Your Gut: A Delicate Garden?

Reasons Why the Digestive System is Important

by Christiane Northrup, M.D.

Digestive Health

Your gut is a very delicate ecosystem, with more flora (healthy bacteria) in it than all the other cells in the body put together. When this ecosystem is healthy, your digestive tract has the proper balance of stomach acids and bacteria. This allows your body to breakdown food for nourishment and cell repair. Without the ability to absorb nutrition from your food and eliminate waste, you may experience all kinds of health issues that, on the surface, don’t seem to be related to digestion. These include headaches, mood issues, weight gain, menstrual cramps, fatigue, back pain, frequent colds, estrogen dominance, and more.

Reasons Why the Digestive System is Important

If your digestive health is poor, everything suffers. Here are some things you might not know about the amazing digestive system:

Digestive System and Immunity

The lining in your gut is actually part of your immune system. In fact, it’s your first line of defense against bugs and other organisms that can make you ill. For millennia, this immune mechanism was needed for the survival of the species. Humans lived without refrigeration and didn’t always know enough to practice safe food handling. When your gut is healthy, it keeps any foreign invaders in food from getting into the bloodstream. It also protects you from airborne viruses and bacteria.

Digestive System and The Nervous System

Research done in recent years proves there is a real connection between the digestive tract and the nervous system. (To learn more read Michael Gershon, M.D.’s book The Second Brain.) In addition to the nervous system in the spine, there is a nervous system in the gut called the enteric nervous system, which sends signals to the brain and vice versa. If you are anxious, depressed, or stressed, you may notice that your desire for food is different or your digestion is off. Stress hormones can shut down digestion (which results in constipation) or speed it up (which results in diarrhea).

The digestive system actually produces more neurotransmitters than the brain does. I suspect that many women could avoid antidepressants altogether just by supporting their digestive system. How many of us reach for a sugary treat when stressed? This is a short-term (and unhealthy) way to make the neurotransmitters your body needs to restore your emotional equilibrium.

The phrases “Rely on your gut” and “Gut instinct” make more sense than you may realize! As a second brain, it may be more effective. It doesn’t have to contend with the judgmental “committee,” which lives in your left brain and will often try to talk you out of what you know in your gut to be true.

Digestive System and the Third Chakra

As an energy system, the digestive system is part of the third chakra. This area has to do with self-esteem, self-expression, an appropriate sense of responsibility, and having the confidence to “go with your gut.”

ABCs of Digestion

A few months ago, Gerard Mullin, M.D., a holistic gastroenterologist and professor at Johns Hopkins, was a guest on my Internet radio show Flourish! Dr. Mullin is also the author of Inside Tract: Your Good Gut Guide to Great Digestive Health. We explained to listeners that any time you take medicines that block acid production or kill healthy bacteria, you upset the delicate ecosystem in your gut. I understand the desire to quell your symptoms. But remember that you’re not suffering from an antacid or a laxative deficiency. It’s always better to address the underlying issue than to take medicines that can cause other health problems. Here are some suggestions for addressing three common digestive ailments—acid indigestion, bloating, and constipation—without upsetting the natural balance.

Acid indigestion

Acid indigestion, also known as reflux or heartburn, occurs when your stomach acids back up into the esophagus. The standard treatment is prescribing a proton pump inhibitor to keep the stomach from producing any acid or popping an antacid to reduce symptoms.

Proton pump inhibitors are used to treat ulcers, too. The problem is that your stomach acids help balance the bacterial growth in the gut. Too little acid can result in too much bacteria, which can lead to yeast overgrowth (infection) throughout the body, as well as gas and bloating.

This condition is largely the result of a highly-refined food diet, which is converted into high blood sugar too quickly. Your body also needs stomach acids to break down minerals, including calcium, magnesium, and iron. Insufficient stomach acid can lead to deficiencies in these minerals as well as in vitamin B-12. It’s not uncommon for women to develop low bone mineral density (osteopenia) if they take acid blockers for long periods of time.

Bloating and Gas

Dr. Mullin mentioned a category of foods that you may never have heard of—even though you probably eat these foods often. They’re called FODMAPs, which is short for Fermentable, Oligo-, Di- and Mono-saccharides and Polyols. These common, everyday foods are a type of carbohydrate that ferments during the digestive process causing gas, bloating, and bacterial overgrowth. Following a diet that eliminates FODMAPs has been shown to dramatically improve symptoms for Irritable Bowel Syndrome sufferers.

