#140 How to Heal Your Gut in 5 Simple Steps

How to Heal Your Gut

New research shows that having the wrong gut bacteria may cause weight gain, illnesses, allergies, autoimmune diseases, and problems with your heart.  Indeed, a study this past week showed that within 4 generations on a low fiber “modern diet” your beneficial gut microbes may become forever extinct.  In this article, I will share with you 5 simple things you can do to heal your gut and prevent chronic medical problems.

The Challenge

The number of bacterial cells in your gut out number the rest of the cells in your body by 10 to one.  The modern diet, low in fiber and high in sugar and saturated fat, wipes out healthy gut microbes.  Even worse, modern foods promote unhealthy strains of gut bacteria which may cause chronic medical conditions.

Weight Gain

Regardless of your willpower, you may never lose weight with the wrong gut bacteria in place.  Likewise, pre-diabetes and diabetes may also be caused by these same “bad” bacteria living in your gut.  To better understand the science of gut bacteria and weight gain, please read my previous blog.

Illnesses, Allergies, and Autoimmune Diseases

Do you seem to catch every cold going around?  Do you suffer from allergies?  Are you battling an autoimmune disease?  If so, your immune system challenges may be from the wrong gut bacteria.

Fully 70% of your entire immune system is in your gut.  What is happening to your gut’s immune system may also be affecting the rest of your body.

Cardiovascular Disease

In addition to weight gain and diabetes, new research shows that high cholesterol and heart disease may also be caused by the wrong gut bacteria.  Until recently, researchers were not sure how the bad gut bacteria caused heart attacks.

The link between bad gut bacteria and heart attacks may be due to TMAO.  TMAO, or Trimethylamine N-oxide, is a chemical produced by the wrong strains of gut bacteria.  TMAO in the blood may be a bigger risk for a heart attack than even high cholesterol.

People eating foods high in carnitine and lecithin produce a lot of TMAO.  Carnitine and lecithin are especially high in meat and eggs.  Red meat seems to be the biggest offender of TMAO creation by the gut bacteria.

Interestingly, studies show that people on antibiotics produce little TMAO.  Likewise, a vegan who suddenly eats a big steak also won’t produce much TMAO either.  However, if the vegan starts eating meat daily then their gut bacteria will start making large amounts of TMAO.  The bottom line is that if you eat a lot of meat and eggs on a daily basis, you will grow large amounts of the TMAO producing bacteria in your gut.

One puzzle to the TMAO theory of heart disease is fish.  While fish eaters have long been known to have lower rates of cardiovascular disease, fish eaters also have TMAO in their blood.  One theory to explain this conundrum is that the TMAO produced from fish is eliminated easily by the kidneys.

Are Good Gut Microbes Becoming Extinct?

A very sobering study on the gradual extinction of beneficial gut microbes was just published this past week by Drs. Erica D. Sonnenburg and Justin L. Sonnenburg from Stanford University.  It is well known that beneficial gut microbes thrive on fiber.  Fiber is their fuel source.  If fiber is not available, these healthy microbes die from starvation.

In their place will emerge strains of “bad” gut bacteria causing weight gain, poor immune system function, and heart disease.  These “bad guys” in your gut love the modern diet.  They especially love massive quantities of sugar, artificial sweeteners, refined carbohydrates, and saturated fats from animal products.

Although this Stanford study was done in mice, the findings may apply to you as well.  To study the effects of fiber on the human gut, they bred mice without any bacteria in their guts.  Next, they populated the guts of these germ free mice with healthy gut bacteria taken from humans through a procedure known as a fecal transplant.  In this case, they transplanted healthy “poop” from humans into the guts of these germ free mice.

With healthy human gut microbes in place, the Sonnenburgs then put these mice on a low fiber diet similar to what most Americans eat.  After several generations of mice, here is what they found:

1. A low fiber diet kills off beneficial gut microbes.

2. Healthy gut microbes gradually become extinct on a modern diet.

With each generation of mice on a Western diet, healthy strains of gut microbes became progressively extinct.  By the 4th generation, the mice had forever lost 75% of the beneficial strains of gut microbes.

