Healing Digestion: Part 1 – Restoring the Mucous Layer

Healing Digestion: Part 1 – Restoring the Mucous LayerPhoto credit: Beth Phillips

Click on the following links to read the other posts in this series:

Healing Digestion: Part 2 – Digestive Tonics
The Dangers of Acid Blockers: How to Heal Heartburn Naturally {Healing Digestion: Part 3}
3 Essential Facts about Probiotics [Healing Digestion: Part 4]
Digestive Enzymes [Healing Digestion Part 5]

Healing chronic symptoms begins by healing digestion even for those without obvious digestive disorders.

Our bodies use nutrients to rebuild and maintain proper function. Without proper breakdown and absorption of those nutrients, it cannot function properly no matter how well we eat or what supplements we take.

Eating a nutrient-poor diet and improper digestion can both cause your body to starve in the midst of plenty.

Conditions Connected to Maldigestion
  • adrenal fatigue
  • allergies
  • anxiety
  • autism
  • chronic infections/syndromes/illnesses
  • depression
  • mental disorders including agoraphobia, dyslexia, dyspraxia
  • motion sickness
  • GERD
  • heartburn/reflux
  • H. Pylori overgrowth
  • stomach/duodenal (small intestine) ulcers
  • gut flora imbalance
  • constipation
  • diarrhea
  • hair loss

The entire symptom and syndrome list is extensive.  

What Came First?
Healing Digestion: Part 1 – Restoring the Mucous Layer
Photo Credit: Cheeseslave

Is your condition causing digestive issues at a cellular level or is lack of nutrients and poor digestion causing your condition?

This concept is a bit of the ‘chicken or the egg’ debate.

No matter your view, eating a nutrient-dense diet along with digesting and absorbing those nutrients will improve health and can do so dramatically.

An inadequate diet and improper breakdown and assimilation of nutrients is a classic recipe for body system dysfunction from the subcellular level to the organism as a whole.

Two very famous protocols that demonstrate the body’s ability to heal with nutrients are the GAPS diet and Gerson therapy. Both have shown great success in reversing terminal illnesses and both focus on nutrition as a main pillar of their healing protocols.

Overview of Digestion

There are two main ways incomplete digestion causes dysfunction: 1) by allowing undigested particles of food into the intestines and bloodstream (engages the immune system causing inflammation and food allergies), and 2) by not fully breaking food down into its usable forms (not able to absorb nutrients).

A quick digestion overview will show you that digestion actually begins in the brain.

As soon as you see or smell your food, the brain sends out the order to start the digestive process and, if you are not stressed, switches the body to parasympathetic mode. This state of the body is required for all parts of the digestive process to work.

Your body begins to produce saliva even before that first bite. Breaking food down thoroughly by chewing and mixing it with saliva is the first part of creating the stomach’s ‘soup’.

Saliva contains important solutes like salivary amalayse, a digestive enzyme that breaks down starches and lysozyme that kills bacteria.

If you wolf down a burger in the car or a microwaved, frozen meal at your desk or standing in the kitchen, the digestive process is already compromised. The stomach receives large chunks of food, little liquid or solutes from saliva, no live enzymes from the processed, dead food, and doesn’t even get a heads up that food is on its way.

All of your parents’ or grandparents’ scolding to slow down and chew your food completely was dead on.

Your stomach’s job is to create an acid soup, called chyme, from the food you swallow. It does this by chemical and mechanical means – producing hydrochloric acid (HCl), enzymes, and other solubles and also by squeezing and tossing the food around.

The stomach has no teeth, so, if the food isn’t masticated by chewing, it has little chance of breaking down thoroughly during the next stages. Each stage is designed to break down a different product.

Much of the enzyme action happens in the small intestine.

As soon as the chyme reaches the right consistency, the stomach signals the first part of the small intestine, the duodenum, to open its valve and let the chyme in.

The duodenum immediately begins to lower the pH to neutralize the acid soup and dumps bile from the gall bladder and digestive enzymes from the pancreas to finish turning the food into its usable parts.

