Category: Brain Maker


Gut Bacteria Chart Our Destiny

I have just finished reviewing what I believe is a seminal research article relating to the gut microbiome. The study, written by researchers in Sweden, is titled The Gut Microbiotia– Masters of Host Development and Physiology, and recently appeared in Nature Reviews Microbiology.

If you’ve been following my blog, you are no doubt aware of my keen interest in the role of the gut bacteria, the human microbiome, in the context of how these organisms relate to disease processes. Further, my new book, Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain–for Life, is focused on exploring the underlying research that relates these bacteria to various processes that can then affect the brain, as well as the various lifestyle factors that can be modified to enhance the health of these bacteria, and therefore translate into a better environment for brain health.

I can assure you, there is an abundance of research that is ongoing, exploring the powerful role of the microbiome in human illness. But what these researchers describe is the powerful relationship of the hundred trillion organisms that live within us in terms of our normal bodily function and even with the development of our organ systems.

They eloquently describe how the human microbiome first appears, meaning how we first colonize our gut by passage through the birth canal, and how these bacteria then pave the way for future colonization with healthy bacteria moving forward.

They then explore various modifiable factors that dramatically affect the gut bacteria and are associated with alterations of our physiology. They included a discussion of antibiotics, exercise and other lifestyle issues, diet, and even our obsession with hygiene.

The body of the article is certainly quite in-depth and scientific. But what is so striking is how the authors pursue the relationship of the microbiome not just to various medical conditions, but more importantly, in the actual production of human organs, the development of our immune systems, the function of our gastrointestinal systems, and a variety of other physiologic functions that really aren’t generally associated as yet with the bacteria that living within us.

As they state:

Research over the past decade has accumulated a large body of evidence linking alterations in the gut microbial composition to several diseases, such as inflammatory bowel disease, asthma, arthritis, obesity and cardiovascular disease. Furthermore, it is now clear that the normal intestinal microbiota also influences numerous physiological aspects in the healthy host, including organ morphogenesis, immune system and gastrointestinal tract development and maturation, intestinal vascularization, tissue regeneration, carcinogenesis, bone homeostasis, metabolism and behaviour.

This dramatically raises the importance of our understanding of the microbiome. Basically, this information is breathtaking and clearly serves as a harbinger for defining where science is going to take us in the future.

We live in a time when science is making great progress in developing cures for various illnesses. Unfortunately, at the same time, we are seen issues like Alzheimer’s disease and autism virtually exploding on the scene with no meaningful understanding about what can be done.

As these authors so clearly point out, the changes that are happening to the microbiome may well be associated with these and other unexplained diseases. They make it clear that we are modifying a fundamental control point in our most basic level of physiology. But rather then curse the darkness, lighting the single candle of hope should be what is taken away from this report. That is, we can change so many factors over which we have control to gain a more healthy, robust microbiome. This will no doubt enhance our chances of becoming more disease resistant, and in living a longer and healthier life.

  • ri

    im very curious to know if a long term study has been done on vegans specifically those who follow a high carb low fat lifestyle and the percentage of those who end up developing neurological declines or Alzheimer’s and dementia because these people swear by this lifestyle for longevity and health but their fat intake is usually very restricted and they eat far too many carbohydrates

    • TechnoTriticale

      re: … long term study has been done on vegans …

      Well, they are conducting one themselves, but it’s not clear if anyone is collecting the data. When a premature celebrity departure generates headlines, I usually search to see if there are any dietary clues, and there seems to be a continuing stream of unusual (Harold Ramis) and utterly needless (Robin Williams) deaths, with a vegan diet connection.

      re: … their fat intake is usually very restricted and they eat far too many carbohydrates

      Without careful attention, vegetarian diets inherently omit a multitude of key nutrients. In the context of this blog, perhaps the most important are DHA & EPA Omega 3. This is only available from plant sources from algae (without getting an excess of ALA). I suspect many veg dieters aren’t doing that at all, and even those who are trying for higher fat are getting an overdose Omega 3 ALA and Omega 6.

      Any study of veg outcomes has to perform a pretty deep dive into exactly what they were eating.

