Sequencing DNA for Metagenomics

If someone brought you an odd piece of electronic hardware and you wanted to identify it, you’d probably look for markings on the outside first. If that didn’t work out, you might look under the cover and read some markings on the board or key components. However, in a tough case, you might dump the firmware and try to guess what the device is or what it does by examining the code that makes it run. That’s kind of what [Ciro] did. Wanting to determine the bacteria in a water sample led to using relatively inexpensive DNA sequencing hardware to look at the DNA present in the samples. This would have been a huge undertaking for a well-funded lab just a few short years ago. Now it just takes a USB device and some software.

Of course, inexpensive is in the eye of the beholder. The micropore sequencer costs about $500 and has a one-time use consumable cost of about $500, although that’s enough to process about 10 human genomes. The technology depends on using a small pore only large enough to pass one strand of DNA at a time. Blocks of nucelotides cause different amounts of electrical current to flow through the pore.

A lot of blood cell counters work in a similar fashion, but have an easier mechanism as they look for the tiny aperture’s partial blockage. Determining which DNA components are passing through the pore requires very precise measurements.

Of course, such a thing is hardly plug and play. First, the water samples needed reduction using several filtration and separation techniques. Then a polymerase chain reaction clipped the part of the DNA that would allow for the identification of unique bacteria types. Truly, the work in concentrating the DNA samples seemed to dwarf the actual sequencing.

Honestly, we aren’t as knowledgeable about DNA science as we’d like to be, but we were impressed at the results you could get for less than you’d spend on a big PC. Polymerase chain reaction technology has become cheap and simple, maybe this is the next frontier on biohacking. We’ve looked at how you can get started with PCR several times.