Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:
Anti-Inflammatory Diet and Lifestyle.
There are over 190 articles on diet, inflammation and disease on this blog
(find topics using search [upper left] or index [lower right]), and
more articles by Prof. Ayers on Suite101 .

Wednesday, March 12, 2014

Health in Diagrams I — Gut Flora and Diet

This is the first of three posts to summarize my thoughts on diet, inflammation and disease mediated by gut flora.  I decided that I needed to make my points as explicit as possible by putting them down in diagrams and making references to my other posts.  By the time I finish, I will reach my 200th blog post at Cooling Inflammation.
Everyone Leaves Out Gut Flora
I want to first explain and diagram my current understanding of the relationship between gut flora (the complex community of hundreds of different types of bacteria and fungi in the intestines) and diet.  My impression is that many people have health problems based on diet, but when they try to heal their health, they fix their diet and see only limited benefits.  Medicine provides only a temporary treatment using dairy probiotics.  The problem is that they failed to fix their gut flora, which was also damaged by their unhealthy diet.  

Health Requires a Match between Diet and Gut Flora
It is a myth that gut flora will just adjust to diet and a healthy diet leads to a healthy gut flora.  
A damaged gut flora lacks necessary species of bacteria.  Antibiotics, for example, can permanently delete dozens of particular bacterial species of gut flora that can only be replaced by reintroducing the missing bacteria by eating those bacteria again.  The missing bacteria may be needed to digest particular foods and the result is food intolerances, commonly mistaken for food allergies.  Antibiotic use frequently leads to autoimmune diseases, that are caused by deficient regulatory T cells of the immune system that develop in the lining of the intestines in response to particular gut bacteria.  The natural source of gut bacteria is eating the bacteria clinging to raw or fermented vegetables.
Diagram Showing the Interaction of Food, Gut Flora and the Immune System


