Whole-Genome Shotgun Sequencing of an Indian-Origin Lactobacillus helveticus Strain, MTCC 5463, with Probiotic Potential

Abstract

Lactobacillus helveticus MTCC 5463 was isolated from a vaginal swab from a healthy adult female. The strain exhibited potential probiotic properties, with their beneficial role in the gastrointestinal tract and their ability to reduce cholesterol and stimulate immunity. We sequenced the whole genome and compared it with the published genome sequence of Lactobacillus helveticus DPC4571.Lactobacillus helveticus is present in fermented foods and is also used as a probiotic (4,10,12). Researchers have evaluated the effect of L. helveticus against diseases such as cancer and intestinal inflammation. Milk fermented with L. helveticus R389 delayed breast tumor growth by decreasing interleukin-6 (IL-6) and increasing IL-10 in serum, mammary glands, and tumor-infiltrating immune cells (5). Lactobacillus helveticus strains are normally isolated from milk products and intestinal microflora (6,14). The L. helveticus MTCC 5463 strain was originally isolated from the vaginal tract of a healthy adult female in India at Anand Agricultural University (9). The L. helveticus MTCC 5463 strain, earlier known as Lactobacillus acidophilus V3 (based on biochemical characteristics) was able to grow in the presence of 0.3% sodium taurocholate, deconjugate bile acids, and reduce cholesterol in vitro (1). The strain exhibited significant antimicrobial activity against Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica serovar Typhi, and Escherichia coli (7). The strain produced extracellular polysaccharide and was able to adhere to cells of the human carcinoma cell line HT29. A hypocholesterolemic effect of L. helveticus MTCC 5463 was reported in human subjects with different cholesterol levels (2). The strain has also shown positive immunomodulating effects in a chick model (13).The whole-genome sequencing of L. helveticus MTCC 5463 was performed using GS-FLX Titanium reagents (11). The data generated from the genomic library contained 119,569 reads, and assembly generated a 1,911,350-bp single chromosome. The genome annotation and comparative analysis of the genome were done with the published genome of strain DPC4571 (3). The genomic sequence of L. helveticus MTCC 5463 was somewhat smaller than those of L. helveticus DPC4571 (2.08 Mb) and L. helveticus H10 (2.14 Mb). In total, 2,046 coding sequence (CDS) regions and 71 RNA genes were reported. Of the 71 RNA genes, 59 coded for tRNA, 8 for rRNA, and 4 for 5S RNA. The CDS regions were slightly fewer than in L. helveticus H10 (2,049) and L. helveticus DPC4571 (2,238). Metabolic reconstruction subsystems were assembled to create a metabolic reaction network for L. helveticus MTCC 5463 and L. helveticus DPC4571.The subsystem analysis revealed a common subsystem structure between L. helveticus MTCC 5463 and L. helveticus DPC4571 for seven subsystems, viz., photosynthesis, iron acquisition and metabolism, motility and chemotaxis, secondary metabolism, stress response, nitrogen metabolism, and dormancy and sporulation. The considerable variation observed in the ...

Preparation, characterization and in vitro antioxidative potential of synbiotic fermented dairy products

“…lassi with honey and synbiotic whey with inulin and orange juice. The products were developed in our lab and contained probiotic strain L. helveticus MTCC 5463 (Prajapati et al 2011). Honey and inulin were incorporated as their prebiotic potential has been well established.…”

Effect of Probiotic Dietary Intervention on Calcium and Haematological Parameters in Geriatrics

“…Both the cultures were maintained by propagating in sterilized reconstituted skim milk (10% total solids) and stored at 5±2ºC. Lactobacillus helveticus MTCC 5463(earlier known as L. acidophilus V3) has been proven for its probiotic properties [8][9][10][11] and its whole genome is sequenced [12]. Streptococcus thermophilus MTCC 5460 is a curd isolate, fully characterized and studied extensively for its application in fermented milks preparation such as curd, lassi and yoghurt either alone or in combination with lactobacilli.…”

Feasibility of Genome-Wide Screening for Biosafety Assessment of Probiotics: A Case Study of Lactobacillus helveticus MTCC 5463

“…The culture maintenance and pyrosequencing methodology is explained in our previous publication [17,26]. Each DNA sample was subjected to pyrosequencing (454 Life Sciences technology) based on a high-throughput sequencer (GS-FLX, Roche) according to the manufacturer's instructions.…”

“…On comparing the stress-responsive genes of MTCC 5463 and a cheese starter strain, L. helveticus DPC 4571, gene sets specific to the gut and dairy niche could be identified [27]. Upon completion of genome sequencing of the strain in question [17], we attempted a bioinformatic analysis to provide additional insight into the genetic basis of its safety. The criteria for safety were delineated similarly to the QPS approach (defining the taxonomic unit, collecting the body of knowledge, safety concerns like the presence of antibiotic resistance, likelihood of gene transfer, tolerance to heavy metals, virulence determinants, and production of harmful metabolites).…”

“…L. helveticus strains, used largely in the cheese industry as a starter culture with high proteolytic activity, have been recently characterized at the genomic level [14][15][16][17][18]. Safety assessment can be greatly improvised using mechanistic omics-based data [19,20].…”