Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

Abstract

Bacteria possessing multiple copies of 16S rRNA (rrs) gene demonstrate high intragenomic heterogeneity. It hinders clear distinction at species level and even leads to overestimation of the bacterial diversity. Fifty completely sequenced genomes belonging to 19 species of Lactobacillus species were found to possess 4-9 copies of rrs each. Multiple sequence alignment of 268 rrs genes from all the 19 species could be classified into 20 groups. Lactobacillus sanfranciscensis TMW 1.1304 was the only species where all the 7 copies of rrs were exactly similar and thus formed a distinct group. In order to circumvent the problem of high heterogeneity arising due to multiple copies of rrs, 19 additional genes (732-3645 nucleotides in size) common to Lactobacillus genomes, were selected and digested with 10 Type II restriction endonucleases (RE), under in silico conditions. The following unique gene-RE combinations: recA (1098 nts)-HpyCH4 V, CviAII, BfuCI and RsaI were found to be useful in identifying 29 strains representing 17 species. Digestion patterns of genes-ruvB (1020 nts), dnaA (1368 nts), purA (1290 nts), dnaJ (1140 nts), and gyrB (1944 nts) in combination with REs-AluI, BfuCI, CviAI, Taq1, and Tru9I allowed clear identification of an additional 14 strains belonging to 8 species. Digestion pattern of genes recA, ruvB, dnaA, purA, dnaJ and gyrB can be used as biomarkers for identifying different species of Lactobacillus.

Fish Gut Microbiome: Current Approaches and Future Perspectives

“…The emerging concept of ''forward microbiomics'' that involves manipulating the gut flora to promote fish health finds important applications in aquaculture. Several Lactobacillus species have been identified as probiotics in fish and other animals including humans [105,106]. However, their potential needs to be fully explored.…”

Gene Specific Impedimetric Bacterial DNA Sensor for Rheumatic Heart Disease

“…The similar epitopes of bacteria and host (molecular mimicry), is the major cause of triggering the disease. Kalia and his groups published several papers on genome wide approach for identification of several unique biomarkers for identifying several species (strains) of Streptococcus, Staphylococcus, Yersinia, Vibrio, Clostridium, Lactobacillus and many other bacterial pathogens [6][7][8][9][10][11][12]. Current methods of detection of S. pyogenes infection are bacterial culture test, rapid antigen detection test (RADT), biochemical test, serological test, C-reactive protein (CRP) test, ESR, PCR, bacitracin susceptibility and Phadebact test [13][14][15].…”