Food is just Protein, Fat and Soluble Fiber
The human body produces enzymes to fully digest proteins, fats and one polysaccharide, starch.  All other parts of plants and animals are edible (fermented by gut flora) soluble fiber polysaccharides or insoluble, undigestible fiber consisting of cellulose or lignin, which together also make up the undigested organic matter, humus, of soil.  Grains are problematical for health, because their starch is readily converted to sugar, i.e. high glycemic, and their fiber is insoluble (not fermented by gut flora) and high in phytate.  Phytochemicals, plant polyphenolics, are of questionable value as antioxidants and are of unexplored importance for their antimicrobial impact on gut flora.
Polymers (Protein, Starch) are Hydrolyzed by Enzymes to Oligomers and then Monomers (Amino Acids, Glucose)
The stomach mixes protein digesting enzymes, proteases, and starch digesting amylase, with food protein and starch.  Proteases convert the long chains polypeptides, polymers of protein amino acids, into shorter fragments, oligopeptides.  The specific nature of the stomach proteases leaves groups of basic amino acids (lysine, arginine), heparin-binding domains, intact.  These peptides, similar to the defensins of the microvilli crypts, are anti-microbial and work with residual acidity to reduce bacterial growth in the first part of the small intestines.  Pancreatic enzymes then digest the peptides further and the small peptides are ultimately digested by enzymes on the surface of intestinal epithelial cells just prior to absorption.  Similarly, starch is degraded to oligosaccharide amylodextrins, which are then hydrolyzed to glucose at the intestinal surface prior to absorption.  Amino acids and glucose are not normally available to bacteria in the intestines.
Fats are Dissolved by Bile, Digested by Lipase and Absorbed
Fats are triglycerides, i.e. three fatty acids attached to the three hydroxyl groups of glycerol.  Fats are hard to digest, because they form oily droplets.  The droplets are dissolved in the intestines with bile, which is an acidic form of cholesterol, that is produced in the liver and stored in the gall bladder.  Fat in a meal triggers bile release from the gall bladder into the small intestines.  The bile represents a huge reservoir of the cholesterol that is synthesized by the body and dwarfs the cholesterol content of any meal.  Statins decrease body production of cholesterol, interfere with bile/fat digestion and lower lipid cholesterol levels.  (Unfortunately, lowering lipid cholesterol levels has minimal impact on heart disease and the only impact of statins on cardiovascular disease is through weak anti-inflammatory side effects.)  Pancreatic lipase removes two of the fatty acids from each triglyceride.  The fatty acids (a.k.a. soap) and monoglyceride are absorbed by the intestinal cells and reformed into triglycerides that make their way to lymphatic lacteals and are dumped into the blood, where they circulate as chylomicrons surrounded in lipoprotein.  Lipoprotein lipase binds to heparan sulfate on the surface of blood vessels and gradually removes fatty acids, until the diminished chylomicron is absorbed by the liver and exits as a VLDL.  (Note that this is another connection between lipid metabolism and inflammation, since inflammation decreases heparan sulfate on cell surfaces.  Heparan sulfate also mediates LDL binding to cells and amyloid stacking.)
Plant Polysaccharides are Soluble Fiber and Food for Gut Flora
All that remains of food after the protein, fat and glycemic starch (glycogen) have been removed in the small intestines are plant cell wall polysaccharides, resistant starch, storage polysaccharides, e.g. inulin, plant beta-glucan, animal glycans, e.g. chondroitin sulfate and heparan sulfate, and insoluble fiber.  The insoluble fiber passes on to be a minor contributor to the bulk of stools and the rest of the polysaccharide is potentially fermentable by gut flora into short chain fatty acids (formic, acetic, propionic, butyric acids).  Some of the polysaccharides are simple repeating units of one or two sugars in long chains, but others are made of five to ten different sugars in complex branched structures.  Simple repeating polysaccharides require just a few different enzymes for their initial synthesis and a few for their digestion.  Thus, resistant starch can be digested by a couple of enzymes into glucose that can be used by most gut flora.  Arabinogalactan, on the other hand, requires a dozen enzymes for plant synthesis and an equal number of hydrolytic enzymes to produce arabinose and galactose, which require further enzymes for metabolism in a select few of species of gut flora bacteria.  
Food Intolerance/“Allergy” Indicates Missing Bacteria
Gut flora in general can produce several hundred different enzymes for digestion of diverse soluble fiber,  but most soluble fiber polysaccharides can only be digested by certain bacteria and those bacteria increase, if the complementary fiber is present in the diet.  If a fiber is absent from the diet, bacteria that specialize in digesting that polysaccharide will be eliminated.  People living on diets limited to just a few types of soluble fiber can only digest those fibers and a shift in diet to other types of soluble fiber will lead to symptoms of dietary upset, such as bloating, gas production and food intolerance.  Food intolerances reflect inadequate diversity in gut flora and a mismatch between bacteria and food.  Food intolerances can be eliminated by repairing gut flora and the typical repair solution is eating homegrown fermented vegetables that provide the missing species of bacteria.
Immune Cells Develop in Response to Gut Bacteria
Most of the body’s immune cells are in the intestines.  Cells of the immune system are constantly dividing in bones and the thymus gland, developing in the lining of the intestines and migrating to other tissues.  Filamentous bacteria of the gut flora stimulate the development of aggressive immune cells that kill other cells that are infected with pathogens or viruses or are cancerous.  Furrows perpendicular to the flow of food cultivate the growth of Clostridium species that ferment soluble fiber, e.g. resistant starch, and release butyric acid that stimulates the development of regulatory T cells, Tregs.  It is the Tregs that control the aggressive immune cells and prevent attack on self (autoimmunity) or innocuous antigens (allergy).  It appears that merely eating resistant starch, e.g. potato starch, with probiotics that contain butyric acid producing Clostridium bacteria may provide a cure for many autoimmune diseases.
Gut Biofilms Release Vitamins as Quorum Sensing Signals
 The gut flora lines the intestines in numerous biofilm communities, which form from dozens of different species of bacteria that communicate by exchanging molecules called quorum sensing signals.  These signals from the biofilms intimately attached to the lining of the intestines are vitamins.  Thus, healthy gut flora are the major source of vitamins and other sources, such as fruits and vegetables are only needed, if the gut flora is damaged, e.g. by antibiotics.
Volume of Stools Reflects Gut Flora Fermenting Soluble Fiber
The bulk of bowel movements, stools, is bacteria, the compressed gut flora that accumulated in the colon while fermenting soluble fiber.  We always hear that we need to eat fiber for regularity, but since insoluble fiber is only a minor contributor to stool volume and it is associated with anti-nutritive attributes, such as the binding and removal of zinc and iron by phytate, the fiber that counts for regularity is soluble fiber.  Regularity results from the fermentation of soluble fiber polysaccharides producing short chain fatty acids, such as butyrate, that are the major source of energy for colon cells.  And the growing bacteria in the colon provide most of the bulk of the hydrated stools.  Inadequate dietary soluble fiber or damaged gut flora, dysbiosis, leave only dehydrated insoluble fiber and compact stools of constipation.  Constipation can result from dehydration or excessive retention, but chronic constipation, even in the presence of adequate dietary soluble fiber, is an indication of damaged gut flora and an increased risk for diseases resulting from deficiencies of Treg production:  autoimmune diseases and allergies.  Constipation and associated autoimmune diseases can be cured by repairing gut flora and supplying adequate dietary soluble fiber.

