Researchers from Russia have created visual profiles of bacteria that inhabit the gut microbiome of patients in intensive care units. Understanding these bacteria matters because some may carry traits associated with higher mortality risk when the immune system is weakened.
Looking ahead, scientists anticipate the possibility of precisely guiding the microbiome’s composition. Such control could be crucial for improving resilience in critically ill individuals.
Alexander Tyakht, head of the bioinformatics group at the Institute of Gene Biology of the Russian Academy of Sciences, noted that long stays in intensive care often correlate with disruptions in the gut microbiome. He explained that the bacterial community in the gut can include species that trigger infections or amplify death risk under weakened immunity. Consequently, researchers aim to identify which strains are present and what genes they carry to gauge their potential impact.
The gut microbiome influences multiple bodily systems, including digestive, immune, hormonal, and nervous systems, through interactions among hundreds of microbial species. When illness disrupts this balance, the condition can deteriorate further.
The study brought together experts from Moscow State University, the Institute of Genetic Biology at the Russian Academy of Sciences, Lomonosov Moscow State University, the Federal Research and Clinical Center for Resuscitation and Rehabilitation, St. Petersburg State University Center for Algorithmic Biotechnology, ITMO University, and the Research Center for Medical Genetics. The work involved two critically ill ICU patients as a preliminary test, during which metagenomic data from the microbiome were collected and analyzed for gene content. The reconstructed genomes included bacteria historically linked to human disease, such as Klebsiella, Enterococcus, and pathogenic Clostridia.
The researchers demonstrated how the Hi-C metagenomic method enables deeper insights into bacteria that heighten death risk for ICU patients. Although the sample size is small, the cases illustrate that patients often exhibit a gut microbial community reduced to far fewer species than is typical in a healthy gut, sometimes around a dozen instead of hundreds.
The approach allowed scientists to pinpoint gene clusters within each bacterium and to assign specific genes to their respective organisms with greater accuracy. With the genome as a map, better understanding emerges about how a given microbe can compromise health in individuals with diminished immunity.
Researchers believe that augmenting traditional metagenomics with genome-wide spatial information can expand knowledge about microbiome composition and function in both healthy individuals and those with various diseases. In the future, analyzing a large repository of genomes could pave the way for cheaper, faster diagnostic methods for infections that may be deployed directly in hospitals.
Beyond critical illness, the investigation hints at mechanisms underlying the onset and progression of conditions such as diabetes, cardiovascular diseases, and complications related to viral infections like COVID-19.
“Brushes” and “paints”
The study marks an early clinical application of Hi-C metagenomics, a technique that blends conventional metagenomic sequencing with three-dimensional genome information. This combination enables the generation of more complete and accurate bacterial genomes. By applying new graph-based algorithms, researchers could more reliably associate mobile genetic elements with the bacteria that harbor them—elements that often move between species and contribute to the spread of drug resistance and other important genes among pathogenic bacteria.
Future work with this method aims to link transferable genetic elements to their bacterial hosts more consistently, improving pathogen detection and characterization. Such progress could support targeted diagnostic approaches, including real-time PCR, to identify dangerous bacteria with greater speed and precision.
As the technique evolves, scientists are also applying it to study other microbiomes, including environmental and food-related communities, broadening its potential impact.
The Hi-C approach is ambitious and not without challenges; it has historically been used to map chromosome regions in multicellular organisms. Applying it to bacteria and complex microbial ecosystems requires careful adaptation, according to experts who emphasize that extracting meaningful conclusions from a microbial soup is a significant achievement in itself.
The research was published in a peer-reviewed journal and supported by national science funding bodies. The work highlights the ongoing effort to connect genomic structure with microbial function to better understand health and disease.