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Heal Your Gut, Heal Your Brain


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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.

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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.

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Join the conversation

  1. Pro-biotics, yoghurt, Kefir, have never done anything for any of my health issues that are caused supposedly from a dybiosis. Different brands, different strains, etc etc, no difference.

  2. I’ve just read the book “The Skinny Gut Diet”. I remember a few years ago my then naturopath telling me I needed to heal my gut before looking at managing my thyroid and I dismissed it.

    I’m now seeing how important it is to heal my gut, especially since nothing else has really improved my health much.

    Being 30 lbs overweight has crept up over the last 15 years and my doctor recently said I was pretty healthy and had ONLY detected low grade inflammation in my body. That’s from an unbalanced microbiome in my gut!

    I’ve been down the path of treating just the thyroid but have recently started (just this week) on a course of probiotics, digestive enzymes, fibre (from fruit, veg, linseed, chia etc – no grains at all – no/low sugar – paleo basic, I guess).

    I’m hopeful. I see being overweight as unhealthy these days (rather than not looking good).


    • The change in both mine and my husband’s mood and affect has been astonishing since we both started taking Plexus products. I did NOT expect any effect, and have been totally stunned at what we have experienced. Their ProBio5 probiotic actually contains both probiotics AND prebiotics. My husband is experiencing relief from severe IBS symptoms, and our energy level is double or greater. We are blow away by it and are thrilled beyond measure. I am in my 60’s and he is about to turn 60. I still marvel every day at how GOOD I feel!!! As a health care professional myself, I can’t believe I ‘missed’ all this research. I guess when we specialize, we tend to stay within that field and not notice others as much. Now, the more I read on this, the more I am convinced that the developers of the Plexus products have hit upon a combination of probiotics that apparently helps the majority of people–and their “Pink Drink” is truly amazing. I tried it out of curiosity after watching people rave about it for over a year and a half. Now I’m worse than they are, LOL!!

      • I have had anxiety on and off for 20 years just started investigating the link between the vagus nerve which comes from the brain right down into the stomach where the messages go back and forth I am looking at gut health for the first time I have never heard of this before but looking at the research about ithe I going to be reading up on everything and trying each new food group and idea u can as i want to get of the drugs as they are crap and only give me bad side affects and an increase in weight

    • A good way to get some good probiotics in your gut, I think , is to start fermenting your own sauerkraut, pickles , etc. This method is going to have multiple times more Probiotics in a live state as opposed to a capsule.

    • Acidophilus is a good one. Years ago when my children were young (and so was I) I developed IBS which was probably caused by my anxiety and also my very stressful and time intensive career as a court reporter. I took acidophilus for a couple years every day, pill form, and also a tablespoon of Citrucel in water. My IBS resolved, my bowels were corrected. I felt great! Well, here I am now 60 with one adult child with a severe mental illness (schizophrenia) and we have the genetic predisposition for Sz so while I was not shocked I was dismayed because I never believed this would ever actually happen! Sooo long story short, I am now so very sad and also extremely anxious and have been self-isolating and my health has started to suffer. I’m looking into this gut-brain connection lately because I just can’t go on like this. I started back on the acidophilus just a few days ago and praying this helps.

  3. Fluoroquinolone antibiotics – cipro, levaquin, avelox, floxin and their generic equivalents – are particularly hard on the brain. They mess up GABA receptors and cause anxiety, insomnia, depersonalization, and worse. In a survey of 94 people who experienced adverse reactions to Levaquin/levofloxacin, a fluoroquinolone antibiotic, 72% reported experiencing anxiety, 62% reported depression, 48% reported insomnia, 37% reported panic attacks, 33% reported brain fog and/or cognitive impairment, 29% reported depersonalization and/or derealization, 24% reported thoughts of suicide and 22% reported psychosis. DO NOT TAKE FLUOROQUINOLONES IF YOU VALUE YOUR MENTAL HEALTH!! Very little can be done to repair the damage done. They don’t tell you that in the commercials when they say, “see your doctor if __ occurs.” http://floxiehope.com/2014/12/08/fda-petitioned-to-add-psychiatric-side-effects-to-black-box-warning-for-fluoroquinolones/