The rest of the small intestine is used to absorb nutrients directly into the bloodstream, and the large intestine is used to reabsorb the extra water needed for digestion after its job is complete.

The bacterial layer, or intestinal flora, in the large intestine work on the very last stage of breaking down the food particles that we don’t use into their food sources. In the process, they create vitamins that we can use.

Then, waste leaves the body via the colon.

This is the healthy workings of a digestive system. If the process doesn’t begin correctly, then the dysfunction compounds as it works its way through the digestive system and we start to see things like holes in the intestinal lining, inflammation, undigested food that feeds the wrong yeasts and bacteria.

This causes havoc on many levels and is a good example of how important it is to have holistic medical care. The individual parts cannot be successfully treated without addressing dysfunction of the body as a whole.

Part 1: Restoring the Mucous Layer

It’s likely that the protective lining of the stomach is not optimal if you are dealing with chronic symptoms.

The first step to a properly functioning stomach is by healing the protective layer so you can then ramp up the acidity of the stomach. If you think you already have too much stomach acid, be sure you read part 2. I’ll explain why the mainstream medicine and pharmaceutical industries have it wrong.

Stomach pH has an ideal range of 1.5-3.5 or acid enough to burn through your floor. Mucosa is the mucous membrane of the stomach and what protects the stomach lining from that extremely acidic environment that we require to break down our food.

Healing the Stomach Lining

The mucosa can often be healed in just a few days because the turnover of new cell growth is so rapid. For those with ulcers, bacterial overgrowth, and significant damage, this process can take longer and should be monitored by a qualified health professional.

The fastest way to heal this lining is by removing irritants and introducing healing compounds. Irritants can be spices, grains/nuts/seeds, dairy, high fiber foods, or food allergens.

  • Focusing on a diet of gut-healing meat stocks, meat and vegetables well-cooked in stock, and eliminating processed foods during this time is key to a quick turnaround.

Long-cooking, mineral-rich bone broths are wonderful nourishing foods, but do not have the same healing components as a meat stock and the abundance of minerals can be hard on a stomach that already has compromised digestion.

  • Many people will also benefit from removing raw fruits and vegetables during this time. Raw animal products like liver, egg yolks, and fish eggs are generally well digested.

This restricted style of eating can usually heal the stomach lining and allow it to regenerate in 3-4 days, though for some people, it can take up to a month. A properly functioning mucosa also allows for a healthy layer of the cells that produce stomach acid. We address that function in Part 2 of healing digestion.

The GAPS Diet

The GAPS Introduction Diet: Stage 1 has a very thorough example of some foods that promote fast healing if you need an example to follow. The entire intro diet is difficult for many people to follow and can cause further health problems, so I don’t recommend following it to the letter unless you are working with a qualified holistic health professional skilled in the GAPS Diet and gut healing.

Each person’s bioindividuality needs to be addressed and supported when following any health protocol.

Some people may need a small amount of grains and starch from the beginning. Many people need to heal the stomach lining and restore proper stomach digestion before beginning a probiotics program. Other factors also need to be considered.

[If you are embarking on GAPS intro, feel free to use this GAPS Intro Quick Guide for easy reference.]

Healing Digestion: Part 2 will discuss how heartburn and GERD are actually caused by low stomach acid and begin to focus on improving stomach acid production naturally.

These are general recommendations and not meant to diagnose or treat a condition. Because of our bioindividuality and individual circumstances, full healing protocols will vary.

If you are not comfortable treating your own condition, please see a holistic practitioner who practices nutritional therapy. If you would like to work with me as a distance client, please contact me here.


[Note: I earn a small commission to help maintain this website if you make an Amazon purchase through the links provided – learn more here.]

