University of Vienna: Watch intestinal bacteria eat – and learn from it for medicine

Microbiomes shape human and environmental health. How they do this is revealed by an analysis of the functions that individual microbes perform in these communities of microorganisms. Scientists from the University of Vienna, in collaboration with photonics scientists from the University of Boston, have developed a microscopy method with which they can identify bacterial cells in milliseconds and at the same time determine their metabolic activity. Your method for functional analysis is 100 to 1,000 times faster than previously available approaches. It enabled the researchers to gain new insights into the breakdown of mucus, an essential component of the intestinal mucosa, by the human intestinal microbiome. The findings may help explain some people’s susceptibility to inflammatory bowel disease.

Hundreds of different types of bacteria thrive in the human gut. They are part of the gut microbiome and their diverse functions affect human health. One of the most important tasks of microbiome research is therefore to decode the functions of our microbial co-inhabitants and to research how these can be specifically influenced. Since bacteria in the laboratory in pure culture often behave completely differently than in complex communities, the direct functional analysis, which records the functions of individual microbes in complex microbiome samples and thus in their natural habitat, is particularly meaningful.

The direct functional analysis makes bacteria and the feeding behavior of individual bacterial cells visible using chemical imaging. For this purpose, the microbiome sample is mixed with a substrate that is labeled with a stable (non-radioactive) isotope. Microbes that metabolize this substrate are tagged with the stable isotope along the “you are what you eat” principle. Their feeding behavior can thus be analyzed via the isotope content of individual bacterial cells. At the same time, different types of bacteria are marked in color with the help of fluorescently labeled gene probes, which attach themselves to the ribosomes of very specific bacteria.

Due to the large amount of time required for the measurement itself, researchers have so far only ever been able to examine relatively few cells per sample, even with the most modern analysis methods. “This is problematic because microbiome samples contain hundreds of bacterial species in different frequencies. The analyzes available so far were therefore only suitable for the dominant microbiome members. Many more were overlooked,” explains Michael Wagner, microbiologist and deputy head of the Center for Microbiology and Environmental Systems Science . He initiated the collaboration with the imaging experts from the USA. By combining stimulated Raman scattering microscopy (SRS) and two-photon microscopy, the international research team reduced the measurement time required for the identification and determination of the isotope content to milliseconds and thus by 2 to 3 orders of magnitude compared to conventional Raman spectroscopy. “With this high-speed method, we were able to determine the isotope content of more than 30,000 bacterial cells from human intestinal samples after incubation with various sugars that occur in the intestinal mucus in a very short time,” reports Wagner.

“To our surprise, it turned out that certain clostridia – a type of intestinal bacteria – play an important and previously unknown role in the breakdown of the mucosal sugar fucose,” adds Fátima Pereira, co-first author of the study and Senior PostDoc in the Vienna research group. The finding is remarkable as fucose represents the interface between the mucosa and the gut microbiome. However, every fifth person cannot perform fucosylation of the intestinal mucus and shows an increased risk of inflammatory bowel diseases. Current research projects are attempting, among other things, to use probiotics in a targeted manner in order to reduce the risk of these people becoming ill. In order for this to be successful, it is important to understand which microbes benefit from fucose degradation in the gut and which individuals may be missing.

In a current research project, the research team from Vienna and Boston is now using the newly developed method to investigate how drugs that are commonly prescribed to treat Parkinson’s disease and schizophrenia affect the human gut microbiome. “However, the use of this new method is not limited to human microbiomes, but also opens up completely new possibilities in the research of environmental microbiomes,” explains Michael Wagner. Due to this promising potential, the Center for Microbiology and Environmental Systems Science has purchased an SRS fluorescence microscopy microscope.