IChip: high-throughput technology to grow soil bacteria brings a new antibiotic

Soil bacterium for blog updated

Imagine the world in 30-40 years, when most people die not from cancer or heart disease, but from trivial infections caused by drug-resistant strains of superbugs? Up to now, this vision has seemed quite likely. The speed at which pathogens evolve to acquire resistance is so much greater than the speed with which we could develop new antibiotics. However, isolation Chip (iChip) is a game-changing, high-throughput technology that tremendously speeds up a process of antibiotic discovery. It works by identifying antibiotics which occur naturally and may have low susceptibility to development of resistance. Therefore, instead of screening libraries of synthetic molecules for their antimicrobial potential, scientists chose to come back to nature and to use bacteria-rich soil as a starting material for their hunt.

Yes, soil is seemingly teeming with potentially beneficial bacteria that naturally produce potent, antimicrobial compounds, as a weapon against their rivals. Unfortunately, soil remains an untapped source of potential antibiotics because 99% of its microorganisms die soon after being brought to the lab and subjected to conventional in vitro culture techniques. A solution to this hurdle is to first pre-cultivate soil bacteria directly in situ in the soil, with free access to essential nutrients and growth factors; this is what iChIP is doing. This pre-step enables the biologists to obtain a first bacteria colony, which can be then transferred to the lab to multiply on traditional petri dishes, providing scientists with enough material for a screening for interesting antimicrobial metabolites.

The design of the iChiP is quite simple – it is an assembly of several plastic plates containing nearly 400 through holes; when a diluted soil sample is applied onto them each hole traps only a single bacterium. A plate is then wrapped from two sides by a semi-permeable membrane, which creates a miniature diffusion chamber for each individual cell, allowing passage of essential nutrients from soil. Thanks to this device, not 1% but 50% of the microbes in the soil sample can be further grown in the lab and screened for potential antibiotics. So far, iChip has yielded a new antibiotic, teixobactin; some of the most persistent microorganisms seem unable to develop resistance to this (at least in the controlled laboratory setting). So simple, yet so ingenious!

Articles:

http://www.ncbi.nlm.nih.gov/pubmed/?term=20173072

http://www.ncbi.nlm.nih.gov/pubmed/?term=25561178

Picture of iCHIP:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849220/figure/f1/

http://www.brockpress.com/2015/01/oddly-enough-antibiotics-gain-new-life-in-the-21st-century-236/

 

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Ewa Soltysinska

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