A streamlined stack of supplements designed to meet your most critical needs - Adapt Naturals is now live. Learn more

Heal Your Gut, Heal Your Brain


Last updated on

Are you among the 20 percent of adults suffering from anxiety and depression? Find out how nourishing your gut microbiome can make you happier and more relaxed.

leaky gut and anxiety
There is a strong connection between the gut and the brain. AntonioGuillem/istock/Thinkstock

In my work, a significant number of patients list anxiety or depression as one of their top three health concerns. This is not at all surprising given that anxiety and depression are two of the most common mental health issues in our society, with anxiety disorders affecting approximately 18% of adults in the U.S. (1) Anxiety and depression are not the same, but they are often experienced together as a complex set of emotional and functional changes. (2)

Both anxiety and depression, along with other mood and neuropsychiatric disorders, such as eating disorders, bipolar disorder or sleep disorders, generally result from a complex interplay of factors. These may include a combination of nutritional, physical, environmental, social, emotional, and spiritual factors, affecting your genetic tendencies and brain biochemistry (meaning that your neurotransmitters, or the chemical messengers within your brain, can be affected by these key components of well-being). You can think of anxiety and depression as disruptions in brain health.

Treating the Cause Not Just the Symptoms

While conventional medicine, not surprisingly, offers medications to treat the symptoms of anxiety and depression with somewhat limited success (data suggests that 30 to 40% of patients do not respond to current drug strategies), we take a very different approach in functional medicine. (3, 4) It’s important to recognize that medication, particularly antidepressants, can be essential for some people, particularly those with more severe depression, and a decision to start or stop antidepressants needs to be discussed with your health care provider. I never recommend coming off antidepressants too quickly, and there are times when patients clearly benefit from the support of these medications.

What surprises many new patients who ask for help with their anxiety or depression is that we start by looking at the health of the gut. For those of you who have followed this blog for any amount of time, you’ve probably picked up on a common theme here that you have to have a healthy gut microbiome for optimal well-being.

Having trained in conventional medicine, this idea was not intuitive to me even five years ago. But now, after reading the scientific literature on the microbiome-gut-brain axis, and working with patients to heal their gut and seeing the incredible improvements in mood, I’m convinced this is the starting place to heal anxiety and depression.

Anxious, stressed, or depressed? Healing your gut may be the solution. #guthealth #microbiome #mentalhealth

A Growing Body of Evidence Shows That Our Beneficial Gut Bacteria Support Positive Mood and Emotional Well-Being

The gut microbiome, which we’ve discussed in a number of prior articles and podcasts (here and here), refers to the microorganisms, predominately bacteria (somewhere on the order of 10 to 100 trillion) and their genes, living within the human gut. Many of these microorganisms are in fact essential for good health. When the balance of beneficial bacteria in the gut is disrupted, disease can occur.

The relatively new understanding of how microorganisms affect every system of our body, along with the incredible volume of research on the microbiome is leading to a shift within medicine, and specifically a shift towards appreciating how important it is to care for our healthy gut bacteria.

Differences in the Gut Microbiome Exist between People with Anxiety and Depression and Those Without

Numerous studies in animal models show convincing evidence of a strong relationship between the gut microbiome and mood. For example, studies have found significant differences in the types of gut bacteria in animals exposed to various types of stress such as maternal separation early in life, social stressors, or prolonged restraint. (5, 6, 7)

One study, published this month, examined the specific differences in the bacterial make-up of the microbiome in patients with major depressive disorder in comparison with healthy individuals. (8) Significant differences were identified between these two groups. Additionally, the severity of depressive symptoms was related to the amount of a specific bacterium. A lower relative abundance of Faecalibacterium was associated with more severe depression.

Like what you’re reading? Get my free newsletter, recipes, eBooks, product recommendations, and more!

Altering the Gut Microbiome with Probiotics Can Decrease Feelings of Anxiety and Positively Affect Emotional Processing

Several studies show evidence for reduced feelings of anxiety and improved aspects of well-being after taking probiotics. (9, 10, 11)

One study used functional MRI (magnetic resonance imaging), which is a type of imaging that looks at brain activity, to evaluate the influence of gut microbes on emotional behavior and underlying brain mechanisms. (12) Specifically, three groups of women were given either fermented milk with probiotics, non-fermented milk, or no intervention, twice daily for four weeks. Functional MRI was performed both at the start and completion of the study to look at brain activity in response to an emotional attention task.