Gut and Psychology Syndrome by Dr. Natasha Campbell-McBride, MD, MMedsci(neurology), MMedSci(nutrition)

Introduction to the Human Body: The Essentials of Anatomy and Physiology by Gerard J. Tortora and Bryan Derrickson

Why Stomach Acid Is Good for You: Natural Relief from Heartburn, Indigestion, Reflux and GERD by Jonathan Wright

Jennifer Nervo is a Nutritional Therapy Practitioner, Reiki Master Practitioner & teacher, and Aromatherapist. Her focus is on digestive, nervous, and immune system dysfunction and the fields of functional nutrition & psychoneuroimmunology. She works with all conditions and diseases including environmental and food allergies, autoimmune diseases, multiple chemical sensitivity, diabetes, eczema, anxiety, weight loss as a symptom of dis-ease, and gut-brain disorders like autism.

When she’s not herding her small troupe of monkeys or seeing clients, her free time is packed with researching and perfecting new wellness techniques (her not-so-secret passion). Jennifer is currently a group leader for the newest class of Nutritional Therapy Practitioners out of Ann Arbor, MI, studying for the national board exam in holistic nutrition, and running a combined distance and brick and mortar practice in metro Detroit. She’s also a homeschooling suburbanite, foodie, and mama to two littles and a schnoodle.

56 thoughts on “Healing Digestion: Part 1 – Restoring the Mucous Layer”

    • Thank you so much! you have no idea how this article has helped me! I always read that you should always eat lots of fiber for your stomach and health, but I found this only aggravated my condition. This idea of meat soups is perfect and makes sense for healing because I notices low fiber low fat foods as things my stomach tolerates well.

  • We are in that class of crazy people where GAPS was great for starting our 9mo on solids and caused our 3yo to break out in a full body staph/yeast rash from hell that NOTHING seems to be able to kill. Look forward to reading more!

    • Poor little bunny! I suggest raw organic apple cider (with the mother) vinegar baths [www.20somethingallergies.com/detox-bath-method-and-recipes/] for yeast. The only things that I know work well for staph/broken skin are manuka honey, matcha tea, and bleach baths – similar to pool water, but not on my recommended list – combined with skin wraps. Steroids make is spread, lower the immune system, and are definitely a case of the cure being worse than the cause.

      You many want to look into my skin balm for helping to heal the damaged skin during and after the infection is gone too [www.20somethingallergies.com/diy-healing-skin-balm/].

      • We fought staff with bleach baths for 8 months. Switched to soaking area with organic apple cider vinegar & a week later lots of improvement, 2 weeks later gone. My feeling is the bleach was killing the good bacteria on the skin that the skin needed to fight the infection.

  • This is a great post! Thanks! Can I ask why the intro diet “can cause further health problems, so I don’t recommend following it to the letter”? I was thinking of trying the GAPS diet or just Intro diet to see if my ezcema on my fingers clears up. Can the intro diet make things worse instead of heal?

    • I explained it in general terms in the post but can’t really get into specifics without a full client evaluation. It is based on individual needs, and we’re all different. If you read the previous comment, Leah had great results with her youngest child and very unpleasant results with her oldest.

      I would suggest easing into GAPS and evaluating how you feel and your symptoms as you go. Many of Dr. natasha’s ‘die off’ symptoms she suggest we push through can be toxins that are damaging to the body or allergic reactions that should be addressed in a different way. I suggest a GAPS-like protocol that incorporates a rotation diet. You can find more about how we eat in my ‘What We’re All About” menu pages.

      You can also check out my DIY Healing Skin Balm for your hands while you’re healing if you’re interested (http://www.20somethingallergies.com/diy-healing-skin-balm/).

  • Just ordered the GAPS book and looking forward to it’s arrival. I’ve tried a lot of anti-candida supplements which helped while I was on them. Symptoms returned when I finished them. For some reason, ACV and other fermented foods cause loose stools and digestive problems. Will GAPS help? I’m already gluten free and have given up most processed food.

    • GAPS can help and has helped a great many people. I’m sorry but there is no way of knowing if it is your best option without seeing you as a client. I would definitely recommend reading the book to understand the protocol, the cause of many health issues, and what is happening within body. It is a fantastic book filled with wonderful information.