    • That is NOT necessary to put on these sites how the adverse reactions are hard to repair once damage is done! Have you ever considered how many people are looking for hope and answers. And you ALWAYS post EVERYWHERE about how everyone basically needs to suffer after they have had reactions. YES, they cause damage but so do many other drugs out there. And our bodies are designed to heal with the right things and time. So please reconsider how much fear you put in people who are in fact suffering from these awful side effects. You are adding more fear to everyone with these posts/comments everywhere online. Please consider when you are getting the word out, adding people CAN and DO recover from this…….. God Bless

      • Good point. Nothing is irreversible. Of course some things take more time than others. But robbing people of hope is wrong. On that note, I can’t stand the conventional mindset around “bad news” and “diagnoses”. My limited experience has taught me telling someone they’re going to die or giving them a diagnosis of ANYTHING is a sin. And I don’t mean that in the dogmatic religious fanatic way. I mean it in spirit. When they do that, it is no different than casting g a spell. In fact, it literally IS spellcasting. For anyone who doesn’t matter” get that”, you’re sorely misguided. Blind followers. There is no such thing as “false hope”. Hope is inspired. Hope is gratitude. Giving up, a sin.

        • Did you know that the body is designed to heal itself? As long as you are alive there is always hope. I have a friend that duke University doctors put him on a machine for 10 days in a coma and his organs were renewed. You can go on a 21 day and night fast and you body will renew itself. Research it find out for yourself. The God I serve (his name is Jesus), can do anything but fail.

      • It is my thought that the body can be very unforgiving however, I am convinced that a ph. balanced body recovers from most everything. The one thing that may not be reversable is scar tissue, for example, in the stomach or lungs etc??? I am convinced that sickness, disease, cancer etc. cannot thrive in a healthy host or ph. balanced body. I’ve never seen a sick fish in a ph. balanced fish tank. But what a sewer it is when the tank has not been cleaned. MikeRyan.

        • Again, just my thought but, if everyone were to ph. balance their body’s, I suspect more than half the Dr’s In the world would be out of business, as well as, pharmacists and pharmacy related companies. Forgive the comma’s in the wrong place, I had stomach issues that day in grammer school. MikeRyan.

    • I had the reaction of anxiety, panic, depression, and depersonalization from Prilosec. I have been off of it for 5 months and am still suffering months later.

      • Me too. I have taken Prilosec for years, but have recently quit.
        I have anxiety and depression which have come and gone but have kept me from maintaining a job.
        I have recently, over the past 6 months, have seen the best days of my life. I am 48 years old and turbo charged.
        I have noticed my depression is directly related to city water. Of course! City water has chlorine and flouride designed to kill bacteria. Therefore probiotics do not work. I started treating my acid reflux with Apple cider vinegar, my new balance has increased my energy and I take Maximum Vibrance and have cut out all foods consisting of antibiotics (designed to kill bacteria). Thanksgiving went without turkey and ham. I fill a 5 gallon water bottle from a friends well and eat nothing but fish and venison (what I catch).
        I must admit it takes about a month to feel the diference but I have never felt this alive.
        Good luck to you.

  4. I suffer from both Depression, and H pylori. Due to the medication I am on and can not quit taking for the depression ( citalopram SSRI) I can not take the triple threat treatment for the h pylori. The h pylori is causing the depression to get worse (being in constant pain) my GI doctor has offered no other treatment or solution for the h pylori, saying that the triple threat treatment is the only treatment. Any suggestions?

    • It might be worth your while to look at the website http://www.walshinstitute.org and see if you can speak to one of the doctors listed to see if they could suggest something. They are mainly mental health (Depression) doctors, but deal with a lot of other complaints as well.

    • @Holly Comment
      I don’t know what meds you’re on, so you must figure out if this might help or not.
      But in our family, we’ve repeatedly used GSE to kill off H.Pylori VERY effectively, usually with usually only one serving.
      GSE = Grapefruit Seed Extract.
      It’s very bitter, mixes well in about 1/2 cup water.
      We always buffer that bitterness by adding a packet of Tangerine EmergenC powder to it, too. Citrus flavors help camouflage the bitterness.
      GSE has a VERY long shelf-life. I used some that had been stored at a remote cabin for over 13 yrs, and it was still very strong and effective….it had just turned a darker amber color, over time.
      GSE fixed this way, also kills off most food poisoning.
      My Doctor had always told her patients who were traveling, to use 1 or 2 drops in citrus juice every morning, to avoid catching “Montezuma’s Revenge” [parasites].
      We’ve used it topically and internally, and for disinfecting countertops, etc.
      I’ve also soaked lemons [bot from Costco–those always get moldy too fast] in it in a large bowl, overnight, to help prevent them getting moldy.

