Russian scientists have compiled “portraits” of bacteria living in the intestinal flora of patients in intensive care units. Information about these bacteria is important because they may contain those that potentially increase the risk of death.
In the future, scientists believe it will be possible to precisely control the composition of their microbiome, which is severe and will help them survive.
“In patients who have been in intensive care for a long time, there are serious violations in the composition of the microbiome,” said Alexander Tyakht, head of the bioinformatics group at the Institute of Gene Biology of the Russian Academy of Sciences. , told socialbites.ca. “The bacterial community living in their gut may contain species that can cause infections and increase the risk of death when their immune systems are weakened. Therefore, it is important to investigate which strains patients have and what specific genes they carry. ability).”
The microbial community (microbiome) of the human gut is involved in the regulation of various organ systems: digestive, immune, hormonal, nervous and others. This is achieved by the coordinated interaction of hundreds of species of microorganisms. When a person gets sick, the balance of the microbiome is disrupted, which can cause the condition to worsen.
The study involved experts from Moscow State University, Institute of Genetic Biology of the Russian Academy of Sciences. Lomonosov, Federal Research and Clinical Center for Resuscitation and Rehabilitation, St. Petersburg State University Center for Algorithmic Biotechnology, ITMO University and Research Center for Medical Genetics. Academician NP Bochkov.
As a “trial balloon”, the microbiomes of two critically ill patients in the ICU were examined. From the metagenomes—data from DNA sequencing of the microbiome—several dozen bacterial genomes were collected and analyzed for gene compositions. Reconstructed include bacterial genomes associated with human disease, such as Klebsiella, Enterococcus, and pathogenic Clostridia.
“We showed how the Hi-C metagenomic method allows us to study at a deeper level the bacteria that increase the risk of death in a person in intensive care,” Tyaht explains. – Although the sample is small, the examples are illustrative – both patients had a significantly depleted gut community, each without the hundreds of bacterial species in their guts as usual in a healthy person, but about a dozen.
Our approach made it possible to identify the gene cluster in each of these bacteria, including more accurately assigning specific genes to a particular bacterium. Knowing the genome allows you to better understand how a particular microorganism poses a threat to the health of a person with reduced immunity.
We believe that complementing traditional metagenomics with genome spatial shape (Hi-C) technology will allow scientists to learn more about the composition and functions of the microbiome in both healthy people and patients with various diseases. In the future, based on the analysis of a large collection of genomes, it will be possible to create cheaper, faster methods for diagnosing infections that will be used directly in the hospital.”
According to the scientists, an in-depth study of the microbiome will also provide a better understanding of the mechanisms of onset and development of diabetes mellitus, cardiovascular diseases and complications of COVID-19.
“Brushes” and “paints”
In this study, Russian scientists, one of the first in the world, conducted a study with the clinical application of Hi-C metagenomics. This is a specialized method that is a combination of conventional metagenomic DNA sequencing and “three-dimensional genome” technology.
Hi-C metagenomics allows researchers to obtain more complete and accurate bacterial genomes. Using the new graphing algorithms, the researchers were able to more accurately attribute mobile genetic elements to a particular bacterium – fragments of DNA that are often transferred between different bacterial species and contribute to the spread of drug resistance genes and other important genes among pathogenic bacteria.
Further application of the method will not only allow us to better understand the genomes of the bacteria causing the infection, but will also better associate the transferable genetic elements with the bacteria to which they belong.
Such an atlas would allow the development of targeted methods for the detection of dangerous bacteria, for example based on approaches such as real-time PCR.
Meanwhile, scientists are more widely applying the method to analyze other microbiomes from the environment and food.
“The Hi-C method itself is quite complex and is often used to identify chromosome regions for metazoans. It’s a pretty bold approach to apply it to bacteria and complex bacterial systems that are microbiomes,” says Pavel Volchkov, head of the MIPT Genomic Engineering Laboratory. “It’s comparable to the analysis of bacteria – just instead of them. If scientists can extract individual bacterial components from such a “soup” and draw useful conclusions from that analysis, that’s a serious feat,” he said. “Otherwise, it’s just implementing the method itself.”
Scientific article published in Frontiers in Microbiology. The work was supported by the Russian Science Foundation and the Russian Ministry of Education and Science.