The community of microorganisms residing in our gut have been shown to affect brain function and behavior. However, scientists still struggle to explain how gut-brain communication occurs.

Chu and colleagues have unraveled mechanisms by which gut microbiota affects mice adaptation to fear conditioning.

By using a classic Pavlovian test, the authors first trained mice to associate a tone with pain in their foot provoked by an electric shock, cringing each time they heard the sound. However, after hearing the tone while not receiving the electrical shock several times, the mice subsequently stopped reacting to the sound stimulus.

The researchers wondered to what extent gut bacteria could play a role in these learning and forgetting responses.

For this objective, mice were treated with antibiotics and then a tone was played, with a mild shock given multiple times right after. The animals therefore learned to associate the noise with pain. But while mice colonized by gut bacteria forgot the association between the noise and the shock from the third day, the antibiotic-treated mice continued to react to the tone.

Next, the scientists performed in vivo brain imaging and single cell RNA sequencing to study individual brain cell structure and gene activity. They observed differences in the process of formation and elimination of dendritic spines—structures involved in learning and memory through the formation of synaptic connections between neurons—in neurons from the prefrontal cortex, which is a key region implicated in neuropsychiatric disorders including depression, schizophrenia and autism.

Thus, mice treated with antibiotics showed more dendritic-spine elimination and less spine formation than control animals with gut microbiota. As such, the higher spine elimination might explain why the antibiotic-treated mice were not able to extinguish the fearful stimulus over time.

RNA sequencing on individual neurons from the medial prefrontal cortex revealed that antibiotic treatment had a more pronounced effect on excitatory over inhibitory neurons. That is in line with previous data showing gut microbiota’s impact on regulating prefrontal cortex myelination. Moreover, evaluation of microglia suggested that these cells are also affected by microbiome changes and herewith alter microglia-mediated synaptic pruning.

In addition, the authors found that the levels of 4 gut microbiota-derived metabolites—phenylsulfate, pyrocatechol sulfate, 3-(3-sulfooxyphenyl)propanoic acid and indoxyl sulfate—were depleted in the cerebrospinal fluid, serum and fecal samples of gut microbiota-deficient mice when compared with controls. Within these metabolites, a derivative of 3-(3-sulfooxyphenyl)propanoic acid and indoxyl sulfate have been associated with schizophrenia and autism in humans.

On the whole, these findings show that mice need gut microbiota to update their behavior in response to environmental stimulus. The gut microbiota-related changes reported here in both the shape and activity of neurons involved in learning and forgetting may help better understand human neuropsychiatric diseases that have alterations in cognition and synaptic plasticity as a common hallmark.



Chu C, Murdock MH, Jing D, et al. The microbiota regulate neuronal function and fear extinction learning. Nature. 2019; 574(7779):543-8. doi: 10.1038/s41586-019-1644-y.