    • I got rid of h pylori by taking mastic gum for a month. Testing proved it was removed. Look into it! Hth

  5. I dont know if this conversation is still being looked at but I hope to get a little feedback. This past winter I experienced (for the first time in my life) feelings of severe depression. I have, all of my adult life lived with anxiety disorder, but never depression. I also have, for the past year, been having chronic loose stools (by chronic, I mean all of my BMs are loose, not that I sit on the toilet all day!) In researching the depression, I came across the idea of the link between brain and gut health, so, I have been working with a functional medicine FNP, who has had me on an elimination diet, and now a elimination/candida diet, as well as, a strict probiotic (100b cfus/day) plus specific probiotics, herbal, and vitamin regime. For the past 3 months I have eliminated gluten, corn, soy, sugar and sweeteners, most oils, starches, mushrooms, citrus, limited fruit, several grains, nuts, all white and processed foods, plus I have been vegan for many years. Needless to say, my diet is very clean and I consider it healthy, although I might not really get enough calories, as I am a yoga teacher by trade and probably burn more than I consume. My whole point is, I dont feel any better. Each bowel movement is still loose and almost always urgent. The feelings of depression still linger (although I havent had an episode of severe depression like I did in the winter). Frankly, I havent noticed any benefit at all to this new way of life. Do I need to give it more time? My NP thought for sure I would have celiacs, but gluten free hasnt improved any symptoms nor did it show on tests. My fecal test results show over abundance of some beneficial bacteria, way too high triglycerides but healthy pancreatic enzymes, on the border of too low e.coli. She says my various test results point to malabsorption and leaky gut, but we cant figure out what’s causing it. I just turned forty, am in good physical shape, healthy BMI, healthy diet and lifestyle, practice stress reduction techniques ( am not very stressed anyway), have a healthy self-esteem, spiritual life, financial life, etc. If I could improve one area of life, I guess it would be going to sleep earlier, I stay up late but do get 7-9 hours of sleep everyday…maybe earlier bedtime is important? Should I just be patient to see if the diet and probiotic/herbs/vitamin regime eventually make a difference? Should I visit a more allopathic minded physician to see what they say? I am willing to try anything and happy to hear any suggestions and ideas…this messy poop and lingering odd depressed feeling has got to go! Thanks for reading, I hope to hear some thoughts 🙂

      • I have to agree with you. That book is packed with information if you are looking to understand your gut and its’ relationship with your brain. I recently did a 3 week cleanse from a book called “Clean” and I feel great. I don’t have the book handy so I don’t know the author. I learned from a nurse practitioner that l-glutamine is needed to heal the gut lining. Probiotics as well, but more so after you heal the gut.

    • Hi Lili,
      I appreciate the amount of info you are providing here. 3 months is not very long when it comes to healing the gut and turning things around.
      What comes to my mind is NOURISHMENT. If you are eliminating so many things in order to reduce the irritants and to detox, what are you adding to provide deep nourishment? It might just take time for your body to absorb the good stuff you are providing it. If you have leaky gut then it takes time to heal that. If you are vegan it might take even more time to heal leaky gut. if you are eating a lot of raw then it might not be easiest for the gut to deal with. If you are not opposed to consuming meat broth or fish broth that might do wonders for healing your gut lining at the same time providing deep nourishment that is easy to absorb.
      Are you border line at the low end of your healthy weight? if you have loose bowels every day then you might be depressed from not absorbing enough nutrition. Combination of borderline low healthy weight and loose bowels can result in depression in my experience.
      Tests are tricky to interpret. go for multiple tests over a length of time. Learn this from Chris. Keep going and relax into the process. Getting second and third opinions can’t hurt but might be exspensive.

      • Hi Lili, looking at your diet, like Angela, I’d suspect possible malnutrition. Also, sorry to introduce a new varable, you could be suffering from an intestinal parasite (I had Giardia for years – have you been abroad, could be years ago ?).
        Personally, I think if you’re following the right path, you ought to be feeling much better in a month let alone 3. So I am not convinced of the wisdom of your current regimen. Also, I hadnever heard of so many people suffering on some sort of fructose intollerance. If you haven’t observed any obvious adverse effects yourself, I’d go for more fruits (and the meat or fish Angela suggested). Have a look at the movie Superjuice me and become convinced of its power. Lifethreatening, complex diseases turned around in a month. I did sth similar in one week and it was very powerful. It will confront you though. I practice EFT for that.
        Good luck !

