Scientists have discovered that the gut functions like a “second brain” and is connected to the brain in ways that go far beyond digestion.[1] Well-known examples of this connection include getting butterflies or “following your gut,” but there are many other links too.
These lesser-known connections between the gut microbiome and mental health can have a major impact on your life. This article will cover:
- How the brain and gut communicate via the enteric nervous system.
- How gut bacteria produce neurotransmitters.
- The link between specific gut bacteria and mood disorders.
- Dietary changes that support both gut and mental health.
- How to find treatment that supports mental health well-being.
Connection Between Gut Microbiome and Mental Health
Scientists have found that the gut and brain are connected in multiple ways, and they’re still discovering new connections. In general, these connections can be split into two specifics:[1]
- How the gut and brain communicate via the nervous system.
- How specific bacterial species influence brain chemistry and overall health.
Both of these are significant for what we know about mental health.
Enteric Nervous System
Many people know that the sympathetic nervous system is responsible for our “fight or flight” reactions, particularly if they’ve had therapy for anxiety. However, the enteric nervous system (ENS) is less widely known. The ENS is made up of 100 million nerve cells that line the gastrointestinal tract and communicate back and forth with the brain.[1] It’s sometimes called the “second brain” because it can operate independently of the central nervous system, sending and receiving signals without waiting for instructions.
Recent research has found that the ENS is capable of triggering big emotional shifts, particularly in people with:
- Irritable bowel syndrome (IBS).
- Constipation.
- Diarrhea.
- Bloating.
Experts used to think that mental health conditions like anxiety and depression contributed to these sorts of stomach problems. However, their new understanding of the ENS suggests the connection also goes the other way around.[1]
As we’ll explore throughout this article, this connection means that stomach irritation may trigger signals to be sent to the brain, which result in mood changes.[1]
Impacts of the Microbiome
Beyond the ENS, the gut-brain connection is also influenced by the gut microbiome. This is the name for the billions of bacteria that live in your intestines. These bacteria help digest food, with different bacteria excelling at breaking down complex sugars or fats.[2]
The foods we eat change the species of bacteria that thrive in our guts. For example, someone who eats a wide variety of fruits and vegetables will have a different gut microbiome than someone else who eats mostly meat and other low-fiber foods.[2]
Your microbiome is also shaped by the diversity of foods you eat. Low diversity (known as dysbiosis) is connected to many diseases, such as type 2 diabetes and anxiety.[2]
Our microbiomes play key roles in immune function, metabolism, and susceptibility to stress. Experts have also discovered that gut bacteria are responsible for producing neurally active substances, which means they affect the brain and nervous system in various ways, including:[2][3]
- Gut bacteria that interact with fiber-rich foods produce short-chain fatty acids, which help us react to stress.
- Other gut bacteria produce neurotransmitters like serotonin, which influence mood, cognition, and sleep.
- During adolescence, gut bacteria influence brain development by stimulating the growth of new neurons. These play a role in social behavior, memory, and stress reactivity.
- Gut bacteria continue to influence neural connections throughout life, stimulating new neural connections in the brain.
- Having more of one type of bacteria (Firmicutes) and less of another (Bacteroides) may contribute to major depressive disorder.
- 90% of the body’s serotonin is produced in the gut.
As a result of these brain-gut connections, there is significant interest in how diet may impact psychiatric disorders. We’ll now explore this more deeply by looking at the symptoms of poor gut health and mental health.
Gut Microbiome Imbalance Signs and Symptoms
Many people with mental health conditions experience some digestive issues, but don’t connect the two. If you have both, it’s worth considering whether they might be related.
Microbiome imbalance symptoms can show up as various digestive issues, including:[4]
- Bloating.
- Gasiness.
- Irregular bowel movements.
- Constipation.
- Diarrhea.
However, a gut microbiome imbalance can show up in other ways too. For instance, if you have frequent cravings for sugary foods or feel fatigued after eating, there may be an imbalance of bacteria in your gut. Sugary foods feed certain bacterial species. The more sugar you eat, the more those bacteria thrive.
Your skin can also be affected, with people reporting eczema, acne, and unexplained rashes. You may also be ill more frequently due to how your microbiome influences your immune system.[4]
Researchers find that gut bacterial imbalances can lead to and worsen mental health conditions.[5] Specific species of gut bacteria have been linked to specific mental health conditions. For example, the following gut bacteria and mood disorders are found to be linked:[5]
- Anxiety and increased Prevotella
- Depression and increased Dialister and Coproccus
- Post-traumatic stress disorder (PTSD) and higher levels of Mitsuokella and Odoribacter
- Bipolar disorder and increased Clostridiaceae and Flavonifractor
- Schizophrenia and reduced Ruminococcus and Roseburia
- Anorexia and reduced Bacterioidetes
There’s no need to know the exact species of gut bacteria living inside you. But it is useful to understand that specific types (influenced by the foods we eat) are more prevalent in people with specific mental health conditions. The research is still developing, but the pattern is consistent enough to take seriously.
If you’ve noticed symptoms of both a mental health condition and a gut imbalance, you might consider the advice in the next section.
Improving Diet and Gut Microbiome for Mental Health
The gut responds to dietary change faster than most people expect. Research finds that changes in the gut microbiome can occur within two weeks of changing a “typical American diet” to a plant-rich one.[2]
Here are our top three tips:
1. Track Your Symptoms
To address the IBS and mental health link, you should first keep track of your various symptoms. Seeing how inflammation, microbiome, and mental health are connected for you will create a helpful map for understanding what’s going on. You might find that certain foods consistently precede anxiety or digestive discomfort.
