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Wondering about the connection between the gut microbiome and mental health? Research has shown that the brain and gut interact and that changes in the microbiome are linked to mood and mental health.
The gut and the brain are deeply interconnected—and, as a therapist, it’s important to understand how the gut can impact mental health and how to work with clients whose mental health symptoms may be directly tied to gut dysregulation.
But the gut isn’t just a mental health issue, and it’s also important to recognize when a client needs support that extends beyond therapy.
So, the question is, how does the gut-brain connection factor into your work with clients? How can you identify when gut issues might be contributing to your clients’ mental health challenges? And, how can you support them in addressing those issues and feeling better—without stepping outside your scope of practice?
Let’s take a look into the microbiome and mental health, including gut-brain connection therapy, ihow to work with clients to identify and address gut issues that could be contributing to ongoing mental health concerns or interfering with therapy, and how to determine when to refer to nutritionists, doctors, or other medical professionals.
Summary
The microbiome and mental health are deeply interconnected through the gut-brain axis, with gut bacteria directly influencing neurotransmitter production, stress responses, and mood regulation through bidirectional communication pathways.
Gut-brain connection therapy encompasses evidence-based approaches including gut-directed hypnotherapy, diaphragmatic breathing, mindfulness interventions, and adaptations of CBT and ACT that address how emotional distress and GI symptoms fuel each other.
Therapists can how to assess gut health through clinical questioning about bloating, digestive patterns, stress-symptom connections, and lifestyle factors without crossing into medical diagnosis or treatment.
Understanding when to refer to nutritionists or medical professionals is crucial when clients present with serious physical symptoms, complex dietary questions, or requests for medical testing beyond the therapist's scope of practice.
What is the gut-brain connection—and how does it impact mental health?
Before we get into gut-brain connection therapy, let’s first cover what, exactly, the gut-brain connection is—and what impact that connection has on mental health.
“The gut–brain connection refers to the two-way communication between the central nervous system and the gut microbiome through the vagus nerve, immune signaling, microbial metabolites, and endocrine pathways,” says Christina P. Kantzavelos, LCSW, founder of Begin Within Today.
So, what role does this back-and-forth communication play in mental health?
The microbiome helps regulate neurotransmitters and stress signals—meaning the health and balance of your gut can directly influence things like mood, anxiety levels, and focus.
“The tiny microbes living in your gut help make brain chemicals like serotonin, which boosts mood, and GABA, which calms the nervous system,” says Jenny Hughes, PhD, trauma psychologist and founder of The BRAVE Trauma Therapist Collective.
When your gut is healthy and balanced, it works together with your brain to keep you feeling and functioning your best. “When your gut is balanced and diverse, the signals it sends tend to support steadier moods, less anxiety, and better focus,” Hughes continues.
However, when the microbiome is out of balance—also known as gut dysbiosis—mental health can take a hit.
“When the gut is out of balance…the signals can be more like alarms,” says Hughes. “This can leave you feeling more anxious, down, or stressed.”
How an out-of-balance gut can impact mental health
Research has linked gut dysbiosis and inflammation to increased anxiety and depression.
But, what’s actually happening? How does an out-of-balance microbiome contribute to mental health symptoms?
According to Hughes, when the gut is out of balance:
Helpful bacteria decline, and harmful bacteria take over.
The gut lining becomes more “leaky,” allowing irritation and inflammation to spread.
The gut stops producing enough building blocks for mood-regulating neurotransmitters.
“When this happens, people are more likely to feel anxious, depressed, stressed, or have trouble with sleep and focus,” Hughes explains.
The stress of those symptoms can throw the microbiome even more out of balance—setting up a negative feedback loop that keeps people stuck with poor gut health and mental health.
“Stress...can make this cycle worse by irritating the gut even more—so it turns into a back-and-forth loop between body and mind,” Hughes adds.
How to incorporate the gut-brain connection into therapy
Clearly, the microbiome can play a significant role in mental health.
But how should therapists integrate the microbiome and mental health connection into therapy and behavioral health treatment in a way that supports clients?
How to explain connection between the microbiome and mental health to clients
The conversation around the gut-brain connection and mental health is fairly new, and the concept might be completely new to your clients.
And, like any new concept, it’s important to introduce it in a way that’s easy for clients to understand and apply to their own therapeutic journey.
When talking with clients about the microbiome and mental health, avoid any explanations that are too technical or scientific, which could be overwhelming and/or confusing. Instead, break down the concept in a more accessible way.
For example, when Hughes introduces the gut-brain connection to clients, she uses a metaphor that compares the gut to an active neighborhood group chat.
“If the neighbors—microbes—are diverse and cooperative, messages trend calm, focused, and steady,” says Hughes. But “if the neighborhood loses diversity or gets too heated—[or in other words] inflamed—the messages come across as alarmed and irritable.”
How you talk to your clients about the microbiome and mental health is up to you—but make sure you talk to them about it in a way that’s clear, uncomplicated, and easy to digest (pun intended!).
Use therapeutic assessment tools
As a therapist, you never want to cross the line into medical treatment or diagnosis.
But, if you want to get a sense of whether gut issues may be impacting your clients’ mental health, there is a way to explore your clients’ gut health without veering out of your lane.
“Therapists can use clinical questions rather than medical tests,” says Kantzavelos.
When it comes to how to assess gut health as a therapist, consider “asking about everyday signs [about their gut-brain connection and health],” Hughes says.
For example, you might ask questions like:
Do you notice frequent bloating, stomach pain, or irregular bowel habits?