39 comments:

Lola said...

HI. I've been reading your blog for a long time now and I've been putting in to practice everything that I can to help overcome my antibiotic induced autoimmune diseases. I was a vibrantly healthy farm girl until I was fifteen and ended up needing to go on high dose, broad spectrum antibiotics for over a year for what they thought was a bone infection (it wasn't). Anyway, after that, my health fell apart. Acne, horrible digestive disorders, depression migraines and headaches and Psoriasis all over my scalp. I'm thirty now and have been eating a weston a price diet/gluten free/casein free diet for over nine years. i have a healthy husband and four healthy children and we live on an organic farm in Nova Scotia. I am able to somewhat manage my symptoms with an anti-inflammatory diet and good sleep but I would love to overcome the psoriasis for good and eliminate the Fructose Malabsorption and subsequent headaches and moodiness. We ferment our own foods, eat completely gluten free and mostly grain free except for occasional rice. I've started on Potato starch and have noticed an improvement. Since reading your blog, we go out of our way to live dirty lives :) We are around our farm animals, manure and general dirt all day. I'm just wondering if I will slowly get better or if I need to do something more drastic. None of my children have ever had any antibiotics or have ever been sick at all. I've considered using them as donors for a fecal transplant but have been told that because I gave birth to them, they are missing the same bacteria I am. Do you think that is true? I'm willing to try anything. Because I want to be healthy and free from inflammation but also because it just drives me crazy that I can't fix myself. I appreciate every post you write. Thank you so much!

Raj said...
This comment has been removed by the author.
Anonymous said...

Dr. Ayers, first time commenter here. I have seen the statement that vitamins are produced by bacteria in numerous posts of yours, and I would like clarification. Do you mean ALL vitamins, or just the B complex plus the K complex? I have a hard time imagining that retinol, D3 and ascorbic acid are produced in the gut from potato starch.

Anonymous said...

Any thoughts on the racial differences that exist between humans and how that might affect dietary choice?

Asians have larger salivary glands to break down starch. Does this mean that Asians will do better on a diet that has more starch compared to other races?

Anonymous said...

Dr Ayers,

Just wanted to say thanks for putting everything down so concisely. I think this is an extremely clear summary of a complicated issue, and your blog is much appreciated.

mk07 said...
This comment has been removed by the author.
LeonRover said...

Dr Ayers,

I do like your notion that:

The natural source of gut bacteria is eating the bacteria clinging to raw or fermented vegetables.

Reminds me of the poetic description:

Tasting of flora and the country green

which engenders:

Dance and Provencal song and sunburnt mirth

I hope you enjoy this conceit.

Sláinte

S Carton said...

Thanks for your always interesting posts. I must admit a lot of it goes over my head, but I like trying to keep up.

So if butyric acid producing Clostridium probiotics coupled with potato starch (does this mean potatoes too, or just the starch?) can help heal auto-immune diseases, where do I find said probiotics? Suggestions?

