30,000 drops per second
Packing bacteria into drops helped find antibiotics in the bear's saliva
Daria Spasskaya, N+1
Russian biologists have developed a method for functional analysis of complex microbial communities using a high-performance microfluidic platform. The method allows to determine the composition of communities by multiplying individual cells inside drops of water-fat emulsion. In this way, you can search for producers of new antibiotics and determine the resistance of bacteria to them from any exotic sources. As an example of such an analysis, in an article published in the Proceedings of the National Academy of Sciences, researchers studied the microbiota from the oral cavity of a brown bear and found there a substance that suppresses the growth of methicillin-resistant Staphylococcus aureus.
Traditional microbiological methods of bacterial research imply the isolation of a pure (isolated) culture of a microorganism and further work with it. When studying microbial communities from different ecological niches, from human feces to Kamchatka hot springs, scientists often evaluate them by the total genome of all bacteria in the sample. Genomic analysis can be quite informative, but it does not always allow us to fully assess the functional capabilities of microorganisms, for example, the ability to produce new antibiotics or resistance to them.
Employees of Alexander Gabibov's laboratory at the Moscow Institute of Bioorganic Chemistry named after Academicians Shemyakin and Ovchinnikov, in particular, Stanislav Terekhov, Ilya Osterman and Ivan Smirnov, together with colleagues from Skoltech, including Konstantin Severinov, have developed a method that allows analyzing the properties of individual cells using a microfluidic platform. The method involves packing individual cells into droplets of water-fat emulsion, and subsequent high-performance sorting of droplets, for example, by fluorescence of reporter proteins. The sorting speed reaches 30 thousand drops per second, so in a short time you can "view" a huge number of bacteria from any exotic source and select cells with the desired properties. At the same time, cells can divide inside the droplets.
To demonstrate the capabilities of the platform, the authors analyzed the microbiota of the oral cavity of a wild Siberian brown bear. Scientists have set themselves the task of finding in the saliva of a bear producers of antibiotics active against methicillin-resistant Staphylococcus aureus – the causative agent of dangerous nosocomial infections. To do this, the cells of microorganisms from the bear's mouth were packed into droplets together with staphylococcus cells that carried the green fluorescent protein gene. Then, using a sorter, scientists selected those cells where staphylococcus did not multiply, and determined what kind of microorganism was there. It turned out that the strain of Bacillus pumilus, a producer of the antibiotic amikumacin A, has the greatest antimicrobial activity in bear saliva.
This antibiotic was already known to scientists, but an additional analysis of the genome of bacilli from the bear revealed a new gene of resistance to it – AmiN kinase, which phosphorylates the antibiotic and makes it inactive.
Stanislav S. Terekhov et al.,
PNAS 2018 (with changes)
At the next stage of the work, the researchers used their platform to test all participants of the microbial community from the bear's mouth for resistance to amicumacin, as well as, for comparison, microbes from the feces of a healthy person and a person with intestinal inflammation. To do this, individual cells were packed into drops together with different concentrations of the antibiotic, or without it. Sensitivity to the substance was determined by staining for the presence of living cells. After incubation with an antibiotic, the contents of the droplets were sequenced and determined which microorganisms are in the community at all, and which of them are sensitive to the antibiotic. It turned out that amikumacin is active mainly against gram-positive microorganisms, and in addition, it acts against groups of microbes characteristic of a person with intestinal inflammation. Scientists have suggested that the amicumacin-producing bacillus may become a component of probiotics to prevent intestinal diseases.
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