The women who consumed the fermented milk with probiotics showed changes in regions of the brain crucial in emotional processing. This study provides further evidence that supporting the gut microbiome can provide measurable changes in emotional processing within the brain.

Additional support for the connection between the gut microbiome and mood came from a study that showed the use of specific probiotics significantly decreased anxiety-like behavior in rats and reduced psychological distress in humans. (13)

Nourishing Your Beneficial Gut Bacteria Will Also Reduce Anxiety and Decrease Stressishing your beneficial gut bacteria will also reduce anxiety and decrease stress

A recent study evaluating the effects of prebiotics on well-being provided additional evidence of the gut bacteria positively affecting mental health. (14)  Prebiotics are carbohydrates that humans cannot digest, but bacteria in our guts can.

In this study, 45 healthy individuals were asked to take either a prebiotic or placebo every other day for three weeks. Cortisol measurements were taken from saliva samples at the beginning and end of the study to evaluate the hypothalamic-pituitary-adrenal (HPA) axis activity (an important factor contributing to anxiety and depression). After three weeks, the participants completed a series of tests designed to assess how they processed emotional information, such as processing facial expressions of the six basic emotions, and responding to positive and negatively charged words.

The results showed that individuals who had taken the prebiotic had significantly lower cortisol after three weeks, meaning they showed physiologic evidence of a decreased stress response. And the prebiotic group paid more attention to positive information and less attention to negative information when compared to the participants who were given placebo. This suggests that when confronted with negative stimuli, the prebiotic group would have less anxiety, similar to that which has been observed in some people taking antidepressant or anti-anxiety medication.

Use an Integrated Approach

Therapy and, in some cases, antidepressant or anti-anxiety medications can be important pieces of treatment. But if underlying imbalances in the gut microbiome are to blame (which is often the case in our experience), you won’t heal until they are addressed.  This functional medicine approach to mood disorders is something that I frequently find to be more effective than conventional treatments, allowing many patients relief from their symptoms of anxiety and depression.

Amy Nett

About Amy:  Amy Nett, MD, graduated from Georgetown University School of Medicine in 2007.  She subsequently completed a year of internal medicine training at Santa Barbara Cottage Hospital, followed by five years of specialty training in radiology at Stanford University Hospital, with additional subspecialty training in pediatric radiology.

Along the course of her medical training and working through her own personal health issues, she found her passion for Functional Medicine. She works with patients through a Functional Medicine approach, working to identify and treat the root causes of illness.  She uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.

ADAPT Naturals logo

Better supplementation. Fewer supplements.

Close the nutrient gap to feel and perform your best. 

A daily stack of supplements designed to meet your most critical needs.

Chris Kresser in kitchen


Join the conversation

  1. I have celiac disease and Hashimoto’s thyroiditis. Can anyone suggest a good pre/probiotic for individuals with autoimmune diseases? When I was making kombucha that seemed to help a lot.

    • I would highly encourage you to look at Plexus products. There are private testimonials groups on Facebook for individuals who have Hashimoto’s. In fact, I have a friend whose in remission. you can find her testimony on my FB group page, Ragan’s Be Well Plexus.

  2. Please know that I am not at all disputing a role for gut health in underlying conditions that conventional medicine often insists are solely emotional/psychological in origin and are “all in your head.”

    BUT: in terms of addressing the root cause, and not just the symptoms, I think we should also address the ugly & scary 800-pound gorilla in the room — that is, it’s possible there’s so much anxiety, depression, and other brain/mood issues in our world these days because we are much unhappier, more discontent, and far less fulfilled in and by our daily lives than many of us would like to contemplate.

    I’m not saying *everybody* is unhappy, just that there might be some difficult questions that we are disinclined to ask ourselves, because probing so deeply might reveal things we are uncomfortable with or afraid of. (Perhaps we don’t like our jobs/spouses/family/homes/cities/selves as much as we might pretend to on the outside, and something — or multiple somethings — are lacking.)

    I addressed this a while back in a (very, very long) blog post:

    There’s also the mismatch between the go-go-go pace of the industrialized world in 2015, and the (presumed) human need for relaxation, stargazing, being quiet and still, getting fresh air, listening to the birds chirp and a breeze rustle the leaves, feeling loved and valued, etc. I talked about this in a response to a question about depression on the infamous Paleohacks site a few years ago. The perma-link to my reply isn’t working, but you can find the question here and just scroll down to my answer: https://www.paleohacks.com/depression/how-wide-spread-is-depression-17428#answer-143133

    I would imagine that for people who *are* very happy and fulfilled in their lives, and can’t imagine any reason why they might *still* nevertheless feel anxious, depressed, or some other way that interferes with daily life, then there’s probably a larger role for gut health or other unknown underlying physical/physiological cause.