Have you noticed any other gut symptoms? If so, what/when/how often?
Do you often feel tired, foggy, or inflamed?
Do your gut symptoms flare up when you’re stressed?
What are your typical routines (diet, sleep, exercise, etc.)?
Have you noticed any connections between gut symptoms, mental health symptoms, and your routines? (For example, do certain foods cause you to feel bloated immediately after eating them—and then tired and sad a few hours later?)
These questions can open the door for your client to start exploring their current gut health and how it may (or may not) be impacting their mental and emotional well-being. =For you, as their therapist, it can help you to better understand that connection and how it may play into therapy and treatment.
Gut-brain connection therapy
Clinical approaches derived from this science, known as gut-brain connection therapy or brain-gut-behavior therapies (BGBTs), are short-term and skills-based, focusing directly on regulating the nervous system to improve symptoms.
For clinicians, this means integrating psychological techniques with a focus on bodily regulation using evidence-based modalities like gut-directed hypnotherapy, diaphragmatic breathing, mindfulness-based interventions, and GI-focused adaptations of cognitive behavioral therapy (CBT) and acceptance and commitment therapy (ACT).
These interventions are particularly effective for clients presenting with co-occurring stress-sensitive GI conditions, such as irritable bowel syndrome (IBS), as they address how emotional distress and physiological discomfort fuel each other, thereby fostering long-term resilience and symptom reduction.
Work together to create an improvement plan
If your client suspects their gut may be negatively impacting their mental well-being—and is open and willing to explore ways to address it—you can work with them to create a plan to support better gut health.
The plan should center around evidence-based lifestyle changes proven to support better gut functioning over time, like:
Eat more whole foods. A diet of fresh, healthy, whole foods supports optimal gut health. For example, the Mediterranean-style diet—which includes a variety of high-fiber foods, plants, beans, fish, nuts, and olive oil—has been linked to increased microbiome diversity.
Add fermented foods. Fermented foods can also support improved gut health. “Things like yogurt, kefir, kimchi, and sauerkraut help build gut diversity,” says Hughes.
Keep stress at bay. Stress can cause all sorts of gut issues, including “leaky” gut. As such, managing stress is an important part of any plan for improving gut health. “Mindful movement, breath work, and stress reduction also support gut health,” adds Kantzavelos. “
Once the client has identified a few changes they’d like to incorporate into their routine, encourage them to figure out how to track improvements and progress.For example, they may keep a journal documenting how eating changes impact their gut and mental health symptoms. Keeping a behavior log can help them identify trends and patterns over time and figure out which changes are having the biggest impact.
Refer out when needed
As a therapist, you can absolutely support your clients in exploring the gut-brain connection.
But some clients will need a different kind of support and/or a higher level of care, requiring you to refer out to a qualified medical professional.
You’ll need to assess each client to determine if and when they need a referral. Generally speaking, you’ll want to refer a client out if they:
Have serious physical symptoms. If your client is struggling with physical symptoms—like significant and/or persistent gastrointestinal symptoms, unexplained weight change, and/or a diagnosed gut disorder—it’s important to refer them to a doctor to get the support and treatment they need.
Have advanced or complex medical, dietary, or lifestyle questions. While it’s typically fine to address basic questions like “What dietary recommendations can you share?” or “Does gut health impact sleep?” with your clients, you’ll want to refer them to a qualified professional for more advanced or specific questions about gut health and how to treat it.
Request medical testing. If your client wants to get deeper insight into their gut health through medical testing (for example, blood work or a stool analysis), you’ll need to refer them out to someone who can order and interpret those tests.
Understanding the gut-brain connection can help you better support clients
The gut-brain connection plays a powerful role in mental health—and sometimes, the key to improving mental health lies in treating the gut.
You can use that understanding about the connection between the microbiome and mental health to better assess and treat your clients as they work toward better emotional and mental well-being.
By incorporating gut-brain connection therapy principles, asking the right clinical questions, providing evidence-based lifestyle guidance, and knowing when to refer out, you can offer comprehensive support that addresses the full spectrum of factors influencing your clients' mental health.
Sources
An, E., Delgadillo, D., Yang, J., et al (2024). Stress-resilience impacts psychological wellbeing as evidenced by brain–gut microbiome interactions. Nature Mental Health.
Carabotti, M., Scirocco, A., Maselli, M. A., & Severi, C. (2015). The gut-brain axis: Interactions between enteric microbiota, central nervous system, and enteric nervous system. Annals of Gastroenterology.
Yano, J. M., Yu, K., Donaldson, G. P., Shastri, G. G., Ann, P., & Ma, L., et al. (2015). Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell.
Clapp, M., Aurora, N., Herrera, L., et al. (2017). Gut microbiota's effect on mental health: The gut-brain axis. Clinics and Practice.
Asad, A., Kirk, M., Zhu, S., Dong, X., & Gao, M. (2024). Effects of Prebiotics and Probiotics on Symptoms of Depression and Anxiety in Clinically Diagnosed Samples: Systematic Review and Meta-analysis of Randomized Controlled Trials. Nutrition Reviews.
Weaver, J. (2021) Fermented-food diet increases microbiome diversity, decreases inflammatory proteins, study finds. Stanford Medicine News Center.
Madison, A., & Kiecolt-Glaser, J. K. (2019). Stress, depression, diet, and the gut microbiota: human–bacteria interactions at the core of psychoneuroimmunology and nutrition. Curr Opin Behav Sci.
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