{c}
{numbered}
{scope}
{tag=DNA sequencing}
{tag=Metagenomics}
{tag=Polymerase chain reaction}
{tag=articles}

This article gives an idea of how this kind of biological experiment feels like to a <software engineer> who has never done any <biology> like <Ciro Santilli>.


How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it

{wiki}

Experiments that involve sequencing bulk DNA found in a sample to determine what species are present, as opposed to sequencing just a single specific specimen. Examples of samples that are often used:
* river water to determine which bacteria are present, notably to determine if the water is free of dangerous bacteria. A concrete example is shown at: <oxford nanopore river bacteria>{full}.
* sea water biodiversity: http://ocean-microbiome.embl.de/companion.html
* <food>, including searching for desirable microorganisms such as in cheese or bread <yeast>
* <poo>, e.g. to study how the human microbiome influences health. There are companies actively working on this, e.g.: https://www.microbiotica.com/

One related application which most people would not consider metagenomics, is that of finding https://en.wikipedia.org/wiki/Circulating_tumor_DNA[circulating tumor DNA] in blood to detect tumors.


Ciro Santilli @cirosantilli 37

 Tagged: Metagenomics