Scientists uncover brain’s “profound molecular changes” stemming from gut bacteria

A new study from the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, reveals gut bacteria can bring about “profound molecular changes” in the brain.

The new study, published in the journal Nature Structural and Molecular Biology, is the first to show that bacteria living in the gut can influence how proteins in the brain are modified by carbohydrates — a process called glycosylation.

“Glycosylation can affect how cells attach to each other (adhesion), how they move (motility), and even how they talk to one another (communication),” explains Clément Potel, first author of the study and a research scientist part of EMBL’s Savitski team.

“It is involved in the pathogenesis of several diseases, including cancer and neuronal disorders.”

The study was made possible by a new method the scientists developed — DQGlyco — which allows them to study glycosylation at a much higher scale and resolution than previous studies.

New pathway to measure glycosylation

Sugars, or carbohydrates, are among the body’s main sources of energy. However, in a process called glycosylation, the cell also uses sugars to chemically modify proteins, altering their functions.

However, glycosylation has traditionally been notoriously difficult to study, note the researchers. Only a small portion of proteins in the cell are glycosylated. Concentrating enough of them in a sample for studying — a process called “enriching” — tends to be laborious, expensive, and time-consuming.

“So far, it’s not been possible to do such studies on a systematic scale, in a quantitative fashion, and with high reproducibility,” says Mikhail Savitski, team leader, senior scientist, and head of the Proteomics Core Facility at EMBL Heidelberg.

“These are the challenges we managed to overcome with the new method.”

Bacteria living in the gut can influence how proteins in the brain are modified by carbohydrates — a process called glycosylation.Looking at microheterogeneity

DQGlyco uses easily available and low-cost laboratory materials, such as functionalized silica beads, to selectively enrich glycosylated proteins from biological samples, which can then be precisely identified and measured.

Applying the method to brain tissue samples from mice, the researchers could identify over 150,000 glycosylated forms of proteins (“proteoforms”), an increase of over 25-fold compared to previous studies.

The quantitative nature of the new method means that researchers can compare and measure differences between samples from different tissues, cell lines, species, etc. This also allows them to study the pattern of “microheterogeneity,” the phenomenon where the same part of a protein can be modified by many — sometimes hundreds of —different sugar groups.

One of the most common examples of microheterogeneity is human blood groups, where the presence of different sugar groups on proteins in red blood cells determines blood type (A, B, O, and AB). This plays a major role in deciding the success of blood transfusions from one individual to the other.

The new method allowed the team to identify such microheterogeneity across hundreds of protein sites.

“I think the widespread prevalence of microheterogeneity is something people had always assumed, but that had never been clearly demonstrated since you need to have enough coverage of glycosylated proteins to be able to make the statement,” says Mira Burtscher, another first author of the study and a Savitski Team PhD student.

Gut-brain axis

Given the method’s precision and power, the researchers decided to use it to address an outstanding biological question. In collaboration with Michael Zimmermann’s group at EMBL, they next tested whether the gut microbiome had any effect on the glycosylation signatures they had observed in the brain.

“It is known that gut microbiomes can affect neural functions, but the molecular details are largely unknown,” says Potel. “Glycosylation is implicated in many processes, such as neurotransmission and axon guidance, so we wanted to test if this was a mechanism by which gut bacteria influenced molecular pathways in the brain.”

The team is exploring whether the data can be used to inform predictions about glycosylation sites, especially in different species. For this, they have been using machine learning approaches such as AlphaFold — the AI-based tool for predicting protein structures recognized with the 2024 Nobel Prize in Chemistry.

Mice with gut bacteria showed different brain glycosylation patterns compared to bacteria-free mice, suggesting a gut-brain connection influencing neural functions.Interestingly, the team found that when compared to “germ-free mice” — mice grown in a sterile environment such that they completely lack any microbes in and on their body — mice that were colonized with various gut bacteria had different glycosylation patterns in the brain.

These altered patterns were particularly apparent in proteins known to be important in neural functions, such as cognitive processing and axon growth.

Deeper dive into glycosylation

Martin Garrido, a postdoc in the Savitski and Saez-Rodriguez groups at EMBL and another first author of the study, says that training the models on mouse data allows the scientists to start predicting what the variability of glycosylation sites in humans could be, for example.

“It could be very useful for people studying other organisms to help them identify glycosylation sites in their proteins of interest,” he notes.

The researchers are also working toward applying the new method to answer more fundamental biological questions and to understand the functional role glycosylation plays in cells.

In other recent gut science advances, Biohm Technologies launched its Longevity Gut Report functionality, an addition to the company’s microbiome test kit solution. The upgrade leverages AI and bioinformatics to provide deeper insights into how an individual’s gut microbiome may influence the aging process.

Meanwhile, Nimble Science is upgrading healthcare services with its SIMBA Capsule, which collects and preserves precise samples directly from the small intestine when swallowed to advance personalized microbiome research.