Genome Wide Analysis for Rapid Identification of Vibrio Species

Abstract

The highly conserved 16S rRNA (rrs) gene is generally used for bacterial identification. In organisms possessing multiple copies of rrs, high intra-genomic heterogeneity does not allow easy distinction among different species. In order to identify Vibrio species, a wide range of genes have been employed. There is an urgent requirement of a consensus gene, which can be used as biomarker for rapid identification. Eight sequenced genomes of Vibrio species were screened for selecting genes which were common among all the genomes. Out of 108 common genes, 24 genes of sizes varying from 0.11 to 3.94 kb were subjected to in silico digestion with 10 type II restriction endonucleases (RE). A few unique genes-dapF, fadA, hisD, ilvH, lpxC, recF, recR, rph and ruvB in combination with certain REs provided unique digestion patterns, which can be used as biomarkers. This protocol can be exploited for rapid diagnosis of Vibrio species.

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

“…However, in cases where bacterial genomes contain multiple copies of rrs, such as in Clostridium, Staphylococcus, Streptococcus, Vibrio, and Yersinia species, a high level of heterogeneity is seen. It is difficult to identify these bacterial species on the basis of their rrs gene alone [5][6][7][8][9][10]. The same problem has been faced in the case of Lactobacillus as well.…”

“…Another limitation generally encountered in the usage of rrs is in the case of organisms which harbour it in multiple copies: Clostridium, Yersinia, Vibrio, Staphylococcus, Streptococcus, etc. Here, high intragenomic heterogeneity leads to mis-identification and even overestimation of bacterial populations [5][6][7][8][9][10].…”

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

“…A total of 10 Type II REs were considered for digestion on the basis of our previous works [18][19][20]. The following REs were used: (1) 4 base cutters AluI (AG'CT), BfaI (C'TA_G), BfuCI (_GATC'), CviAII (C_AT'G), HpyCH4V (TG'CA), RsaI (GT'AC), TaqI (T_CG'A), Tru9I (T_TA'A), and (2) 6 base cutters HaeI (WGG'CCW), Hin1I (GR_CG'YC).…”

“…net/) was used to get RE digestion patterns of the 27 common gene sequences (Table S2). Data matrices of REs producing 5-15 fragments were taken into consideration for further analysis [18][19][20].…”

“…These features enable easy identification of organisms up to the species level. However, rrs gene does not prove helpful in the following scenarios: (1) in phylogenetically very closely related strains, which differ in less than 1 % nts along their length, and (2) in strains with multiple copies of this gene in each genome [17][18][19][20]. An obvious solution to circumvent this problem is to use other HKGs [13,21].…”