Oliver Magoo said...

I'm curious about the vitamins as well. Could one eat nothing but potato starch and lard and get all the vitamins they need from gut bacteria?

Garett Howardson said...

Any suggestions for where to find "butyric acid producing Clostridium probiotics?" I am HLAB27 positive and suspect an autoimmune spondylarthritis. Potato starch has been a huge help but I want to take it the next step. However, I have not had much like finding Clostridium-based probiotics.

Heka said...

Yes, I would like to know where to find butyric acid producing Clostridium probiotics as well - can you give us further information on how to increase this in our guts?

Dr. Art Ayers said...

Lola,
It sounds like you are doing everything that I can think of except waiting for the full impact of the RS. It will take weeks to months for normal Treg suppression of autoimmunity.

You may still be deficient in the Clostridium spp. that would digest the RS. There are probiotics that might supply that. Check Amazon under probiotics Clostridium.

You might also use PEG based laxative to do a complete bowel irrigation and strip off biofilms. When they reform, you might have a healthy gut flora based on a better environment, diet, etc.

I assume that your homemade fermented veggies just start with veggies, salt and water?

Let me know how you progress.

Dr. Art Ayers said...

Hi Raj,
I really appreciate your knowledgeable vote of confidence. It keeps me writing.
Gut flora can be grown with more or less difficulty, but I fear for loss of diversity and the gigantic increase in cost and reduced availability from pharmaceutical exploitation.
Big pharmacy will only get into it if they can exclude cheap competition. The $10M company will replace $10B in medicine. That won't happen unless the decisions get taken out of the lobby-dominated politics.
Thanks

Dr. Art Ayers said...

Vitamins
I wrote a post on vitamins as quorum sensing signals and excluded vit.D as a steroid hormone that is not present in significant amounts in food, and vit.C that probably supplied by parasitic worms. Vit.D is a problem only if chronic inflammation blocks normal solar skin production. Vitamin C you probably need to supplement. You can figure out retinoic acid.
The major point is the proviso of healthy gut flora. Damage by antibiotic or consumption of processed food will lead to vitamin deficiency. Most modern people have vitamin D and C deficiencies.

Thanks for the comments.

Dr. Art Ayers said...

Race
I don't think that most genetic differences make much difference, since the gut flora just optimize to fit the diet, as long as free access to new bacteria is encouraged.
Hygiene is usually the confounder.

Thanks for the questions.

Dr. Art Ayers said...

mko7,
I think that Hashimoto's thyroiditis is essentially an autoimmune disease based on celiac. Treatment requires fixing gut flora. Iodine may be helpful, but is not the main point. If the autoimmune problem is not fixed, other autoimmune diseases will follow.

Thanks for the questions.

Dr. Art Ayers said...

LeonRover,
Thanks for the pleasant imagery.

Dr. Art Ayers said...

S Carton,
I think that Clostridium is a popular probiotic outside of the Western world. I just checked Amazon under Clostridium and they list Probiotics-3.

Thanks for your comments.

Dr. Art Ayers said...

Garett,
Those HLA predispositions are nothing more than that and can be completely eclipsed by good diet, gut flora and exercise.

Look at my other posts on repairing gut flora and start fermenting your own veggies. Autoimmune diseases can be cured. My next post will address that.

Thanks for your comments and let me know how you do.

Anonymous said...

Many thanks for the explanation Dr. Ayers. I went back and read all your posts on quorum sensing. It states clearly that vitamins C and D need to be provided externally. Maybe one day we will master the art of building good intestinal floras to the point where we can turn our attention to the fauna (the worms), but given how ignorant we are of flora, I will eat a kiwi a day.

That leaves us with retinol. AFAIK carotenoids are formed into retinol inside the human body, and the presence of dietary fats assists in the absorption of carotenoids. So I do not see how bacteria help.

There is also the matter of our very shortened digestive tract. We have, what, 1/4 the length of a gorilla's tract, right? And the tract of a gorilla is plenty long to generate and absorb all those nice vitamins, but what about us? Can we really produce and absorb 100% RDA vitamin B12 in 7 meters of intestine? Also why would people get beriberi or pellagra from a diet so very rich in resistant starches?