3. A healthy diet alone can’t bring back healthy gut microbes.

While a high fiber diet allows the surviving beneficial gut microbes to multiply, a healthy diet alone could not bring back healthy gut microbes from extinction.

The finding that healthy strains of gut microbes can become extinct is a new scientific finding.  This finding has serious implications for the health of your children and grandchildren.  On a bigger scale, if healthy strains of gut microbes are forever lost from the human race, chronic medical conditions will afflict even more people.

Of course, it is possible that after thousands or possibly even millions of years your body may learn to adapt to a low fiber diet.  In the meantime, what can you do to prevent the extinction of healthy gut microbes from your family line?

Heal Your Gut in 5 Simple Steps

1. Eat a High Fiber Diet

While our ancestors once ate more than 100 grams of fiber daily, the average American now eats just 15 grams of fiber each day.  Even our government has set the bar very low by recommending just 14 grams of fiber for every 1,000 calories you eat.  Thus, a person eating a 2,000 calorie diet only needs a mere 28 grams of fiber daily according to our government.

Since reading this article, I have tried to significantly increase my fiber intake.  Even while traveling most of last week, I still averaged 81.1 grams of fiber each day.  All of this fiber was from natural whole foods.  No supplements were taken.

To increase your fiber intake, eat more fruit, vegetables, legumes, nuts, and seeds.  If you enjoy grains, make sure they are only whole grains which are high in fiber.

If you currently don’t eat much fiber, talk with your doctor first.  Suddenly switching from a low fiber diet to a high fiber diet could cause abdominal distress and possibly even an intestinal blockage.  You may need to gradually increase your fiber intake.

2. Eat More Fermented Foods

While fiber allows good bacteria to multiply, to introduce new healthy strains of gut bacteria you will need to eat more fermented foods.  Some examples of fermented foods include yogurt, kefir, natto, sauerkraut, kimchi, etc.  One ray of hope from the Stanford mouse study was that if researchers did a fecal transplant and fed the mice a high fiber diet they could restore a healthy gut.

Most of my patients are not willing to sign up for a fecal transplant.  Besides, a fecal transplant is still considered “experimental” and is only indicated to treat the most severe cases of C. diff colitis.

Thus, to introduce more healthy gut bacteria, eat more fermented foods. While I still don’t like fermented foods, I make it a point to eat them on most days.

If you have a weak immune system, talk with your doctor first to make sure it is safe to consume fermented foods.

3. Avoid Unnecessary Antibiotics

While antibiotics can be life-saving, most antibiotics currently used in the United States are unnecessary.  Unnecessary antibiotics in human and animals are breeding superbugs that can no longer be treated.

In addition to killing harmful bacteria, each course of antibiotics also wipes out billions of healthy gut microbes.  These healthy gut microbes may forever be eliminated from your gut and family line.

Work with your doctor to make sure any prescribed antibiotics are absolutely necessary.  Also, if you must take an antibiotic, be sure to quickly replenish your healthy gut microbes with plenty of fiber and fermented foods.

4. Give Your  Children Every Advantage

Many mothers have no choice but to undergo a C-section or feed their baby formula.  The beneficial gut microbes a baby starts this life with is determined, to a large extent, by a normal delivery and drinking mother’s milk.

As children grow older, do everything possible to encourage high fiber and fermented foods.  Work under the direction of your pediatrician as to when these healthy foods can be safely introduced.

Yes, children will fuss about eating healthy foods.  Don’t give up.  Starting off life with a healthy gut can help them to avoid weight gain, allergies, and future heart problems.

5. Don’t Live in Too Sterile of an Environment

Anti-bacterial soaps, toxic cleaners, hand sanitizers, and too much time spent inside may wreck havoc on your immune system and your gut.  Sadly, your contact with the microbial world is shrinking with each new generation.

It has long been recognized that farmers, children from big families, or people with pets suffer less from allergies and asthma.  Indeed, exposure to microbes in the dirt, microbes from a sick sibling, or microbes from a pet may help to fine tune your immune system.