      You can start the program and determine if there are any changes you need to make while you are on it based on how you feel over time or see a qualified holistic practitioner to help you with the process and make any needed modifications.

  • Just found your site…thanks for all the great information. I’m looking for a way to proceed with mine and my daughter’s terrible allergies/asthma, and her overactive thyroid. I was wondering if you had a gut permeability test done to be sure you had a leaky gut before starting the GAPS program?

  • “Many people will also benefit from removing raw fruits and vegetables during this time. Raw animal products like liver, egg yolks, and fish eggs are generally well digested.”

    Should raw, fermented vegetables be eliminated? And are there any other good protein sources appropriate for this stage besides raw meat?

    • For those people who can’t digest raw fruits and veggies, I would also suggest removing fermented for a time during the healing phase. For most people, it will only be for a short time. The juice from fermented veggies should be a good source of vitamins, minerals, and friendly bacteria if well tolerated.

      Cooked meats are still a good source of protein.

  • Thank you so much for all your information, it is great!
    I have a question about the GAPS intro. I am doing it now for 2 weeks and the only difference I notice is that my bowel movements are less frequent (around the other day instead once or twice a day as it used to be), but my stool is still sticky and sometimes rather thin. I do not experience any die off. Any idea if this is okay? I am having 3 Biokult capsules a day, 1/2 cup whey and sauerkraut juice/portion soup or stock, egg yolks, FCLO 1 tbsp/day and I had some fermented fish. Can I go on with the next stage or should I wait?

    • I am certainly not the GAPS expert, but I do know that each stage should take 1-4 days. It sounds like you’re doing a great job so far and are in good shape to move to the next stage.

      Though there is a lot of debate over whether dietary fiber is a necessary part of colon health, I feel that your changes are resulting from a lack of dietary fiber and will likely resolve once you are eating a balanced diet that includes raw plant fibers again. Dr. Natasha suggests enemas if you are not having a movement within 24 hours to keep toxins from reabsorbing. I prefer to start with vegetable juicing before moving to the enema stage, but the important thing is that things stay moving.

    • I’m not sure exactly what information you are looking for. If it’s about GAPS, let your practitioner know your symptoms and situation and see if s/he has any input and ask any questions that you may have. Be sure to read Gut and Psychology Syndrome before starting the protocol or speaking to your doctor, and write down any questions you may have to ask him/her when you do discuss it.

  • How can you tell when your stomach mucosa is healed? I know you said more severe cases need guidance from a holistic practitioner; how do you tell if you are one of the people who only needs 3 or 4 days? And thank you for sharing this great information! I just found your blog and am really looking forward to looking through all your posts 🙂

    • I’m so glad you found me Jodi! If you have had digestive distress for some time, you may need more time to heal. It takes some people months, but we all heal at a different rate. A good rule of thumb is to work on this step for 4-7 days, and then begin to introduce the digestive tonics of step 2 while continuing with the gut nourishing foods of step 1. If the tonics are well tolerated (no burning or pain), then your stomach is ready to handle the acidic environment that it needs to properly digest your food.

      Personally, I needed to work through both stages slowly. I started with supplementing a small amount of HCl and worked my way up as my mucous layer healed.

  • Is it normal to have a herxheimer reaction to this protocol? I started this morning and had chicken broth with carrots, onions, and peppers (all well cooked) for breakfast and lunch with a little salt and had a teaspoon of honey (raw, local, good honey) in between because I tend towards low blood sugar, and now I’m feeling dizzy, feverish, with sharp stabbing pains on and off in my stomach and joint and muscle pain throughout my body. Oh and I feel nauseous. With my health, all of these separately are actually rather normal, but all together and so intense is unusual. I’m just wondering if I should ease into it with maybe one cup of bone broth a day instead. Thank you!

  • Are you suggesting to eat nothing but meat stock for 3-4 days? If so, what about taking prescribed meds during this time. I am on a ppi. H2 blocker, & carafate?

