Our brains may seem physically far removed from our guts, but in recent years, research has strongly suggested that the vast communities of microbes concentrated in our digestive tract open lines of communication between the two. The intestinal microbiome has been shown to influence cognition and emotion, affecting moods and the state of psychiatric disorders, and even information processing. But how it could do so has been elusive.

Until recently, studies of the gut-brain relationship have mostly shown only correlations between the state of the microbiome and operations in the brain. But new findings are digging deeper, building on research that demonstrates the microbiome’s involvement in responses to stress. Focusing on fear, and specifically on how fear fades over time, researchers have now tracked how behavior differs in mice with diminished microbiomes. They identified differences in cell wiring, brain activity and gene expression, and they pinpointed a brief window after birth when restoring the microbiome could still prevent the adult behavioral deficits. They even tracked four particular compounds that may help to account for these changes. While it may be too early to predict what therapies could arise once we understand this relationship between the microbiome and the brain, these concrete differences substantiate the theory that the two systems are deeply entwined.

Pinning down these mechanisms of interaction with the brain is a central challenge in microbiome research, said Christopher Lowry, an associate professor of integrative physiology at the University of Colorado, Boulder. “They have some tantalizing leads,” he added.

Coco Chu, the new study’s lead author and a postdoctoral associate at Weill Cornell Medicine, was intrigued by the concept that microbes inhabiting our bodies could affect both our feelings and our actions. Several years ago, she set out to examine these interactions in fine-grained detail with the help of psychiatrists, microbiologists, immunologists and scientists from other fields.

The researchers performed classical behavioral training on mice, some of which had been given antibiotics to dramatically diminish their microbiomes and some of which had been raised in isolation so that they had no microbiome at all. All the mice learned equally well to fear the sound of a tone that was followed by an electric shock. When the scientists discontinued the shocks, the ordinary mice gradually learned not to fear the sound. But in the mice with depleted or nonexistent microbiomes, the fear persisted — they remained more likely to freeze at the sound of the tone than the untreated mice did.

Peering inside the medial prefrontal cortex, an area of the outer brain that processes fear responses, the researchers noticed distinct differences in the mice with impoverished microbiomes: Some genes were expressed less. One type of glial cell never developed properly. Spiny protrusions on the neurons associated with learning grew less plentifully and were eliminated more often. One type of cell showed lower levels of neural activity. It’s as if the mice without healthy microbiomes couldn’t learn to be unafraid, and the researchers could see it on a cellular level.

The researchers also set out to learn how the condition of the microbiome in the gut caused these changes. One possibility was that microbes send signals to the brain through the long vagus nerve, which carries sensations from the digestive tract to the brain stem. But snipping the vagus didn’t alter the behavior of the mice. It also seemed possible that the microbiomes might stir up responses in the immune system that affect the brain, but the numbers and proportions of immune cells in all the mice were similar.

But the researchers did pinpoint four metabolic compounds with neurological effects that were far less common in the blood serum, cerebrospinal fluid and stool of the mice with impaired microbiomes. Some of the compounds were already linked to neurological disorders in humans. The team speculated that the microbiome might produce certain substances in abundance, with some molecules making their way into the brain, according to the microbiologist David Artis, the director of the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine and the senior author on the study.