    But there might be some people out there who are actually *just fine,* and feeling anxious or depressed is almost a “normal” response to the wackiness of the modern world. (I’m not saying this very well. What I’m trying to say is, I think it’s probably far more common to feel anxious, depressed, or emotionally sapped in our crazy environment, than it is to *not* feel that way.)

    • Certainly there is abundant discord and imbalance in our daily lives! It can be totally overwhelming. What goes on in our minds seems so real, like there is no way to fix it. It’s so real, it seems the very substance of reality, and therefore nothing can fix it….except there are things that can!
      However, IF one’s gut biome is good, and IF proper nutrients are being consumed in beneficial quantities, all that helps the mind/emotions/brain/hormones/nutrition, to function more optimally, therefore handle the terrible stresses more effectively.
      For instance, some research is showing that L.Rhamnosus bacteria, even alone, decreases anxiety and depression.
      Nutrients like 5-HTP are wonderful for helping balance neurotransmitters, as is Rhodiola Rosea. As are B Vitamins.
      But more basic that those, even, is getting really therapeutic levels of a broad-spectrum of chelated minerals [No oxides! No carbonate!], something which has a large list of trace minerals too [there are far more than 20]. Products such as Mt. Capra Mineral Whey, Kelp/sea veggies work great. Even the non-chelated Mezotrace mineral powder works very nicely, sprinkled into all one’s foods.
      There has been some research which shows that things like allergy/sensitivity to things like MSG and Aspartame, can be fixed by taking more Molybdenum and Selenium [Clinical Pearls book–a compendium of synopses of researches] . I’ve extrapolated that to taking a good, broad spectrum of minerals in more therapeutic amounts, to markedly diminish all my allergies, and those of clients [MCS, and other allergies, depending on total load].
      Imho, most people are drastically deficient in minerals and probiotics. . Fixing those can fix a great deal of what ails most folks, helping them better coping with whatever the world throws at us. . We’ve been doing this in our household and for clients; it works very well. . It’s like night and day, often: . One has serious emotional imbalance, takes 5-HTP and/or GABA, and suddenly, they don’t. . Or, has unrelenting knee pain, takes 2 heaping Tblsp. of Mt. Capra Mineral Whey in a liter of alkaline water, and in a few hours, measurable decreased in pain, and better ability to walk. . Or, person with severe allergic asthma, nearly ready for E.R., does avoidance measures, and starts takes 2 heaping Tblsp of Mineral Whey in a liter of alkaline water 2x daily, and wow–the symptoms reduce markedly; triggers no longer cause severe symptoms, no alupent needed.
      Indeed, there are problems which might SEEM like they are mostly due to the stresses we all must endure daily…..some more than others. . But while under that stress, and these measures relieve them so markedly….that would seem to indicate these measures DO have a major role in relief of those issues, and more.

  3. As soon as I take probiotics or probiotics I get a SIBO reoccurrence. Therefore, I stay away.
    I also feel that because I have an impaired immune system, the good bacteria, turn to bad guys.

  4. It is a shame in order to eat healthy organic food and see functional or homeopathic doctors one needs to be way above the average pay scale. It is unfortunate that most supplements and food are too expensive to afford.

  5. Amy,

    I avoid antimicrobials as much as possible, despite having Lyme Disease. The past 2 weeks I’ve had a bacterial respiratory tract infection and I do take antimicrobials, not without hesitation.

    I am on the fence about pro-biotics. Not that they don’t work. But they certainly don’t provide us with the 1000’s of strains that create the ecology of the gut pre-antibiotics. I will continue to take them, however I am eager to get passed this cold so I can get off antimicrobials and re-focus on adding to my health instead of removing from it.

  6. I completely agree with this article and have personally benefited from adding a daily probiotic to my regimen. I started using Plexus products about 10 months ago and I can not begin to tell you the changes in the way I feel physically, emotionally and mentally. I have often complained about chronic fatigue, feeling run down and crappy and most doctors have just prescribed an anti-depression/anxiety medication. While this helped temporarily, I still continued to struggle. Up until 10 months ago, I had never heard of the connection between poor gut health and the effects it can have on your entire body. I was TEXTBOOK case of poor gut health and no physician ever said anything to me about it. They always attributed it to circumstantial situations (new job, small kids, stress) or mild depression. Since I have been treating my gut health with Plexus Probio 5, I feel better than I have in YEARS.