        • Hi David,
          I know it’s been a few years since your post but… I have a quick (yeah right :-)) question… How long did you suffer from giardiasis? I recently tested positive for giardia to my surprise (an earlier stool test showed nothing). I have been suffering from chronic diarrhea for 7 months now and was told it was probably due to mold exposure (I have CIRS as a result), SIBO and collagenous colitis (also a recent diagnosis which some research suggests may be a result of some kind of infection (like giardia maybe?). I’m wondering if the root cause of my problem may be a chronic giardia infection that’s led to these other issues. Just wondered if you would be willing to share your story. Looking for answers. Thanks!

    • You mention depression this past winter – which points to seasonal affected disorder. The best treatment for that is usually vitamin D. I need at least 3000IU to prevent becoming ‘SAD’ late winter. I don’t think the time of day you sleep matters much, as long as you get enough hours and see daylight at regular times to regulate your body clock. A dawn simulator can help to regulate your body clock. I function better keeping later hours. Whatever works best for the individual.

    • It says you are vegan in your post. I’m not a massive fan of meat eating but know on a paleo diet I feel much better. Leaky gut is very sensitive to carbs and carbs do have a massive impact on the gut when it’s leaky. What proteins are you eating? And fats?

    • Get your Vitamin D level checked. We don’t get enough D in the Winter, and that can cause depression. Either supplements or eating a lot of mushrooms will help.

    • Hi Lili, you sound like a classic case of Clostridium Difficile (c-diff) which can cause anxiety and depression. I would ask to be tested via stool stample asap!

      • If you have c. diff you will want to seriously investigate fecal microbial transplant (FMT). It’s an extraordinary approach.

    • Hi Lili,
      Have just seen these posts and not sure if this response is too late…but the first thing that comes to mind when you talk about loose stools and symptoms that worsen in winter (depression) is internal cold (referring to concepts in chinese medicine.) Your digestive tract is a burner that breaks down foods to extract nutrients – internal cold slows this process and it sounds like the foods that are left in your diet would probably be mostly raw and cooling foods, which would make it worse. I would look to warm and nourish your system to support digestion. Look for warming and nourishing foods such as sweet potato, warming broths with garlic and ginger.
      Hope you are doing well.

    • You might want to check out a genetic mutation, the MTHFR 677 that effects the ability of the gut to manufacture adequate enzymes such as methionine, SAMe, serotonin, dopamine and the body’s major detox substance glutathione.

      Everyone gets a Methyl Tetra Hydro Folate Reductase
      gene from each parent. Two mutations ( homozygous) significantly reduce essential enzymes, creating health
      risks. Search Dr. Amy Yasko and Dr. Ben Lynch for
      treatment suggestions ( supplement a methylized folate).

    • Hi Lilli, been there too, for me the answer lay In an inbalance in my Neurotransmitters in part due to a vegan diet. Try increasing GABA with the amino acids Taurine and L glutamine and Glycine for inhibiting Noradrenaline.

  6. i really enjoyed this article, I’m hoping by improving my gut health I can reduce the impact of my ADD to my life.
    I see my biggest challenge as my gastric sleave procedure. I had it done before I knew better and after years of following conventional advise and not making any progress.

    So my stomach is just over a cup in capacity and I’ve lost all the rest of it (literally) so I must repopulate what I have left.
    Apparently I don’t absorb my nutrients properly either (labs to be done next week)
    There’s so much I want to work on but I think gut is the first thing I should work on since it has received the worst treatment from me (I butchered it and have a crazy insane sweet tooth ( I’ll literally eat chocolate till I feel sick and keep going till its all gone, knowing the whole time I should stop but not being able to)
    Tomorrow I quit gluten and start my cross reactive foods research.
    I also brew kombucha and have started trying to involve sauerkraut in at least one meal a day.

    Are there any people like you guys in Australia?

  7. I find that by eating properly maintaining nutrients and recommend everybody do a juicy smoothie once a day, with your veggies, and fruits to keeps the doctor away.

    When growing up my grandparents my grandma Carrie who lived to be in her nineties, family member’s aunt Daisy, who lived to be 106 outlived 2 younger husbands, did not follow all of this stuff and she ate responsibly, but made sure she had that fiber every morning or in her diet.

    My siblings and myself know what good farm fed food is about and were blessed to go to Grandma and Grandpa Cheers farm where they raised and grew every single thing we put into our lives. Thank God for them!

