How to analyse a DNA sequence

In Step 2.5, you watched Harriet demonstrate how to isolate bacteria from a sample, make a pure bacterial culture and perform a Gram stain.

When we were watching Harriet demonstrate these techniques, we started to identify the species of soil bacteria by observing some of its characteristic traits, including: the appearance of the colonies on agar, which we refer to as the colony morphology; and the appearance of the Gram stained cells under the microscope, which we refer to as the cellular morphology. These two features of our bacterial soil isolate are part of a set of observable traits that we refer to as a phenotype.

In order to identify the soil bacteria, we could continue working with the pure culture in the laboratory and perform a variety of tests to determine other phenotypic traits (eg oxygen requirement, ability to ferment different sugars, production of antibiotics or toxins, motility). You will learn more about some of these tests and how they can be used to identify microbes later in the course.

A microbe’s phenotype is largely determined by its genetic material, and so an alternative strategy is to use molecular techniques such as PCR and DNA sequencing to analyse the microbial genome directly. In this video Dr Soon Gweon, Lecturer in Bioinformatics for Genomics, explains how computer software can be used to analyse DNA sequencing results to identify microbes and detect genetic mutations, including single base changes (called single nucleotide polymorphisms, SNPs).

In the next Step, you’ll have an opportunity to identify a different soil isolate using the BLAST software. Don’t forget to mark this one as complete before you move on.