Armenian fermented dairy product “Narine”: characterization of the whole-genome sequence of starter bacteria Lactobacillus helveticus and potential probiotic marker genes

Abstract

Background: The starter monoculture used in “Narine” dairy products was first isolated in 1954 in Armenia by Professor Levon Erzinkyan's team. The strain was later named after the author's granddaughter, Narine, who, according to family legend, was cured of an acute intestinal infection—likely rotavirus-related—through the use of this bacterium. Her condition improved rapidly, and the strain’s demonstrated effectiveness prompted further research into its potential for treating intestinal infections. Today, the “Narine” product contains not a commercially formulated mixture but a single strain, with over 60 years of practical use—particularly in fermented milk products and food supplements aimed at both treating and preventing digestive disorders. The strain has shown probiotic properties as well as potential medical applications.

Objective: To elucidate the molecular mechanisms underlying the probiotic and prebiotic properties of this well-known strain, whole-genome sequencing was conducted. Based on the sequence data, potential explanations for its established characteristics were explored.

Methods: Whole-genome sequencing was conducted following Oxford Nanopore Technologies (UK) guidelines, using a Flongle R10.4.1 flow cell and the ligation sequencing kit SQK-LSK114 as specified in the g-dna-by-ligation-sqk-lsk114 protocol. High-molecular-weight, high-purity DNA was extracted via the traditional phenol-chloroform method. Raw sequencing data were processed with Flye (version 2.9.1) and annotated using Prokka (version 1.14.5), a bacterial genome annotation tool.

Results: Based on NGS sequencing, the “Narine” starter culture was identified as Lactobacillus helveticus. At this stage, the genome of our strain comprises 1,923,890 nucleotides across 490 contigs, without circular structures, representing 94.3% of the reference strain genome. Preliminary genome analysis reveals several genes associated with known probiotic characteristics of the strain. These include surface layer proteases (2 genes), cell division proteins (6 genes), bile salt hydrolase, biofilm regulatory protein A, exopolysaccharide synthases (3 genes), lipoteichoic acid synthases (3 genes), GroEL and Clp stress protein genes (10 genes), folate metabolism genes (11 genes), lactose metabolism genes (18 genes), peptidases (36 genes), and others. 

Novelty: The complete genome of the starter culture of the 'Narine' dairy product, which has been used as a prophylactic nutritional supplement for newborns in the Soviet Union since the 1960s, has been characterized for the first time. The probiotic properties of the starter culture have been demonstrated.

Conclusion: Preliminary studies of the newly sequenced Lactobacillus helveticus genome demonstrate the excellent probiotic potential of the well-known “Narine” dairy product’s starter culture.

Keywords: Dairy product, “Narine”, Lactobacillus helveticus, whole bacterial genome, Oxford Nanopore Technologies, probiotic