These observations provide the basis for the hygiene hypothesis.  The hygiene hypothesis states that if your hygiene is too sterile then your immune system may not function properly.  If your immune system doesn’t get enough exposure to the microbial world then it could look for the wrong things to attack and cause conditions like allergies and autoimmune diseases.

The Big Picture

More and more studies are pointing to a healthy gut as one of the most important things you can do to maintain an ideal weight and prevent chronic medical problems.  The study by Erica and Justin Sonnenburg is a call to action now to prevent healthy gut microbes from forever becoming extinct in your family.

Please leave your experiences below on how you have healed your gut.  Also, if you have any questions about what you have just read, please leave your questions below.  I will do my best to answer every question.

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Disclaimer Policy: This website is intended to give general information and does not provide medical advice. This website does not create a doctor-patient relationship between you and Dr. John Day. If you have a medical problem, immediately contact your healthcare provider. Information on this website is not intended to diagnose or treat any condition. Dr. John Day is not responsible for any losses, damages or claims that may result from your medical decisions.

  1. What about subsidizing one’s fiber with psyllium husks or another type of fiber in a glass. If so what type do you recommend? Thanx.

    • Hi Bill,

      Great question! I am always a fan of getting all of your nutrients, including fiber, from real food sources whenever possible. Unless your doctor has specifically prescribed a fiber supplement for you, I would first try to see if you can meet your fiber needs from real whole foods.

      Hope this helps!


  2. Great information, thanks so much Dr Day!
    So how much can probiotics help, and which type is best? Can they replace missing bacteria?

    Thanks in advance

    • Hi Bernie,

      Great questions! The problem with all the probiotics is that they are not well regulated and the types of microbes tend to be very limited. This is why I specially suggested fermented foods. With “real” fermented foods you are much more likely to get many more different strains of beneficial microbes.

      While probiotics/fermented foods may help to replace the beneficial gut microbes, this may not be where most of the benefit comes. It may be that the greatest benefit comes from fine tuning the immune system. In other words, as these microbes from fermented foods come in contact with the gut’s immune system it may help to keep the immune system functioning properly.


  3. Hi dr John day

    thank you for this good article . I follow most of it . I also take a small amount of kefir every morning . Just wondering about your thought on this fermented drink . It is widely drank in Eastern Europe but not popular in the west . I believe it as help me a lot

    • Hi Dave,

      As long as there is no added sugar to kefir, it is a great fermented food. Many of my patients even make their own kefir. Despite a slow start, kefir is rapidly growing in popularity here in the U.S.


  4. Hi Dr. Day
    I have been taking Prilosec for the last 2 years to quiet ulcer-like stomach pain. The pain stopped about 1 month after I started taking the Prilosec but I kept on taking the Prilosec. I recently felt like I should stop taking the Prilosec to restore my normal stomach acid level. With the ok of my Primary Dr. I have now stopped the Prilosec but have been experiencing acid rebound. The high acid level is slow going away. Have others experienced this acid rebound?

    • Hi Leon,

      Prilosec and the other proton pump inhibitor medications (Prevacid, Nexium) are great at reducing stomach acid but also block the absorption of many key things such as magnesium, vitamin B12, etc. Some people do experience an acid rebound when stopping this medication.

      The real answer may be to find the cause of your acid reflux symptoms. I also took Prilosec for years (I had eosinophilic esophagitis). In my case, losing weight and stopping dairy were key in putting an end to my acid reflux symptoms and for putting my eosinophilic esophagitis into remission.

      Don’t give up! Work with your gastroenterologist to find a way to get off these medications if possible! Here is an article I previously wrote on this topic: https://drjohnday.com/5-reasons-to-get-off-acid-reducing-meds/

      Best of luck!


    • Hi Brent,

      Yes, prebiotics (fiber) and probiotics (fermented foods) can definitely help to restore a proper balance!



  5. Hi Dr. Day,
    Would you recommend a particular fast to reset your gut? Or is it good enough to just follow the above 5 steps?
    Thank you.

    • Hi Beth,

      A great question. There are lots of popular fasts, cleanses, etc. to help people reset their gut. Despite the popularity of these approaches, there are little scientific data supporting this approach. While there are certainly cases where people may need a reset, for most people these 5 steps should help considerably.