A new database of thousands of microbial species and culturing conditions enables the prediction of appropriate culture media recipes for the growth of new microbes, reports an article published in Nature Communications. The database will facilitate research into the biology and biotechnology-related potential of these new microorganisms. Most microbes that live in the environment or in our bodies cannot yet be grown in the lab, constituting the so-called ‘microbial dark matter’ of which we know very little. Matthew Oberhardt and colleagues extracted recipes with which to prepare media for microbes to grow on from a large repository, to build a database dubbed KOMODO. The database includes information from 18,049 different microbes and 3,335 media recipes, allowing a systematic study of principles determining microbial growth in the lab.
The researchers found that using specific trace metals and vitamins in the media is often crucial for growing new microbes. They also validated the common, yet untested, assumption that closely related microbes tend to grow in similar media. Finally, they developed an online tool (GROWREC) that can predict appropriate media recipes found in KOMODO for new microbes. GROWREC uses available knowledge on the evolutionary relatedness of known microorganisms, together with a piece of the microbe’s genetic information (16S rDNA sequence) that can be readily obtained from any environmental or clinical sample containing the microbe of interest.
The database and online tool developed by the authors will be useful for growing and studying in the lab many microorganisms that remain uncultivated up to now. The researchers see their work as a first step towards the goal of a more predictive science of microbial nutrition.