    I am not here to pitch a product, but since some of you have asked for recommendations, I feel compelled share with you Plexus Probio5 “helps replenish internal flora to its proper state of balance in the body, which may create an intestinal system that is less likely to promote the overgrowth of ‘less healthy’ bacteria…..provides 5 strains of probiotic bacteria for supporting the immune system…..contains enzymes to aid in the breakdown of proteins and fibrous foods during digestion, contributing to a balanced intestinal system….and…may help inactivate free radicals or free radical-initiated chemical reactions in the body”

    I would be happy to send additional information about the ingredients in Probio5 and I would welcome feedback from the authors regarding this product. Again, it has changed my life and feel its a good quality probiotic that you may want to consider. http://www.bewellplexus.com

  7. So many prescription drugs also kill off gut bacteria, both good and bad.

    Metformin prescribed for blood sugar issues is one of those.

    Dr. Hyla Cass has a book called “Supplement Your Prescription” that lists several frequently prescribed drugs and the nutrients they deplete.

    She is a psychiatrist who recognized that nutrient deficiencies CAN cause psychological problems.

    • Absolutely, nutrition plays a big part in mental stability. There have been growing numbers of Psych Docs who advise nutritional changes for their patients, with good results, if and when the patients use them. That’s the tricky part.
      Imho, if a person can only grasp taking one or two things, #1 is a broad-spectrum Probiotic daily, and #2 is a broad-spectrum mineral powder [like Mt. Capra mineral whey, or Mezotrace mineral powder], or Kelp/Sea Veggies, daily. Alkalinizing the body using a simple, cheap measure like a bit of baking soda in one’s drinking water, helps too.

      • Hi Chimonger: I would like to add probiotics to my daily regimen and have been looking for one to take. There are so many available and I would appreciate any helpful suggestions you may have. Thanks

  8. I’ve being treated for SIBO by a gastroenterologist. I’m on a low FODMAP diet and taking psyllium (Konsul) and Mirilax for motility, which helps, but prebiotics like resistant starch still cause gas and bloating. And probiotics cause flu-like symptoms, weakness, and feelings of despair. I noticed a white coating on my tongue, a doctor cultured it and said it was candida albicans, now being treated with Griseofulvin and capryllic acid to deal with that. Hopeful that once the candida is in check I can add a beneficial yeast, S. boulardii, in order to keep the candida in check in the future. If anyone has further advice on how to proceed, glad to hear feedback.

  9. I’ve had a fascinating journey with depression/medication/food. I’d have to write a book here to talk about all of it, but basically I’ll just say here that changing my diet at age 51, following the principles of Mark Sisson (The Primal Blueprint), allowed me to significantly lower the amount of depression medication I was taking. I’ve tried twice (unsuccessfully) to completely wean off of medication. I eat a very clean diet but I suspect my gut is not 100% healed. I’d love to be able to afford to work with a holistic/naturopathic doctor but unfortunately I cannot. So I glean what I can from the internet, and have resigned myself to the possibility that I may never be 100% free from depression mediation.

  10. Very interesting article. I too am very interested in which probiotics and supplements are recommended.

  11. This is fascinating – as I’m currently working on my Biome and currently in “hold back” with drugs (on a tapering cortisone treatment – and triple therapy – my UC flare of 8 months is showing signs of not holding as I decrease dose – as I expected. Thus confirming this is a band-aid – giving me time to rehydrate and stabilise from the long term loss. However I am working on all levels with healing – food, stress, meds and natural therapies. The cortisol treatment is definitely affecting my mood and thoughts in an amazingly positive fashion. So this is an induced state, most likely will pass with the taper of drugs which highlights the feedback from Chris re the cortisol response. Interesting.

  12. Hello,
    Like Nathan, I would love some recommendations for where to start with good quality prebiotics and probiotcis. Thank you.

  13. This was a very interesting article. It just makes sense that the foods you eat will affect your mood. My point is that those foods affect your gut and as a result your health.

    I have a friend who´s kid has a mild level of autism and the Dr. gave him a especial diet, targeting the gut´s health with the idea of helping him with his anxiety and stress level.

