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New Tool Could Help Scientists Grow the 99% of Bacteria Currently Ungrowable in the Lab

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Posted October 21, 2015

One of the major problems facing the science of basic microbiology today is the overwhelmingly specific feeding habits of many bacteria, requiring long and complex recipes of various nutrients, ions and vitamins. As a result, despite the work done over the past century and a half, scientists are still unable to culture some 99% of bacteria, which constitute the so-called “bacterial dark matter” of which we known very little.

Around 99 percent of all bacteria on our planet are currently impossible to grow in the lab due to their peculiar feeding habits. If the new tool, developed by a team of researchers led by Matthew Oberhardt and Eytan Ruppin, proves as powerful as it’s thought to be, this hurdle might finally be overcome, opening the door to the study of a vast world of microorganisms that potentially harness useful compounds. Image credit: Bill Shrout via Wikimedia.org, CC0 Public Domain.

Around 99 percent of all bacteria on our planet are currently impossible to grow in the lab due to their peculiar feeding habits. If the new tool, developed by a team of researchers led by Matthew Oberhardt and Eytan Ruppin, proves as powerful as it’s thought to be, this hurdle might finally be overcome, opening the door to the study of a vast world of microorganisms that potentially harness useful compounds. Image credit: Bill Shrout via Wikimedia.org, CC0 Public Domain.

Thanks to the efforts of molecular biologists, most of the bacteria present in any single ocean water or soil sample can be identified by sequencing a particular gene, called 16S rDNA, present in all bacterial species. Useful as it is, however, it still doesn’t help scientists grow these microorganisms in the lab.

But now, thanks to an international team of researchers led by Matthew Oberhardt and Eytan Ruppin from Tel Aviv University, that may be about to change. If successful, their research could represent nothing short of a revolution in basic microbiology.

Working together, the team has developed a massive relational database of 18,049 different microbes, 3,335 media recipes and 20,824 organism-media pairings, dubbed Known Media Database (or KOMODO), as well as an algorithm – called GROWREC – that predicts the breeding requirements of a bacterium using its 16S rDNA sequence and data pertaining to the evolutionary relatedness of known microorganisms.

To see just how accurate their tool is, the researchers tested how 61 different bacteria grew in their projected culture conditions. Almost half (26) of these were confirmed by existing literature, 29 were confirmed when the authors grew the bacteria in their own labs, and only 6 failed to grow altogether.

Even though there haven’t yet been any attempts at growing any of the “ungrowable” species, the authors believe they have demonstrated the usefulness of their tool, which they hope to prove beyond reasonable doubt as soon as more data becomes available.

For now, GROWREC has been made available as an online tool for microbiologists to use.

If it’s actually as powerful as they believe it to be, these findings could have an enormous impact not only on basic microbiology, but biotechnology as well. A number of the literally millions of as-yet-uncultured microbes on our planet likely produce novel antibiotics or possess metabolic pathways useful for everything from creating biofuels and bioplastics to degrading toxic compounds. And tapping into the potential of these microorganisms usually starts by growing them in the lab.

The study was published on October 13th in the journal Nature Communications.

Sources: study, realclearscience.com, natureasia.com.

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