National Institute of Advanced Industrial Science and Technology (AIST)
Phenotypic screening brings unculturable microbes out of a million droplets
The challenge in searching for microbes is shifting from finding bacteria in nature to selecting large numbers of candidates based on what they actually do. A research group including Nagaoka University of Technology has developed a phenotypic screening system that searches for and collects useful microbes at the scale of one million droplets. If the technology works reliably, ingredients for bottles could be made at a detergent factory from chemical feedstocks produced by selected microbes in a fermenter.
Many microbes that perform useful functions are alive in nature but cannot be grown in a test tube. Researchers can work only with a limited number of cultured strains, and finding microbes that produce chemicals from carbon feedstocks takes time and money because candidates must be cultured and examined one at a time. It is still not easy to take microbes from nature and turn them into candidates that can be used in factories.
Selecting invisible microbes by what they do
To grow a microbe, researchers must recreate in the laboratory the conditions in which it lives in nature. For many microbes, that is not possible. Reading a DNA sequence can reveal a microbe’s genetic information, but it cannot directly show whether the microbe will actually produce a desired substance from a particular feedstock.
That is where droplet microfluidics comes in. It is a method that treats tiny droplets as small reaction vessels, one by one, and tests many cells and conditions at the same time. Did the microbe grow? Did its color change? Did it emit light? Did it produce the desired product? Selecting candidates based on such actual functions is called phenotypic screening.
Screening one million droplets in sequence
A joint research group from Nagaoka University of Technology, the National Institute of Advanced Industrial Science and Technology (AIST), Hiroshima University, On-chip Biotechnologies, and Nikon Solutions says it has developed a technology that makes uncultured and difficult-to-culture microbes culturable, then searches for and collects droplets containing microbes with useful functions.
At the center of the technology is the “Million Screening Technology,” which searches at the scale of one million droplets. First, many droplets are screened; next, their condition is examined using images; finally, promising droplets are collected. By turning primary screening, image-based secondary screening, and collection into a device that operates as a single sequence of steps, the technology makes it possible to move from searching by manually testing a small number of cultured strains one after another to searching for more microbes based on what they actually do.
Until they become microbes that can be used in factories
If this process can be used reproducibly, microbes that were difficult to select based only on genetic information can become candidates based on their actual functions. For researchers and biotech companies that want to use uncultured microbes as materials, it opens up a broader path to biological resources that cannot be obtained from collections of cultured strains alone. It should also become easier to automate the primary screening of microbes that make chemicals, materials, and feedstocks from carbon resources.
For example, at a detergent factory, one can imagine making ingredients for bottles from chemical feedstocks produced in a fermenter by selected microbes, rather than relying only on petroleum-derived feedstocks. To make that possible, however, the collected microbes must work reliably even in large-scale culture tanks and meet requirements for manufacturing costs and safety. Optimizing culture conditions and moving to mass-production processes will also be necessary; finding a microbe does not turn it into a product immediately.