This means cutting out eleven fruits, including apples, pears, and peaches; twenty vegetables, including asparagus, cauliflower, and peas; six lactose-containing foods, including milk and ice cream; four legumes, including lentils and kidney beans; two whole grains, including wheat and rye; and seven sweeteners, including fructose and high-fructose corn syrup.

It’s very common for women to experience more gas and bloating as they go through menopause. These women often become intolerant to foods they’ve eaten all their lives, particularly wheat and gluten. Cutting out these foods can drastically improve bloating, gas, and indigestion for many women. Your normal production of stomach acids declines as you age, too. Taking a digestive enzyme can help you break down and absorb the nutrients in food better.


Magnesium is a miracle mineral. It’s used by virtually every cell in the body and can be particularly beneficial for muscle spasms, migraines, and anxiety. It’s also great for constipation. So instead of reaching for a stool softener or laxative, try 500 mg to 1500 mg of magnesium aspartate (or a blend of different forms of magnesium).

Finally, I always recommend a diet of whole foods that is low in sugar and includes lots of fresh vegetables and greens, lean protein, and healthy fats as well as plenty of water. Processed foods wreak havoc with the digestive system, and can cause acid indigestion, bloating and gas, and constipation. Plus they can rob the body of magnesium.

Last Updated: July 1, 2012

Christiane Northrup, M.D.

Christiane Northrup, M.D., is a visionary pioneer and a leading authority in the field of women’s health and wellness. Recognizing the unity of body, mind, and spirit, she empowers women to trust their inner wisdom, their connection with Source, and their ability to truly flourish.


Add comment
  1. holly
    4 years ago

    You have not talked about chronic diarrea ……I’ve suffered with this for years, tried every holistic modality to help it, have been gluten free, dairy free all this time as well… one has been able to help me, and its just called IBS-D. But it has messed with my quality of life. I have to constantly take Immodium or Pepto Bismol, or make sure there is a bathroom nearby….long trips? No happening. Please help guide me on this

  2. Spencer
    5 years ago

    Thank you so much for this article! I have just started a journey of changing the way I think about my body (particularly the stomach) in order to better take care of myself. Your article has helped me rewrite the narrative of my life by viewing my body as a nation with the brain as the governing center and the stomach as production or agriculture. When the government (my brain) forgets the little people (the delicate ecosystem of the stomach), that’s where the majority of stress arises. If I can’t take care of the parts of me that keep me alive, how can I expand outward to make exciting changes in my life?

  3. Diane
    8 years ago

    Ive recently been prescribed a PPI 20mg – one pill daily. I started to take it but then stopped because I would like to treat my esophagal inflammation naturally.
    Is it possible to to treat GERD naturally. I have mild inflammation, damage to my esophagus. I was prescriped Raberprazole daily for two months. Im afraid to take this medication.
    Do you recommend HCl acid supplement? Is GERD caused by not enough acid in the stomach?
    Kind regards,

  4. Kimberley
    9 years ago

    First and foremost I am proud to call you a Dr. I so wish that I could find a Dr in my neck of the woods that would help me fix my inner gut instead of readily writing out prescriptions for drugs in my case ppi’s and antidepressants.
    I have for 1 year now been suffering with pancreatic issues the only things that was ever prescribed to me was antidepressants because they felt it was due to nerve endings and stress or shingles!!! My very first attack was last March 2014 my enzymes hit 5,000 second attack 2 weeks later after them telling me the chances were very slim of yet another attack raised my enzymes to 7,000 and a year later the beginning of March this year I had yet another attack raising my enzymes to 10,000.Hospitalized for 16 days days this time they decided to do an ERCP and also they removed my gallbladder (fingers crossed) I never have another pancreatic attack.
    As for PPI’S last year because of my pancreatic attacks they said they had one more test to investigate the issue and that was a endoscopy. That test they claimed showed that I have low grade Barrett’s of the esophagus and right away put me on PPI’S. Later I got educated on the dangers of long term use on them that Doctors claim are safe to take for the rest of my life YET the manufacture of these pills will not claim any truth to this!!! I started taking Slippery Elm,DGL and Alkapure which traditional Doctors while at my last Hospital stay claimed is no good?What am I to do as I do not want to get esophagus cancer.