    • No, only the most severely damaged tissue will require clear broths with no food. In the article, I suggest the types of foods you should be eating. Well-cooked foods allow your body to rest and better absorb nutrients when the intestinal lining is damaged and the digestive organs are dysfunctional.

      Do not go off your meds without being under the care of a health practitioner qualified to monitor your progress. You will likely need to follow this process for some time while continuing to take your GI prescriptions and adding in additional gut healing supplements. The acid blockers and suppressors will need to be slowly weaned off as your mucosal lining heals and is able to handle the additional stomach acid.

      If you have ulcers, I would also recommend looking into an H. Pylori infection. It’s often the cause of ulcers.

  • I have severe digestive issues- nausea, bloating, constipation, diarrhea, heartburn, fatigue, the works. I have flirted with the GAPS diet, but found it quite difficult, as I am a committed vegetarian. Do you have any ideas of how I can adapt the GAPS diet for my lifestyle? Thank you!

    • There is no way to adapt GAPS to a vegetarian lifestyle as our bodies require the nutrients in animal products to heal. For those of us who can’t tolerate eggs and dairy, there is no other way to obtain the proper nutrients.

      Unfortunately, ethical beliefs are often at odds with our bodies needs. :/ I choose to eat local meat fed a proper diet – for that species – raised by a farmer that I know well. It’s the most humane and healthful option for omnivores.

  • Do you have any healthy natural ways that someone with Sjogren’s Syndrome can get a protective mucosal layer back in their tract since SS dries that up? It dries out our digestive enzymes, too, but we have to be careful taking them as supplements because there can be burning and damage to the lining since the mucosal layer is being withered away from the SS. What a situation.

    • I would continue with constant mucosal support while you follow an autoimmune protocol to address the underlying issues. My clients begin with changing to the Autoimmune Paleo diet + white rice with a rotation diet, nutrient supplementation, and additional alternative modalities.

      You can use mucilaginous herbs like in my sore throat lozenges. I use these for my daughter to help calm inflammation and protect when she has a flare.

      Essential oils can also be helpful, since they can act as an adaptogen and quickly help the body to rebalance itself.

  • Hi, for many years I laughed at the “natural remedies” thinking they were BS. I’ve been a martial artist for several years and in the past 4 years or so have gotten into Chinese Martial Arts, and many of the other students have sold me on the idea of holistics after numerous conversations. 5 years ago I had to have a huge vocal chord polyp surgically removed and the ENT put my on Nexium, even though i was only getting periodic heartburn from eating garbage occasionally. I took this for about 6 months and abruptly stopped, which I’ve since learned is a mistake, and experienced severe rebound symptoms. Ever since going on the Nexium, I’ve experienced severe GERD-like symptoms, even when on the medication (although i do not get heartburn on the medication). When I’m off the medication I generally have severe heartburn and GERD symptoms. I went to a specialist for this, who scoped my esophagus and stomach and found no issues. The answer? More Nexium? If 20mg and 40mg and 80mg are doing nothing, then how is 80mg + a Pepsid going to do anything? I’ve sinced weened myself off the Nexium and have been having significant heartburn after every meal. I think the GERD symptoms actually have subsided a bit (hoarsness, lump in throat, heavy stomach feeling, etc). The more I’ve been reading on the natural sites the more everything is starting to make sense to me. As of today, I started supplementing with a Multi-Enzyme with a dose of HCL built in at the suggestion of one of the other students in my Wing Chun class. My reflux symptoms were barely evident after the meal. Your site is exactly what I’ve been looking for. I am sure that I damaged my stomach lining from that initial phase of Nexium. I’d like to start from the beginning and try to heal that first (if there is any damage) and then move onto the HCL treatment. Should I cease the Multi-Enzyme/HCL supplement and do the 3-4 day broth diet? Also, Is it OK to eat the actual chicken in the broth when doing this? I noticed you say no spices. Does this mean no onion or anything in the broth for flavor? Sorry for all the newbie questions, but I literally am just starting to wrap my head around this stuff. The “low stomach acid” explanation absolutely makes so much more sense with my symptoms. For example, i kept explaining that i have a “discomfort” in my stomach after eating, but its not heartburn. It just feels like pressure. The doctor kept insisting that he wasnt sure what it was and just take more Nexium. Well duh! When I read that Nexium is blocking my acid production, then wouldnt it be obvious that the uncomfortable feeling is just a ball of undigested food sitting in there??

