.