    I really do feel what one persons stomach may need for complete well-being does not mean that another’s stomach requires the same.

    I am 62, walk everyday, eat what I practically want, but am a health nut and have weighed the same most of my life which maintains a young person of age 34 BMI, blood pressure fluctuates, but due to whether I am sitting, lying or standing and live life to the fullest!

    I thank you for your posts Chris and keep them coming!

  8. Wow – interesting article! I have suffered with anxiety from time to time over the last year or so (perhaps it was related to going on the pill and the effects on my gut?)…so I’m encouraged that starting on fermented foods more regularly could help me out!

  9. Any views on feacal transplants (FBT)? Early sparse literature seems to hold some promise in a number of ares including Autism.

  10. Are you aware of any studies that compare the effects of introducing a variety of so-called “pro”-biotics into the human gut? For example, does drinking kombucha interfere with the action of Bulgaricus cultured yogurts? Or how do “pre”biotics affect L. acidophilus colonization? Does B. longum interact competitively with inulin? And do all these biologicals inhabit different parts of the GI system or are they all competing in the same biome?

    It seems to me that many of us are “playing doctor” with our intestinal flora — perhaps to our detriment.

    I know that whenever I take pre and/or probiotics I end up gassy and bloated, often sluggish and low-energy, and craving massive amounts of grain-based carbohydrates — even after several months of use. Given the vast number of these supplements on the market, do you think there should be some sort of watchdog to make sure we’re not inadvertently wreaking havoc in our bowels?


    • The trick to probiotics is human strain. Good quality. Not off the shelf supermarket ones or yakult and all those useless brands. I think unless you have no problems with your guts then taking a good quality probiotic can help many problems.

  11. Splenda has recently been linked to the gut biome, and not in a good way. It seems that Splenda may do enough damage to warrant most physicians in the know to say “no” to the sugar substitute. If you consider the emotional shrapnel as well, the logic holds water. This throws an interesting twist into the fitness industry, where we are fighting an uphill battle against people’s emotions, obsessions, and habits. The best advice is usually the hardest for people to swallow. You shouldn’t be consuming so much sugar in the first place, like maybe 10% of your current intake for most people, so you shouldn’t need to substitute it. We need a whole new appraoch.

    • Adam,

      Great points! I agree with you that it’s often best to learn to favor savory foods and decrease sugar, even sugar substitutes. In working with patients it seems that initially this can take a lot of effort and will power, but eventually most people seem to “retrain” their taste buds. I was surprised that even Stevia was linked to harming the good gut bacteria in one study described here:


      • Very interesting. I wonder how plausible it is that many foods actually do some kind of “damage” to the gut bacteria, as a small part of a larger ecosystem? If I only had a lab and some backing! Thanks for the reply.

      • I read the entire article you referenced. I have to say I’m wondering if you did. The damage was “slight” at best and reading further showed studies revealing many studies showing beneficial results. Just thought I would throw that in. Perhaps it’s all in how we read it?

  12. What is one to do when there are no functional medical doctors in the area?

    • “Functional medicine” is a new (trendy) term, not a formal field of study. Many practitioners in alternative fields (Chinese medicine, naturopathy, etc.) have extensive training in nutrition and establishing a healthy gut biome. Call up some LAcs or NDs in your town and ask!

    • Hi Jackie,

      I wish I had an easy answer for you! And this is why Chris is spending a lot of time right now putting together the Clinician Training program, so that we can get more functional medicine practitioners throughout the country!

      Many of our patients at the California Center for Functional Medicine come from out of state because of the paucity of functional medicine physicians. So, you are of course always welcome to work with us, but I do understand that the investment in both time and expense in traveling to California can be prohibitive.

    • The best answer is, read books and blogs, and watch videos at YouTube. You’re taking a major positive step by being here, reading the excellent blogs at this site. There are other great sites too.

  13. In the study conducted, the subjects were given fermented milk (kefir) twice daily for four weeks with very good results.

    You refer to kefir as having too much sugar to have much benefit (a contradiction to the study). I believe you are referring to manufactured kefir bought in a store. Kefir is the only food that cannot be manufactured, if you are buying it in a store, it is a processed, adulterated version of the real product. The only way to get the fully beneficial kefir is to acquire kefir grains and make it at home.

    My question is: What was the twice daily doseage amount?

