There’s a highway that connects our intestine to our mental state – and it flows in both directions.
There are so many neuron cells connected to our intestine that it’s often described as a “second brain.”
Through these neurons, our brain and our gut are closely tied to each other in expressions and anatomy. When we get bad news, we’re “sick to our stomach.” When we’re mentally sure, we have “a gut feeling.” When we get a stomachache, it’s difficult to focus – and when we’re anxious or stressed, we often have gut issues.
What’s the nature of this brain-gut connection, and what other surprising factors influence our mental state?
Those are great questions. Let’s start with a little anatomy lesson.
A Look Beneath our Belly Button

Our intestine is the long, snaky tube that follows the stomach in our digestive tract. And made up of two parts. The small intestine is filled with water and absorbs most nutrients from our food. The large intestine focuses on reclaiming water and salt. Both of these areas contain huge, diverse populations of bacteria known as the gut microbiome.
In many ways, our digestive system is vital to daily life. We need it to help pull in nutrients for energy and carry away waste, but we also use the bacteria it holds to train our immune system.
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Your body monitors that vital process via tons of neurons. A large nerve called the vagus nerve directly plugs our intestinal sensors into our brain. Many signals travel along the vagus nerve. It monitors our heart, lungs, stomach and intestines. It relays signals in relation to how our gut is doing – and since it’s connected to our amygdala (our brain’s emotion center), we feel good or bad based on those signals.
What sends these signals up the vagus nerve?
At least a portion of these signals come from the bacteria in our gut. Here’s what they do, and how they may help us.
The Bacteria Flying this Human Spaceship

As mentioned, our large and small intestine, inhabited by a massive population of bacteria collectively called a microbiome. There are more bacteria living inside each of us than there are human cells making up our entire body. Each of us has a slightly different balance of bacteria, making each microbiome unique.
Our gut microbiome lives off the food we eat. They synthesize some of the vitamins we absorb, but they also have plenty of interactions with the host (that’s us). Your microbiome produces hormones and other signal molecules that help regulate your daily biological balance.
This is still an area of active research, but scientists have discovered that the profile of different bacteria in our microbiome changes along with our mental state.
Depressed people show to host a majority of bacteria in the Bacteroidetes, Proteobacteria, and Actinobacteria phyla, and fewer bacteria from the Firmicutes phylum. Similarly, people with irritable bowel syndrome (IBS) have a different microbiome profile, and the condition can certainly contribute to stress and anxiety.
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This is an area of ongoing research, and there’s an important phrase to repeat in science: correlation does not equal causation. Two observations may be linked, but that doesn’t mean one thing is responsible for the other.
Research shows that our gut microbiome changes when our mental state changes, but we can’t say definitively if the gut microbiome is responsible for directly controlling our mood.
Some preliminary research suggests that gut bacteria could have some control. When researchers took the gut bacteria from depressed mice and transplanted them into healthy mice, the previously happy mice became depressed. This suggests that some part of depression may come from signals our gut bacteria produce.
Scientists continue to study the mechanisms these bacteria may use to affect our mood and mindset. We’re a long way from understanding the details enough to propose a microbiome-based cure for depression.
Gut Bacteria Reach Beyond Their Home

We don’t know exactly how gut bacteria alter our mood, but we know they can do a few things, including:
Produce signal molecules. Some of the molecules our gut bacteria make can cross into our bloodstream and create a hormonal reaction. For example, some bacteria can produce a metabolite of dopamine, the feel-good hormone that our brains release when we’re having fun.
Decrease inflammation. Some signal molecules produced by bacteria can help calm our body’s immune response, keeping the immune system from attacking our gut, thus preventing the pain, cramps, constipation, and/or diarrhea that comes along with inflammation.
Alter gut permeability. Our gut wall is like a fence, keeping bacteria inside while letting nutrients through. We suspect that some diseases may be linked to holes in this fence, letting bacteria slip into our body. Some diseases related to various microbiome bacteria compared to the profiles found in healthy people.
Our gut is important to us, and our brain carefully monitors it, receiving constant updates through the connecting vagus nerve.
Scientists don’t fully understand the complex relationship between the gut microbiome, our immune system, and our overall physical and mental health, but we do know these components are linked. Altering the balance of gut bacteria leads to mental and physical changes in mice. It may also play a role in humans.
Perhaps someday soon, a doctor will prescribe a probiotic to accompany antidepressants – or even to replace them. We still need more research to understand exactly how these bacteria influence our mood. And Microbiome-based treatments for anxiety and depression may soon be more than just happy thoughts.