2. Introduce Gut-Healthy Foods
Changing your diet is key to addressing gut issues and may help reduce emotional symptoms too. In particular, the Mediterranean diet has been shown to have particular mental health and gut health benefits.[3] It emphasizes vegetables, legumes, whole grains, olive oil, and fermented foods, many of which directly support a healthy microbiome.
Other foods that are highly beneficial for your gut include:[4]
- Kimchi.
- Miso.
- Kefir.
- Sauerkraut.
These foods introduce beneficial bacteria into your gut microbiome and are known as probiotic foods. They can be paired with other healthy dietary choices to maintain a healthier gut microbiome. For instance, bananas, asparagus, garlic, onions, leeks, and other plant foods will nurture these bacteria to remain and proliferate in your gut.[4] These are called prebiotic foods.
You can also reduce or eliminate foods that harm good gut bacteria. These tend to be sugary and processed foods, such as those with artificial sweeteners, alcohol, white bread, pasta, and sometimes dairy.[4]
As mentioned above, a diversity of foods is another important factor in promoting good gut health. Ensuring that you’re eating a variety of foods week to week helps maintain a healthy microbiome.[2]
3. Promote Good Digestive Function
As well as eating foods that support a healthy gut, there are other things you can do to promote good digestive health. Fiber from vegetables, grains, and legumes helps your bowel move regularly and feeds beneficial bacteria at the same time.[4]
In addition, even something as simple as remaining well-hydrated can support good digestive function. Sufficient water intake helps your body:[4]
- Absorb nutrients.
- Break down foods.
- Prevent constipation.
Many people are mildly dehydrated most of the time without realizing it, which affects digestion and energy levels.
Holistic mental health and gut support typically advocate for lifestyle changes. For instance, you may be advised to:[4]
- Drink peppermint or ginger tea.
- Get enough sleep.
- Practice meditation.
- Exercise regularly.
Find Whole Person Mental Health Treatment With Mission Connection
If you’re experiencing mental health symptoms alongside digestive issues and want to explore the connection, Mission Connection can help you address both. Our personalized treatment plans are built around your full picture.
We also understand the importance of gut health as new research is emerging. For that reason, we can integrate dietary changes into your treatment plan and support you with those adjustments alongside evidence-based therapies (CBT, DBT, and trauma-informed approaches) and medication management.
Our team of licensed mental health professionals goes beyond traditional treatment and provides life-changing care. We offer several options for effective outpatient treatment, including in-person programs at our locations in California, Virginia, and Washington, virtual telehealth, and a hybrid program that combines in-person and virtual care.
Mission Connection is Joint Commission-accredited. We also accept most major insurance providers, so that your recovery is not hindered due to financial issues.
To learn more about our mental health treatment plans, reach out to us online or call us at 866-833-1822 to find out how we can support your long-term recovery. Our compassionate team is available 24/7 to answer your questions and provide guidance with no obligation.
Gut Microbiome FAQ
Do probiotics for depression and anxiety work?
Probiotics for anxiety relief are commonly recommended in the gut-brain connection world, as they can help prevent and manage a variety of diseases. The bacteria Lactobacillus is found to be effective at modulating the gut microbiome and alleviating depression-like behaviors.[5]
It’s one of the most studied probiotic strains, found in yogurt, kefir, and fermented vegetables. The bacteria Pediococcus acidilactici can reduce anxiety-like behaviors.[5] The evidence is promising enough to make probiotic foods a potential addition to any mental health treatment plan.
What kills bad gut bacteria?
It’s more useful to think about shifting the balance of gut bacteria than trying to eliminate specific strains. The different strains of bacteria in your gut are influenced by the foods you eat. By eating less of something, certain bacteria will die off; by eating more of another thing, certain bacteria will flourish.[1][2]
As a result, you will naturally change your gut microbiome through long-term dietary changes. It is possible that this process can be sped up, but research remains limited. For instance, there is some evidence that eating garlic could potentially kill certain gut bacteria without harming the healthy strains.[4]
What is gut health therapy for mental health?
As microbiome psychiatry research has progressed, mental health professionals are increasingly recommending dietary changes alongside medication and psychotherapy. This is because trials for treating depression with dietary changes found a remission rate equivalent to that of antidepressant treatment.[3]
If you’re referred to gut health therapy for mental health, you’ll likely be given much of the advice discussed above, as well as:
- Tests to determine the bacteria in your gut.
- Personalized meal plans.
- Psychoeducation about links between diet and mental health.
- Regular check-ins.
Dietary support is usually delivered alongside counseling or psychotherapy rather than in place of it.
References
- Johns Hopkins Medicine. (2019). The brain-gut connection. Johns Hopkins Medicine. https://www.hopkinsmedicine.org/health/wellness-and-prevention/the-brain-gut-connection
- Psychology Today. (n.d.). Gut-brain axis. https://www.psychologytoday.com/gb/basics/gut-brain-axis
- Liester, M. (2026). The role of food in mental health and mental illness. Psychology Today. https://www.psychologytoday.com/gb/blog/the-leading-edge/202604/the-role-of-food-in-mental-health-and-mental-illness
- McKeever, T. (2025, April 15). How can i tell if my gut is unhealthy? The Gut Clinic UK. https://thegutclinicuk.com/insights/how-can-i-tell-if-my-gut-is-unhealthy/
- Xiong, R.-G. et al. (2023). The role of gut microbiota in anxiety, depression, and other mental disorders as well as the protective effects of dietary components. Nutrients, 15(14), 3258. https://doi.org/10.3390/nu15143258