      • Ri

        thanks techno yeah I definitely think their diets are lacking in the fat intake or they are getting too much ALA. Many seem to thrive and maintain very slim physiques but I think long term they might be doing their bodies a huge disservice by strictly limiting their fat intake and wasn’t Steve Jobs a vegetarian as well? I

        • TechnoTriticale

          re: … they might be doing their bodies a huge disservice by strictly limiting their fat intake …

          If they are doing that, I agree, but it doesn’t necessarily describe all vegans. I’ve also seen it argued that the low fat makes people grumpier and thus much less willing to consider their consequences. That might not be an unexpected side effect of depriving the brain of nutrients it needs.

          re: … and wasn’t Steve Jobs a vegetarian as well?

          His diet was all over the map during his life, including fruitarian. Low fat zealot Ornish was reportedly his doctor up to his premature end.

          • Ri

            thanks for the reply techno- God Bless Jobs but he was quite the bizarre man from what I read.

        • Just a note – I was a vegetarian for 12 years and ate abundant fats in whole coconuts, avocados, olive oils, and raw almonds among other sources. I now include cold water wild caught fish in my diet after my iron levels were found to be too low. According to my doctor, I shouldn’t be able to get out of bed in the morning, my iron is so low, yet I run and walk 5-7 miles every day…so…who to believe?

          • ri

            Hi SL thanks for your reply – im not vegan but my iron levels are low as well. ive had to supplement with iron from time to time. im always very tired but I function daily with the help of stimulants such as coffee

          • ri – I’m sorry to hear about your energy levels. Taking some of the supplements that stimulate mitochondrial growth like coconut oil may help as well (maybe re-read that section in Brain Maker). I find that regular use of a high quality iron supplement such as Floradix helps me, and without the nasty side effect of constipation that regular iron supplements often have. Other than the matcha and green tea I drink, I’m stimulant free and manage to have the energy to hike, play with my children, and walk or jog everyday with my low iron. I understand that in Asian countries, the scale for iron is lower than that in the Western world.

    • mikemarkham

      Yes, there are quite a few, since vegetarianism and veganism has been around for a long time. Most often, clinical trials are looking at a specific set of values. One of the more prevalent and drastic deficiencies is B12 and is directly related to increase risk of dementia and other neurological symptoms. This has a good collection of studies which show the prevalence of B12 deficiencies:


    • ri – I think you will find some fairly interesting research in The China Study on vegan and vegetarian diets long term. Casein, the protein from animal milk, is often implicated as a causative agent for inflammation and other disease processes in the human body.

  • Fiona Sorensen

    I’m curious about the long term effect of supermarkets and their allowance to sell toxic, sugar-filled colourful food. And of course vaccinations and the ongoing pharmaceuticals injected into our bodies from birth in too many situations. Yes gut effecting.

    • MarcusK

      The signs of the long term effects are already showing: the health of Americans is less than the health of Cubans, although the health buget in the USA is the highest in the world. So health is declining and the question is “when will the politicians open their eyes and admit that a couple of laws need to be changed immediately ?”

  • TechnoTriticale

    All over health news today:

    Structural and functional features of central nervous system lymphatic vesselshttp://www.nature.com/nature/journal/vaop/ncurrent/full/nature14432.html

    Turns out the brain has a previously unknown lymph system. Implications for neuro disorders unclear but easily quite profound. And there is an immune system connection, so probably a gut biome connection.

    • Lynn Dell

      Interesting! And sleep is what is required for the previously known “glymphatic” activity. I don’t know what the sleep induced glymphatic drainage and this new discovery have in common, but it sure is fascinating. Any probiotic mixture that aids in a good night of sleep helps the brain to detoxify, via glymphatic drainage (which only happens well with good sleep), and that is my current appreciation of one of a myriad gut brain connections. It will be interesting to see what new, if any, gut brain connections can be made to this new discovery.

  • rev21

    Thank you for making your research available to so many. I am so grateful for all the information.