    1. Mona
      7 years ago

      Did this clear up for you?? I’m have the same problem with my pancreas too and I can’t understand because I eat very healthy ..!

  5. Christa O
    12 years ago

    I too am just finishing a course of antibiotics (Levaquin).
    My nutritional counselor mentioned Ultimate Flora Super Critical. It’s a High Bifido 7-day program with 200 Billion live Probiotic cultures. It does seem to help restore things. I get it in the refrigerated section of my local Health Food store. But I too would be interested in more ideas of how to get the gut back on track and flora restored. Thanks!

  6. Linda
    12 years ago

    I’m anxious to share this info with my sweet 80 year young mom who is suffering, not sleeping and chasing tail with medications. It’s been going on for years…here’s hoping.

  7. David
    12 years ago

    How much are you sleeping? You do rlisaee that you need about 9 hours a night of proper sleep, right?Are you getting enough exercise? Are you eating right? There’s a myriad of reasons that you can be exhausted. If your blood tests came out normal, that rules out any physical ailment. It could be something that you’re doing (or not). Make another appointment with your doctor and discuss it in detail with him/her.

  8. Anne
    12 years ago

    Slippery elm is also good for constipation and Speacial K advantage and All Bran.

  9. AV
    12 years ago

    Can you give a more detailed list of the FODMAP foods you mention?

  10. Karen
    12 years ago

    Thanks for this article. Do you have any suggestions to get a gut back on track? I finished a course of clindamycin for a tooth infection, a terrible bout of c-diff after than from the clindamycin, then flagyl for that and now, a month later my gut is still not right. I’m taking florastor but find I just don’t feel well. I know it will take a long time to repopulate my gut with the good stuff, but anything I can do in the meantime? Thank you!

  11. Christiane Northrup
    12 years ago

    Love the liquid chlorophyll idea. Thanks! For the rash under the breast, try an ointment called Resinol. I’ve used it for years. Also unscented baby powder works well. Deborah- love hearing about your experience with improved digestion!

  12. Donna
    12 years ago


    I would like to know what to do to avoid getting a rash under my breast especially in the summer. Is there anything over the counter that can help.

    Thank you


  13. Judy Keller
    12 years ago

    Thank you Desiree. I shall try liquid Chlorophyll as recommended. I appreciate your suggestion.

  14. Debra Burrell
    12 years ago

    Hi Dr Northrup
    I have just started taken a probiotic , vitamin d supplements and eliminating wheat and sugar from my diet . I have noticed no bloating and regular bowel movements with alot more energy and less fatigue through out my busy day.
    It is the flu season down here in Australia and so far I have not suffered from any sickness that has been going around our work place, so far so good.

    Look forward to your next newsletter.
    Thank you D

  15. Desiree
    12 years ago

    @ Judy – I’ve been adding one/two capfuls of Liquid Chlorophyll to a glass of water once a day (tastes like spearmint). It has numerous benefits but is also a powerful laxative as it flushes your system out (so start with one cap in large glass per day a

  16. michelle
    12 years ago

    Thank you Dr Northrup for your fantastic information its a plaesure to read!

  17. Judy Keller
    12 years ago

    Does taking magnesium oil through the skin have the same effect as orally for constipation? I am on the Fodmap diet as recommended by Dr Sue Shepherd but still have issues intermittently with chronic constipation. Any ideas please.

  18. Sandee
    12 years ago

    well i was hoping for more information on how to repair the stomach lining with Vitamins Slippery Elm ect, as I eat healthy foods already. I like other people can not afford to purchase a book which is all this has talked about, I was years on PPI’s and am now off them trying to heal my stomach.

  19. brigitte
    12 years ago

    good article.

  20. Linda Lewis
    12 years ago

    As always Dr Northrup is spot on with her assessment of the gut and it’s health affecting the whole body’s health. Thank you for sharing this information!

  21. Lindy
    12 years ago

    Magnesium pills via mouth/digestive system can cause more mag deficiency. Try magnesium oil via the skin for a safer alternative.

  22. Karen MANDEL
    12 years ago

    Where is the list of 20 fruits, and the 20 vegetables?

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