Functional genomic analysis of the isolated potential probiotic
Lactobacillus delbrueckii
subsp.
indicus
TY-11 and its comparison with other
Lactobacillus delbrueckii
strains
Authors: Jakaria Al-Mujahidy Sk. Md. , Kryukov Kirill , Ikeo Kazuho , Saito Kei , Uddin Md. Ekhlas , Ibn Sina Abu Ali 
Published: May 2024

ABSTRACT

Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of
Lactobacillus delbrueckii
subsp.

indicus
TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as
Lactobacillus delbrueckii
subsp.
indicus,
whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies
indicus
which were deficient in the core genome of the most popular subsp.
bulgaricus
. During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against
Escherichia coli
ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of
Lactobacillus delbrueckii
subsp.
indicus
.

IMPORTANCE

This study aimed to conduct functional genomic analysis to uncover the probiotic potential of
Lactobacillus delbrueckii
subsp.
indicus
TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic
Lactobacillus delbrueckii
subsp.
indicus
TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of
Lactobacillus delbrueckii
subsp.
indicus
.