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 .

Thursday, January 29, 2015

Healthy Gut Microbiota Means: No Supplements, No Cleanses, No Drugs, No Processed Foods

A healthy, functional gut microbiota (bacteria and fungi) supplies all of the vitamins needed, stimulates the development of a balanced immune system and promotes vitality.  If you feed and maintain the diversity of the pounds of bacteria in your gut, you will be healthy.  If you listen to the medical and food industries, you will be sick, i.e. a good patient/consumer.

Supplements Compensate for Deficiencies/Sickness
The key to this discussion is the functions of the healthy communities of bacteria and fungi called the gut microbiota.  These pounds of bacteria produce all of the vitamins that your body needs, and spiking your diet with multivitamins may disrupt your microbiota, because vitamins are actually the chemical signals used for communications between bacteria in biofilms.  Numerous studies have shown that daily multivitamins are not beneficial, so if you see extra vitamins on the ingredients label, try some whole foods instead.  If, however, you have been exposed to antibiotics or other medications, since most have potent antibiotic activities, then your gut bacteria may not be producing vitamins normally, and you may need to supplement.  Vitamin deficiencies are a symptom of gut dysbiosis, damaged gut microbiota.

Vitamin D is a Steroid Hormone Produced from Cholesterol in Skin by Sunlight
Most people know that sunlight striking skin produces vitamin D, but they still think that they can get a significant amount of vitamin D from their diet.  The confusion comes from the fact that vitamin D is a major hormone that influences many body systems including bone production and immunity.  So in the absence of skin production of vitamin D, the low amounts added to milk are sufficient to prevent deficiency/rickets.  However, chronic inflammation can block solar production of vitamin D, so that even individuals near the equator and basking daily still remain deficient.  Vitamin D deficiency may also, insidiously, be a major source of chronic inflammation.  Thus, most individuals treated for deficiency with supplemental vitamin D3, do not reach high enough levels to suppress chronic inflammation and restart solar production, so they remain deficient.  Chronic inflammation is a symptom of vitamin D deficiency.

Bowel Cleanses Damage Gut Microbiota
The bowels are a long tubelike conveyance and it takes food about a day to travel from table to toilet.  In the colon, all of the plant polysaccharide fibers remaining after removal of sugar, starch, fat and protein, are digested by enzymes of the microbiota and converted into more bacteria and short chain fatty acids that feed the colon tissue. There is nothing toxic left behind in the colon. Protein from meat is readily digested in the stomach and the first part of the small intestines.  Plant materials cannot be digested without the help of a complex array of hundreds of enzymes produced by gut bacteria.  Food intolerances are caused by the loss of particular bacterial species needed for complete digestion of one type of plant fiber.  The bacteria form the stools, and insufficient healthy bowel bacteria, normally fed by the fiber, is the cause of constipation.  Clearly, flushing out bacteria with a "cleanse" is unhealthy and counterproductive.  There is nothing in the colon but gut bacteria and fiber to feed the bacteria. Those bacteria are needed for vitamin production, normal development of the immune system and normal stools.  A cleanse merely removes healthy gut bacteria and leads to constipation or replacement by pathogens. 

Processing Removes Prebiotic Fiber from Food and Starves Gut Microbiota
Diverse and complex plant polysaccharides, e.g. pectin, arabinogalactan, various glucans and fructans, are systematically digested by hundreds of different bacterial enzymes of the healthy gut microbiota.  The sugars that result are eventually converted into short chain fatty acids, such as butyrate, that feed the cells lining the colon.  The plant polysaccharides that feed gut bacteria are called prebiotics.  Unfortunately, prebiotics are removed during food processing to enhance ease of preparation and palatability.  The result of decreased dietary prebiotics is selective starvation and removal of bacterial species needed for the development of the immune system, and autoimmune diseases.

Most Medicines Have Substantial Antibiotic Activity and Damage Gut Microbiota
It is not surprising that antibiotics damage the bacteria in the gut.  What most people don’t realize is that most pharmaceuticals/medicines are developed from the natural antibiotics of plants, phytoalexins.  Numerous recent studies have demonstrated most common medicines, e.g. statins, NSAID, antidepressants, etc. have substantial antibiotic activity and damage gut bacteria.  Surgeons commonly suggest that patients eat yogurt to help repair their gut micro biomes after operations and antibiotics, but they don’t tell them how to fix their gut and immune system as they take medications for the rest of their lives.  The permanently damaged gut just causes further deterioration of the immune system and health.

Damaged Gut Microbiotas/Immune Systems Can Be Fixed
I have several other posts on repair of gut microbiota.

Examination of antimicrobial activity of selected non-antibiotic medicinal preparations.
Kruszewska H1, Zareba T, Tyski S.   Acta Pol Pharm. 2012.  69(6):1368-71.


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

On the topic of food sensitivity .. my daughter appears to be sensitive to a class of acidic foods. These include yogurt, tomato, citrus and vinegar containing foods (mustard, for example). Does this sound to you like a specific species or two is missing, or more like a symptom of a disregulated/overactive immune system more generally?

