1.1 Preparing the genetic material

The process begins with collecting an environmental or biological sample. Different samples are collected in different ways. For example, water from a river is collected by submerging a sterile bottle below the water surface. Regardless of the sample and how it is collected, the important thing is to make sure that the genetic material is not degraded. Scientists usually add chemical preservatives that ‘fix’ DNA and RNA, or keep samples cold and away from heat or direct light.

The genetic material cannot be used as it is directly from a sample but must be isolated and cleaned from contaminants that can interfere with the steps required for metagenomics. These steps also help in making the genetic material more concentrated and easier to sequence later.

During extraction, the cells are opened up (lysed) to release their contents. The DNA and RNA are then purified using specialised chemicals, more often using commercially available extraction kits which come in a column format.

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Figure 2 The steps of DNA/RNA extraction from a sample using silica gel spin columns.

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An illustrated workflow shows DNA/RNA extraction using silica gel spin columns, arranged left to right as a sequence of microcentrifuge tubes with arrows between each step.

On the far left, a tube labelled ‘add lysis buffer to patient sample’ contains blue liquid with small, circular, orange particles. The next tube is labelled ‘lysate’ and shows a uniform orange solution. The following tube is labelled ‘bind DNA/RNA’, with orange liquid added to a white spin column insert. A tube labelled ‘DNA/RNA’ appears after centrifuge, showing dark, coiled DNA/RNA strands retained in the column and orange liquid in the lower tube. Next, a pipette dispenses blue liquid into the column labelled ‘wash buffer’, followed by another tube after centrifuge, with the dark DNA/RNA strands still visible in the column and blue liquid in the lower tube. A second pipette adds blue liquid labelled ‘elution buffer’, followed by another centrifuge step. On the far right, a final tube contains blue liquid with dark DNA/RNA strands at the bottom, with a double-helix icon below and text reading ‘ready to use purified DNA/RNA’.

Figure 2 The steps of DNA/RNA extraction from a sample using silica gel spin columns.

While in most cases scientists look for DNA, there are many viruses (like flu or the Ebola virus) which have a genome made of RNA. The sample extraction process is similar to DNA. However, RNA cannot be sequenced directly and must first be turned into DNA. This is accomplished using a particular chemical reaction called reverse transcription.

Now that the genetic material from the sample is ready, it can proceed for the next step.