    • I agree. Home-made kefir is the stuff of magic. All the author has to do is search on pubmed for the word “kefir” to see studies after studies how potent that thing is (that, and Greek Mountain Tea (herbal), another magic thing that most Paleos don’t know about). I believe that home-made kefir is instrumental is getting the right gut flora back — with time.

      • You are so right Melanie and Eugenia. Kefir is awesome. I start feeling calm after drinking some. And, when you buy the kefir grains you can control the ferment time. A 24-hour ferment will have reduced most of the milk sugars down to 0%. (Plus fermenting alters the milk proteins, which bother some people.) I routinely do a 48-hour ferment cuz I react better to it.

        You can also start making water kefir (if milk is a problem). However, it requires a different set of bacteria/yeasts than milk kefir. Water kefir is our “soda” for the summertime. Once it has fermented (24-48 hours) you remove the water kefir grains, bottle it and add in flavorings: fresh, cut up ginger or turmeric are our favorites. This 2nd ferment develops a real fizz.

        BTW, before I got real milk kefir grains I used the packaged “kefir” grains sold at the co-op. Not ideal, but it still gives you bacteria/yeasts for your gut colonies.

        There is a guy Dom in AU who is an expert on kefir; his FAQ will walk you through how to make it. He also runs a yahoo group about kefir making.

    • Hi Melanie,

      To answer your question about the fermented milk product used in this study, it is described as follows:

      “…fermented milk containing Bifidobacterium animalis subsp lactis (strain number I-2494 in French National Collection of Cultures of Micro-organisms (CNCM, Paris, France), referred as DN-173 010 in a previous publication, together with the 2 classical yogurt starters, Streptococcus thermophilus (CNCM strain number I-1630) and Lactobacillus bulgaricus (CNCM strain numbers I-1632 and I-1519), and Lactococcus lactis subsp lactis (CNCM strain number I-1631). The test product contains 1.25 × 1010 colony-forming units of B lactis CNCM I-2494/DN-173 010 per cup and 1.2 × 109 colony-forming units/cup of S thermophilus and L bulgaricus.”
      This was provided in 125 gram pots consumed twice daily.
      If you follow the link provided this study is accessible for public access, so you should be able to read the full article if you have additional questions regarding the study design.

      And I do agree with you, kefir is a great source of probiotics. I’m sorry if I gave the impression somewhere that I think it’s too high in sugar to be included as part of a healthy diet — I would absolutely recommend homemade kefir!

    • What is the difference between Kefir and yogurt and what are the respective benefits?

      • they have different bugs. I read years ago that kefir can recolonize the gut whereas yoghurt need to be repeatedly consumed (does not colonize). Someone else will have more info in fact, I bet Chris has whole pages on the question of different fermented foods.

  14. Sounds exactly like the information you will find in Dr. Perlmutter’s book Brain Maker.

  15. I have a question. I eat a Paleolithic diet, avoid sugar and processed foods, eat organic, pastured/grass fed meats and tones of vegetables along with fermented vegetables. Exercise and am very healthy, especially for a 62 year old.

    I know young weight lifters and athletic types who have days every week where they consume mostly carbs from sugars, even candy and cakes (carb loading). They are all in excellent shape. Is this diet healthy? How can they get away with it? Thank you in advance.

  16. How very true this is between the gut and our mood! Everything comes from having a heathy intestinal tract. I should know because my is not healthy. I started noticing changes around 50 and by the time I was almost 55 I had been diagnosed with Fibromyalgia, Degenerative Disk Disease, and Ahalasia. Enough said huh ? Does this cause stress ? Yes it’s a definite factor in my life. Medicines for depression do not work for me because my system can’t take it. Two days after trying a medication a bout of terrible diarrhea took place. We have to find other ways of dealing with this. Support groups, family, meditation and additional nutrition. Thanks Jamiep

    • If you haven’t read Mood Cure by Julia Ross, run out and get it right now. I can’t promise it will make everything better, but there’s a decent chance it will help.
      The only thing is, if I recall she doesn’t recommend the dosage of omega-3 that are used in the studies that find it to be effective. Those studies use in the 2000-3000 mg range.

  17. Both my husband and I have found some relief in our anxiety and depression from gut healing. For me, amino acid supplementation is finally what gave me the biggest boost. Though I suspect eating paleo/ancestral/real food type of diet is what allows the amino acids to do their job, along with healing my gut!

      • That’s a big part of the Mood Cure book I just recommended above. She recommends different amino acids for different types of depression (anxious, low energy, etc).