A growing body of scientific literature shows that the gut microbiome can influence the brain in myriad ways. Now, research conducted on mice reveals that a metabolite released from gut bacteria directly binds to a gene in distant microglia and contributes to cognitive decline. The study, published on June 1 in Cell Host & Microbe finds that blocking the metabolite isoamylamine with an oligonucleotide reverses memory loss in the mice. 

“The authors provide an elegant demonstration of the mechanisms by which [the] microbiome-bacteriophage-metabolite axis is dysregulated during aging,” Slavica Krantic, a neuroinflammation researcher at St. Antoine’s Research Center of Sorbonne University in Paris who was not involved in the study, writes in an email to The Scientist. “Maybe most excitingly, this paper brings a proof-of-concept for oligonucleotide-based therapy of cognitive dysfunctions.”  

The metabolite isoamylamine (IAA) is released into the gut by bacteria of the Ruminococcaceae family. The study finds that these bacteria, and therefore IAA, become more prevalent in the guts of both healthy humans and mice as they age. The researchers showed that adding IAA to microglia cells isolated from young, healthy mice promoted the production of so-called apoptotic bodies, suggesting that IAA triggers cell death. 

The researchers initially became curious about IAA because it can pass through the blood-brain barrier and its induction in the guts of older mice correlates with the expression of a gene they were interested in called S100A8, one of several genes that allow microglia to sense and respond to changes in the brains of aging mice. Study coauthor Huang-Ge Zhang, an immunologist at the University of Louisville, explains that the group ran into a roadblock: tagging a small molecule like IAA in the same way they would relatively large proteins would likely disrupt its ability to interact with DNA. To see whether and how IAA directly interacts with S100A8, the researchers had to develop a new technique to screen for the interaction between small metabolites and DNA, Zhang says.

The researchers decided to exploit a simple effect: a single strand of DNA will travel differently during electrophoresis, a process that separates molecules based on size and electrical charge, when bound to a metabolite. By looking for such electrophoretic mobility shifts, researchers can identify “what type of metabolic product binds to your DNA,” says Zhang—a technique the researchers termed single-strand gel shift (SSGS). 

After incubating the gene’s promoter region and the metabolite together, the researchers found that IAA binds to the promoter region of S100A8. Looking closer, Zhang and colleagues found that the hairpin structure of S100A8’s promoter region unwound when bound to IAA, which allows the transcription factor p53 to reach the promoter and induce expression the gene. 

See “Bacteria-Infecting Viruses in Gut Microbiome Linked to Cognition

To understand what this interaction between IAA and S100A8 means functionally, the researchers fed IAA to young mice. Then they ran the mice through three behavioral and cognitive assays. Young mice that had been fed IAA performed worse on the tasks, which included navigating mazes and recognizing objects, than did untreated young controls. The study authors suggest that microglial cell activation may impact the downstream function of neurons in direct or indirect ways, as IAA promoted neuronal loss and neuron death in the brains of young mice. Neuropathologist Thomas Blank of the University Clinic Freiburg in Germany, who was not in involved in the study, writes in an email to The Scientist that “the evidence strongly suggests that IAA is a factor in cognitive decline.” 

“The identification of age-related shifts in the gut microbiome in humans, which caused increases in a bacterial metabolite, isoamylamine, which could directly bind to genomic DNA in the brain of mice is really exciting,” Melanie Gareau, a researcher working on the microbiota-gut-brain axis at the University of California, Davis, who was not involved in the study, writes in an email to The Scientist.

See “Tinkering with Gut Microbes Boosts Brain Plasticity in Mice

Finally, the researchers tested whether blocking the interaction between IAA and S100A8 could reverse cognitive changes. They identified an oligonucleotide, S100p1-G, that competes with IAA to bind the promoter region of S100A8 and prevents the gene from being activated. When the researchers fed the oligonucleotide to aged mice, they found that it improved their performance on cognitive tasks, which the authors say is evidence of improved memory and spatial learning. “The ability to demonstrate cognitive defects following supplementation of the isolated bacterial metabolite and restoration of behavior in mice by blocking it is also very novel,” writes Gareau. However, Blank cautions that “although S100A8 levels rise with age and may activate autophagy and apoptosis, further research is needed to confirm this hypothesis and prove this method of action in the current situation.” 

The new SSGS technology is one of the biggest developments of the paper, says Krantic, who adds that it’s “clearly a huge step towards a new era in the investigation of interactions between small molecules and nucleic acids.” Going forward, the researchers hope this technology can be applied to studies unrelated to aging, such as “any subjects with metabolites involved in the regulation of gene expression,” Zhang says.

The study also suggests that oligonucleotide-based therapies could be applied to cognitive disorders and neurodegenerative diseases, Krantic writes. Zhang suggests that a similar approach may be used to identify oligos that are able to block inflammation in different cell types, as inflammation plays a critical role in different types of disease.