16S rRNA as an applied tool in the molecular characterization of genera and species of bacteria

Abstract

Bacterial identification is carried out by conventional methods based on phenotypic characteristics, since their implementation and costs are more easily accessible. However, molecular identification allows us to know the true identity of the genus and species. The molecular identification of 24 bacterial strains preserved in the Strain Bank of the University Francisco de Paula Santander, Campos Eliseos Experimental Center, identified under macroscopic and microscopic phenotypic criteria, was carried out. Initially, the strains preserved in saline solution were reactivated and characterized macro- and microscopically, then DNA extraction was performed and PCR was done to amplify the 16S rRNA region allowing access to the DNA sequence of interest; the samples were sent to be sequenced and through bioinformatic tools the identity of each bacterium was known. The strains: BLB003, BLB009, BLB011, BLB012, BLB014, BLB016, BLB018, BLB022, BLB023, BLB024, BLB033, were identified as Bacillus cereus; BLB010 as Bacillus thurigiensis; while BLB030, BLB031, BLB032, as Bacillus pumilus; BLB020 as Bacillus amyloliquefaciens; BLB001, BLB004, BLB007, and BLB037, formed the group of Bacillus subtilis; and it is possible that there are divergent ramifications between species of Bacillus in phylogenetic trees. Another grouping that was observed in the phylogenetic tree are the strains BLB019 and BLB029 that correspond to Achromobacter xylosoxidans and Alcaligenes faecalis respectively. Also another group BLB013 and BLB017, were identified as Stenotrophomonas maltophilia. It is important to take into account that sometimes 16S rRNA presents a low discrimination capacity for some genera and species due to recent divergences, it is necessary to complement the identification with the study of other genes.

Molecular Characterization of Native Strains of Bacillus spp. in rhizospheric Soil in Three Regions of Peru

“…Amplification was performed by polymerase chain reaction (PCR) [11] using 2 μl of the DNA sample with the DreamTaq PCR Master Mix kit (2X) and the 16S rRNA 27 F primers (5 ' AGA GTT TGA TCM TGG CTC AG 3') and 1525 R (5' AAG GAG GTG WTC CAR CC 3') [12]. For a negative control, a mix without sample was used.…”