    I also would like to know what prebiotics are good?

  14. Since
    Taking a high strength & quite costly probiotic my anxiety has
    gone. I strongly believe gut health is paramount to mental wellness. Now it’s time to try & re educate my family & friends who don’t believe in it.

    • Just to add, avoiding sugar in my diet has also helped significantly, but it’s not easy!

  15. William J Walsh PhD has written a book ” Nutrient Power Heal Your Biochemistry Heal Your Brain” and has trained 170 doctors in Australia in using Nutrients to rebalance the biochemistry of individuals with mental health issues. Probiotics come into the treatment as well especially for Autism.

  16. This is a very interesting topic that I enjoy reading and learning more about.

    I too would like some more information on which prebiotics and probiotics you would suggest.

    Thanks for the great post

  17. Your article states there is evidence that probiotics caused “changes in regions of the brain crucial in emotional processing”, and “reduced psychological distress”. But thats not the same as depression.

    Has there ever been a study showing that improving gut health improved depression specifically? If no, then with all due respect, I do not think we should suggest it does.

  18. Any recommendations to go along with the article? What supplements do you like? What prebiotics are good to add? Some actionable advice would be appreciated!

    • I learnt from my personal experience that feeding gut bacteria with only prebiotic can heal even Inflammatory bowel disease (Ulcerative colitis). I believe that we have enough good bacteria in our gut, we just need to feed them properly. Alginates from Kelp Jelly, unique carbohydrates from seaweed worked brilliant for me in 2011. My good bacteria started to grow and has built a big colony of happy species during a year 🙂 Since they are happy – I am smiling too.

    • Everybody take kefir make your own don’t buy out of shops it’s all artificially made buy some grains off eBay and make everyday just google kefir it will tell how good this stuff is it’s fantastic been making my own now for 6months I’m off antidepressants I’ve been on for 8yrs it’s magic stuff

      • I buy Kefir that is cultured AFTER the milk is pasteurized; it is made by one of the biggest dairy producers in Canada and sold at Safeway. I expect that they see a market of good stuff and are trying to supply it.

    • Excellent probiotics all available on Amazon:

      Probiotic-3 by AOR
      Ultimate Flora by Renew Life
      Primal Defense Ultra

      Suggest rotating to get the widest variety of strains.

  19. Wonderful article.

    Probiotics are all the rage nowadays don’t forget these bugs can make neither minerals like Ca, Mg, Zn etc. nor retinol.

    Minerals are crucial for bodily functions.

    • Matt, your absolutely right, I believe minerals are crucial. I would love to further discuss this with you. Please reply with contact info if willing.

      • Hello Patty

        The best book on this subject is The Calcium Factor by Robert Barefoot.

        I initially thought he was a quack but now I hold him in high esteem.

  20. Fascinating stuff! This post was perfectly timed since today is the release of Dr. Perlmutter’s new book “Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain–for Life”. If this book makes the best-seller list like Grain Brain did, this will do a lot to bring the brain-gut connection into the public awareness.

    • I have tried “fixing” my biome several times, but the level of depression remains unaltered.

      Maybe my biome isn’t broke or in need of fixing, and the depression has other causes.
      I have found a combo of over the counter lithium and low dosage SSRIs to be the most effective for me.

      Good luck to others.

      • Hi Beesmakehoney, try completely eliminating fructose from your diet (including sucrose). I did this and my depression cleared 95% in a little less than 2 weeks.

        It turns out about 30% of the population can’t digest fructose properly and so it messes with the gut and can cause depression in these susceptible individuals.

        • I suffer from Anxiety, Depression ,and very embarrassing Bad Breath. I have been dealing with this for 5 plus years. I have eliminated dairy, gluten, sugar, fruits. I have had pylori tests done. I have esophageal reflux. I take probiotics on a regular basis. Any suggestions

          • You could try the toungue scraper, and there are capsules/tablets you can order online or in a health food store that usually have chlorophyll in them to help the body naturally cleanse the breath. Here are a few other things to check first: In case you didn’t know, or hadn’t remembered these things, some medications cause dry mouth, and can lead to bad breath, as does smoking. I’ve heard from an allergist that sinusitis or sinus infection could cause bad breath, as could a tonsil issue. Have you checked to see if you have tonsil stones? You can be grossed out by watching videos on YouTube about these, or just avoid and stick with the medical related websites!