Question

You are studying bacterium that grows in a particular ecological niche . you cannot culture it in a particular ecological niche . you can not culture it in the laboratory , but you can isolate small quantities of cells that microscopic analysis indicates are not contaminated with other bacteria How will you obtain the ribosomal RNA gene sequence data to study the taxonomy of the bacterium. How will you determine the complete genome sequence of the bacterium?

Answer 1

PCR with primers to regions of ribosomal RNA genes that are conserved across a wide range of bacteria to amplify the corresponding sequences from the bacterium of interest could be used. If it appeared to be a single band in gel electrophoresis, i.e., the PCR product is sufficiently specific, and was in enough quantity, then the DNA sequence could be determined directly. If the product is not specific, the the PCR might need to be optimised, perhaps by adjusting the concentration of magnesium ions, increasing the annealing temperature or using touchdown PCR. If very little product is obtained in the PCR, then cloning it might be needed before sequencing.