Unknown said...

Thanks for a very informative post.

Do you think gliadin/gluten sensitivity can be cured by fixing the gut flora? And if said sensitivity is the cause of Hashimoto's or other autoimmune disease?

dr j said...

Here is a fun diagram.. poo=zoo in
http://www.probiotictherapy.com.au/pages/concept.html

Ashwin said...

All my thoughts are in this very interesting blog. I find that using Neem Leaf powder to eliminate undesirable gut flora and the introducing Clostridium Probiotic together with potato Starch and Guar gum is really useful for Crohn's disease. I use a probiotic called "BIFILAC HP" that I picked up in India. Probiotics containing Clostridium Butyricum are available in asis, especially Japan. (Clostridium Butyricum Miayiri 588)

Ashwin said...

All my thoughts are in this very interesting blog. I find that using Neem Leaf powder to eliminate undesirable Gut flora and then introducing a Clostridium containing Probiotic together with Potato Starch and Guar gum is really useful for Crohn's disease. I use a probiotic called "BIFILAC HP" that I picked up in India. Probiotics containing Clostridium Butyricum are available in Asia (Japan). (Clostridium Butyricum Miayiri 588)

Marcus Miller said...

Hey Art

I would love to trouble you with a question.

We have been Paleo for around 4 years now due to a fairly aggressive MS diagnosis of my wifes. Blindness, loss of use of one leg, fatigue (brutal)... Not cool and I am sure you get the picture.

So, Paleo has been good for us. No serious relapses, slowed things right down, it's not perfect but it's certainly better than it has ever been and we have reversed the pattern.

The one thing we have learned though is if we take the breaks off then the problems come back. This month after a few big nights (friends hitting 40) and whilst training for a marathon my wife has had a relapse and it is a bit of a lingerer.

So, we know how to put this to bed - paleo with autoimmune tweaks is pretty much proven to us but I don't want to hold this back any longer. It's easy to know the path, but walking it every single day is not always easy.

I want to fix this for Emma and then hopefully move on to help others through a blog or some such.

I have been following the resistant starch angle for a while now and whilst we will always eat Paleo it seems this is a way to steel ourselves against times when we do, naturally fall of the wagon for a night or have an infrequent late & boozy night.

We ferment food. We eat wild fish. We eat 90% grass fed meat with lean meats making up the other 10%. Pastured eggs. No dairy etc. Organic seasonal veg etc. We are not messing around here - three young kids so the stakes are high.

Is there a protocol for the resistant starch? How much? How often? How much probiotics?

It is not proving easy to find these probiotics on amazon.co.uk at least. I found Probiotic-3 but that is on US import only. It seems most probiotics seem to want to fight clostridium difficile rather than provide Clostridium. I even tried searching for Clostridium butyricum and that returned nothing (the strain in Probiotic-3).

Would be great to have a simple protocol to follow here as I am sure left to my own devices I will mess this up and I want to help my wife stay fit and strong and finally beat this illness rather than keep it locked in a Paleo shaped cage.

Thanks for all you do! If there is anything an internet marketing guy can help you do to get your message out then please, give me a shout, I am at your disposal!

Best regards,
Marcus

Garett Howardson said...

Thanks for the response Dr. Ayers. I will give fermenting vegetables a shot. I'll pick up the book you mentioned as well, but do these need to be fresh vegetables or can supermarket ones work? I know that's not ideal but I don't really have access to fresh right now.

I do want to believe that diet and exercise can solve this but things are pretty terrible right now so I'm opting for a shorter term solution (i.e., medication) to help control symptoms and support the longer term fixes. Thanks again for the comments!

Anonymous said...

Are homemade fermented veggies + soluble fiber enough, or do you have to do that AND resistant starch?

Anonymous said...

"Are homemade fermented veggies + soluble fiber enough, or do you have to do that AND resistant starch?"