    I need assistance: Each time I take probiotics (I like Dr. Mercola’s) I feel well emotionally and physically. However, I develop insomnia. People say in blogs it is Herxheimer reaction, but I am not sure that the insomnia is caused by a die-off reaction when every other system in body is working optimally. Needless to say, I have to discontinue the probiotics each time so that I can slee; go to work; live life . . .

    Please help..

    • PBC

      I’ve had problems with Dr. Mercola’s too. I think it’s the Lactobacillus Casei, which is milk derived and also related to the excitotoxin of glutamate or works the same way as glutamate. I have tried a lot of different strains and researched a lot about different strains. Dr. Perlmutter’s probiotic does not cause any problems for me. However, it only has 4 strains. I alternate back and forth between that one and Gut Pro, which has 8 strains but no dairy. I hope that helps.

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  • MarcusK

    Dear Dr Perlmutter, I am a fan and read almost all your posts. I especially like the fact that you always base your clearly formulated statements on scientific evidence and regularly quote articles. Today you wrote “We live in a time when science is making great progress in developing cures for various illnesses.” which made me wonder… which cures are you referring to?

    • Marcus – I believe this refers to all diseases which result from chronic inflammation, which in turn results from an imbalanced gut microbiota and diet. All the “Western” illnesses (diabetes, obesity, heart disease, Alzheimers, autism, arthritis, MS, cancer, autoimmune disorders, allergies, irritable bowel, etc) would be implicated here, the same Dr. Perlmutter refers to in Brain Maker and his previous books.

      I hope this is helpful.

  • enubus

    Hi Doc,
    Are you familiar with the new test that was developed at Cedars-Sinai in LA to determine whether a patient has IBS and if so give a course of antibiotics to rid the gut of the bad bacteria?

    • Midge Tharpe

      I went through the eval at Cedars and it was determined that I had the bad bacteria. I had to breathe or blow into a specific bag. The results were positive but the doctor left Cedars and went to another hospital out of state. I have difficulty with all antibiotics as they make me very sick with diarrhea and stomach cramps by 3 or 4 days. I now take them by IV which makes it somewhat easier but I don’t take them for this condition. Nothing was done so I stopped going.

      • Diane

        Sounds like they were testing you for Helicobacter pylori. The test is for urea in the breath and the treatment is usually metronidazole plus clarithromycin or another antibiotic. Maybe you should get retested and treated if necessary.

      • enubus

        Thanks for the info

  • Diane

    I would like to take probiotic pills and have tried different kinds, different strengths, etc, but taking them always results in severe constipation. Any suggestions?

  • Teresa

    Have you thought of making your own beet Kvass, drinking milk kefir and raw milk? These are power house and are loaded with great nutrients and a lot of strains.

  • Diane

    Thanks for the suggestions, Teresa. I have been drinking goat’s milk kefir and eating sauerkraut and other cultured vegetables. I will definitely add beet Kvass to the list. As for the raw milk, is it safe for someone like myself who has an autoimmune disorder and an impaired immune system?

  • Teresa

    YW Diane. I believe all issues start with the gut and would recommend you reading Brain Maker by the wonderful Dr. Perlmutter as well as Gut and Psychology Syndrome by Dr. Natasha Campbell McBride. Both worth reading.

  • Cynthia Probst

    I have a question. I’m having a colonoscopy next week and am worried that the prep is going to strip my microbiome. I’ve worked really hard to get it in good shape and feel so much better than I ever have. What should I do after the procedure to rebuild quickly. I make homemade kefir and have it daily. Should I consume extra or what? I’d appreciate any thoughts on this.

  • Lori Wise

    I have been put on antibiotics for 2 weeks. I take a Raw Probiotic 3 times a day with a sip of kombochu. In the last year I have gone to a Wheat Belly lifestyle and lost 25 pounds. In 10 days of antibiotics I have gained 3 pounds and am very bloated. Is there anything I can do in the next 4 days to prevent more weight gain and bloating? Thank you

  • janet

    I started taking probiotics, Once Daily Ultra, because it has the strains that Dr. Perlmutter recommends. Does anyone get nauseous or lightheaded from probiotics? Don’t know if I’m having a bad day or if this is a reaction. I usually take after lunch but this time I took an hour before and have felt sick since.

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