She was formula fed (my wife had breast reduction surgery when she was young). I get as much fiber into her as I can, but I can't get her to eat fermented/probiotic foods.

Dr. Art Ayers said...

Hi Raj,
1. Suppression of inflammation is good for gestation. During labor, SCFA production is stopped by bowel clearance.
2. Butyrate is most dominant.
3. Some people show inflammation or immunologically aggressive symptoms when given anti-inflammatory treatments, such as vit.D, since it can repair parts of the immune system that are damaged. I have seen this with rosacea treated with vit.D or omega-3s.
4. ?
5. Suppression of inflammation is not an advantage in all cases of virus infection or cancer, where killing can be good.

Remember that inflammation is a misnomer, since it is cycle and part of many other aspects of anabolism and activation of the immune system. NFkB is nuclear factor controlling transcription of the short (k) chains of immunoglobulins in B cells.

Thanks for the questions.

Dr. Art Ayers said...

It is unlikely that a food "sensitivity" is immunological, since they are rare. Even if it is immunological, the cure is the same as for an intolerance. In both cases missing bacteria needed to be added back.

For kids, I think that it is easiest to repair the gut flora of the entire family and pets. It is unlikely that she alone has dysbiosis, unless she has had antibiotics. Look up my other posts on repair of gut microbiota. Eliminate processed foods, have mud fights, knock off the hyper hygiene, eat veggies from soil to mouth, make sure the dog is digging enough and not washed to much and make your own fermented veggies. If you don't make kraut, you don't really care enough. (That was just for emphasis, to show it is important.)

My view is that the food sensitivities just tell you that there is a problem with gut flora and prebiotic fiber. There is no point in searching out the details of what foods are causing problems, because they all will eventually. It is just easier to cure it with new bacteria and bacteria food/fiber.

Hope this helps. Let me know.

Terri said...

Hi Dr Ayers, first I want to tell you since I had a scare of a deer tick bite and taking antibiotics and then finding out that I just wrecked by gut biome 1 1/2 yrs ago I found your website on how to fix it. Thank you so much for your work. My husband (65) and I (59) changed our diet to a healthy one (no grains, sugar, processed foods, we are farmers and grow our own beef, pork, chicken and eggs, have a vegi garden that supplies our fermented vegis that we eat - thanks to the Shockey's fermented vegi book), I lost 35 lbs and he lost 23 and lowered all his triglycerides/cholesterol levels. Since then my possible candida symptoms with itchiness, 45 yrs of constipation issues, arthritic hip problems and cracking joints, and sinus issues have gone away. My husband went in to the doctors for is lungs hurting when working outdoors and with heavy exertion 5 days ago. The next thing we know he has to go to emergency because of 1.22 enzyme (triponan) levels in his blood. He ended up with an agiogram and two stents in him (one artery was blocked and very calcified - said probably was years old and it started to reroute itself and he will be put on plavix, aspirin, cholesterol lowering drugs (even though all levels are normal except his ldl is 93 and they want him at 70 >), high blood pressure drug (his blood pressure goes from 175/? to 130/?) and some other drug to thin his blood. He experienced no real heart attack and no damage to his heart....they didn't give us any other options. They tell us he'll be on lifelong drugs or otherwise the blood clots/plaques will create another heart attack. We are tweaking the eating further making sure he loses more weight - he carries visceral fat in his abdomen - potbelly

How can I get him off all these drugs? I don't trust the medical field and I'm not sure what to do next, have any suggestions. (BTW...never go to the hospital on the weekend!!)

Raj said...
This comment has been removed by the author.
Dr. Art Ayers said...

Two types of genes are associated with autoimmune diseases: HLAs and inflammatory signals.

I just looked at HLA-B27 structure in Chimera and it is obvious that this presenting structure, which looks like a bun with the peptide presented as hot dog, has unusual heparin-binding basic amino acids along the edges of the bun. This means to me that as the B27/peptide complex is exposed on the surface for Tcells, the presentation is controlled by membrane heparan sulfate proteoglycans. Loading of the B27 with peptides may also be controlled by heparin-like molecules binding.

The upshot of this discussion, is that B27 may predispose to autoimmunity, but the conditions needed for autoimmunity to develop, infammation with Treg deficiency, are determined by the integrity of the gut microbiota. Klebsiella may just be an indicator of gut dysbiosis, inflammation and Treg deficiency.

Thanks for your questions.

Ron said...

Just this week I've read an article about a company which is responsible for inserting probiotics into the ventilation system of closed buildings such as malls etc in few countries.
It was said that the ventilation system of such places is a good place for bad bacteria to develop.
It was also said that it helps with chronic asthma etc.

It made me wonder what about the bacteria of the lungs? Is there such thing as lungs' microbiome and is it as important as the guts'?
It would be very interesting if you write a post or two about the microbiome of the lungs, skin etc.

Anonymous said...

Hey Doc!