    One more thing. Not to get too gross, but I had a stomach bug several weeks ago. I ate broccoli raab at 6 pm on Thursday night. Friday night at about 3 AM i saw that broccoli raab in its recognizable state in the toilet after i threw up. That cant be normal digestion…

    Keep up the good work.


  • Hi I’ve been struggling with digestive issues for a few months now after a few rounds of antibiotics (last one was in january). I’ve been on an anti candida protocol and have been eating an autoimmune paleo diet tho I also have FODMAP intolerances. I am somewhat intolerant to fermented foods along with some other histamine rich foods (massive brain fog, tho I have a constant low grade brain fog, fatigue, muscle weakness, white tongue (not yeast), trouble sleeping, and poor skin quality). I am working with a naturopath on my adrenals and thyroid. I had been taking hcl with foods (I eat about 5 meals a day, 10g or protein or so) just fine and then had stopped recently cause i didnt know if i needed them – this was before I knew I should wait for the burn. I have been taking digestive enzymes which help a lot with gas and bloating tho I am still have trouble with FODMAPS. I tried taking hcl with my meals again (after a couple weeks not on them) and I can’t tolerate them at all! Bad intestinal pain about an hour after taking them. I’m not sure where I should go from here. I have bad constipation and rely on magnesium to go daily, have undigested food in my stool (oh I’ve also recently started removing high oxalate foods from my diet which has helped with joint pains but makes me need to take more magnesium. Given I am low carb for the yeast (actually waiting on a stool test to see if yeast is still an issue, along with a culture of my tongue to see if mold is an issue?), intolerant to fodmaps, have histamine issues, and doing AIP and am avoiding oxalates, finding good foods to eat has been confusing. I have been seeing some improvement but feel stuck now. I have a feeling my stomach acid is still low? Enzymes are helping. I have pain/discomfort around my liver so I know that can affect digestion (been doing castor packs and detox baths that have helped a little tho not hugely). I guess I am just looking for some advice and would greatly appreciate it!

    • This is the first in a series of posts that go through the basics of healing digestion (all of the posts are linked at the top), but I don’t list a one-size-fits-all healing protocol on the blog. My clients all receive individual ones tailored to their biochemical individuality and needs.

  • I know this is an old post, but I have a quick question. I’m weaning off of nsaids for chronic pain and I know they have upset my GI tract and causing problems. Would it be best to start with a meat broth, to heal the lining, and then introduce ACV or HCl? I know I need more stomach acid but don’t want to start with acid if it’ll just irritate things more. thanks!

  • Hi,

    When you say our intestines can have holes does that mean food & waste is sitting in my body? And how does not having a gallbladder affect part one of this protocol?

    • Those tiny perforations do move partially digested food and waste from the intestines into the bloodstream, but your detoxification system works hard to flush out as much as possible. Having compromised digestion also burdens the detoxification and immune systems, and that’s why we feel ill when we aren’t ‘sick’, start reacting to foods and synthetic chemicals, and begin to notice signs of ill health that often seem unrelated to each other.

    • Just above the post there is a gray box with a white envelope inside of it. You can click on it and it will begin the process. That’s the email share icon. You can also share using the adjacent social media icons or copy and paste the web address into an email. I hope that helps!

  • Hello Jennifer, I have burning sensation anytime I eat anything and drink water. I feel heat/burning sensation most times starting from my buttocks, some times down to my foots and sometimes I will be feeling it randomly. Please help me out. I have been very uncomfortable about life.

    • Again, when am taking any cool or hot thing like tea or hot food, I feel it how it descend on me. I feel like pouring water at the surface of one skin.

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