I am not Dr. Ayers, but there are substantial amounts of fermentable fiber left in fermented vegetables, as well as in common vegetables such s beans, beets, and apples. Now some of these are pectin and inulin and some are resistant starches. I am curious what Dr has to say about these. You may need more enzymes, but these polysaccharides are so ubiquitous in the human diet that it seems unlikely our flora has not adapted.

Anonymous said...

Dr. Ayers: is the proper choice of potato starch white potatoes or sweet potatoes? And would it be best to eat them raw or cooked? Or are speaking of processed potato starch? Thanks Ron

Tim Steele said...

Anon - Check out Dr. BGs post on soil-beased probiotics in some real foods:

http://drbganimalpharm.blogspot.jp/2013/09/korean-pepper-paste-burns-visceral-body.html

I am loving all the discussions on probiotics. It's always just been a crapshoot, but now we are narrowing in on some really important ones (c. butyricum, etc..) and learning how to feed them (RS).

Gene ;) said...

Marcus, I think he might mean this one
http://www.amazon.com/Advanced-Orthomolecular-Research-Probiotic-3-Probiotic/dp/B0082DDQH6/ref=sr_1_1?ie=UTF8&qid=1394959165&sr=8-1&keywords=+probiotics+Clostridium

Garett, I'm hla b27 as well and have ankylosing spondylitis. I've been weaning off enbrel for several months and following "The Paleo Approach" written by Sarah Ballantyne for the last two weeks. I am going to implement all of Dr. Ayers' strategies as best I can. I would love a to have another person in the same boat that I could bounce ideas off of and update progression with. Interested? I'll check my temporary email address for your reply and respond with my real one. hlab27r_us@hushmail.com
Good luck either way!

Thank you Dr. Ayers!!! Thank you!!! Thank you!!! I know this is all done by you solely out of kindness but if there's anything I can do to pay it forward, please let me know.

la femme natale said...

Dr. Ayers,

What do you think of this:
I've been making and eating my own sauerkraut with farmer's market cabbage, sea salt, and filtered water. In early January I suddenly had a terribly painful reaction to cabbage, sauerkraut, and kale. The pain felt like what my stomach feels like when I eat gluten - knives twisting in my gut.

I ate kale and sauerkraut nearly daily, as I love how they taste. It's been nearly 6 weeks since I've eaten any cruciferous vegetables, and I miss them terribly. However, enduring 16+ hours of pain after eating them is a scary prospect. What do you think triggered this reaction?

Debbie said...

So, now I'm reading about possibly soil based probiotics becoming pathogenic, and that it may not be a good idea to use them.

I've been eating fermented vegetables for a long time - are you saying that that should be enough with potato starch to fix my gut? The problem is constipation after losing 80 pounds 26 years ago. I kept it off, but - along with vegetables and a little protein ate plenty of hard candy and artificial sweeteners.

Thank you!

Debbie said...

So, now I'm reading about possibly soil based probiotics becoming pathogenic, and that it may not be a good idea to use them.

I've been eating fermented vegetables for a long time - are you saying that that should be enough with potato starch to fix my gut? The problem is constipation after losing 80 pounds 26 years ago. I kept it off, but - along with vegetables and a little protein ate plenty of hard candy and artificial sweeteners.

Thank you!

Anonymous said...

Dr Ayers, I have had many inflammatory diseases throughout my adult life. After a Rea tion to a Rx medication I began having anaphalactoid episodes and histamine intolerance with a diagnosis of Mast Cell Activation Disorder. Also tested positive for SIBO and have IBS for 20 years. With HIT I cannot take fermented foods but I take VSL#3 DS.
I believe that MCAD is the root of all of these or maybe the microbiome is the actual trigger to everything. I am eating a very limited diet......truly afraid to eat after so many Reactions. I had been Autoimmune Paleo prior to the drug reaction.

Any thoughts you have, directions to consider, suggestions are very much appreciated.

Thank you. Catherine

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Evan Marcus said...

This one was really informative. Those who regularly take antibiotics must read this thing as this can lead to serious health disorders. You people can add healthy habits to your regular routine to stay fit and healthy. You can also take help from fruit juices like the Organic Noni Juice to maintain good health for longer hours without any side effect.