Been following your blog for years, and it has really given me a whole new understanding of health and disease. So, thank you!

I hope you can take the time to give me some advice on my condition.

Over the last couple of years I've slowly been rebuilding my gut microbiota (which was completely destroyed) through fermented foods, prebiotics, 1 microbiota transplantation, and several of the other methods you have outlined on this blog.
My gut is now a lot better, but still not 100%.

During these years I've also been experiencing several other health problems, including acne vulgaris, low libido, and "fatigue". All of which I thought were a consequence of my disrupted gut.

As my gut health has improved, so has my acne, and both my skin and gut is now pretty good. However, over the last year my libidio has not gone up, but rather down. I can also feel that I perform poorly in the gym. Compared to before (I've been lifting for many years), my strength gains are poor, and it actualy feels like my body is "resisting" heavy lifting. I can feel that something is not right, and I find it hard to believe that me ageing a couple of years would have such a dramatic effect (I'm in my twenties).

I took a blood test which showed that my testosterone levels had dropped since I last took a test 4-5 years ago, but they are still within the range of what is considered normal.

Do you have any tips for me? It's higly appreciated.

glib said...

All great advice in the title. But why not "no alcohol"? It does kill a lot of bacteria. And I suspect that coffee, too, has a negative effect on the biota.

Anonymous said...

Anynoymous above here: Forgot to add that I also took two courses of Isotretinoin for my acne a couple of years back, but since the fatigue, muscle "weakness", and low libido didn't kick in until more recently, I'm not sure if it is connected. Perhaps it might be.

Anonymous said...

Anon, add some pumpkin seeds or bee pollen to increase low libido and improve testosterone.

Dr. Art Ayers said...

Acne, Accutane and libido,

I thought that Accutane was pulled from the market for being too dangerous. I think it is a stem cell toxin.

Do a Google search for "Accutane libido"

Dr. Art Ayers said...

The lung microbiota is being studied and there is influence from the gut and vice versa. The gut microbiota health is important in the course of lung problems.

Richard said...

Hi Art,

If vitamins are being used for quorum sensing etc, would that mean that taking vitamin K (MK4) for example could create an environment in which the bacteria that used MK4 to communicate were mislead and therefore, presumably, selected against, leaving you with less gut generated exogenous MK4 than you would otherwise have?

Dr. Art Ayers said...

Hi Richard (please don't tell people you are a friend),
You caught me in a slight hyperbole for clarity.

I am trying to provide a different perspective on vitamins to explain why they are produced by our gut bacteria and not us. Bacteria do nothing for gratis or our benefit. They wreak of entitlement and free lunches. And they are very chatty in biofilms and messages that they surreptitiously pass in class are made of vitamins or "chatters."

My generalization has some obvious flaws, since the vitamin designation applied to vitamin D and C doesn't make sense on the outset. So MK4 is probably not a signal like the B vitamins.

But, in general, I think that taking vitamins will mess up healthy biofilms and lead to health issues. Vitamins may be the entry drug for the medical industry. Vitamins start to disrupt your gut microbiota and gradually lead to more interventions to make you a better consumer patient.

Thanks for stopping by.

Dr. Art Ayers said...

I don't think that a little alcohol is a big deal with respect to gut bacteria. Afterall, most of the bacteria are in the colon and most of the alcohol never reaches there. Alcohol is very good for eradicating H. pylori and improves the effectiveness of antibiotic treatments. H. pylori is disappearing in America, probably because of the general antibiotic activity of common medicines. The common American Diet and associated medicines make the stomach too toxic for H. pylori.

Coffee is just a typical plant extract, crude essential oil, so it is loaded with "antioxidants", aka phytoalexins or natural antibiotics.

It is nice to know that plants have lots of naturally toxic chemicals in them, but they are of minimal risk, because your body has ample detox mechanisms and so do your gut bacteria. Biofilms protect many of our gut bacteria from phytochemicals.

Thanks for the questions.

Anna said...

Dr Art Ayers, you've mentioned that pharmaceutical drugs have an antibiotic-like activity and will unfortunately disrupt the gut this also the case for injected insulin too?
It'd be unfortunate to read that it is, especially since its the very thing that keeps Type 1 Diabetics alive.

elliebelly said...

Dr. Ayers,

Do vaccines damage our gut ?

Dr. Art Ayers said...

Most injected drugs have a much lower impact on gut bacteria than those that are taken orally, because the concentration in the gut is dramatically different. In addition, insulin is a protein, so it won't leak from blood to the bacteria in the gut. Also insulin is not like other drugs that started out as a plant polyphenolic and was then repurposed as a drug.

So insulin is no big deal for gut flora.

Note that gut bacteria adapt readily to antibiotics and they will also adapt readily to drugs. Unfortunately, we may not like that one of the common ways that bacteria adapt is by picking up multiple drug resistance plasmids.

Thanks for the question.

Dr. Art Ayers said...

Vaccines are usually proteins from viruses or bacteria, which are injected into tissue and stimulate antibody production. The stimulate part is sometimes enhanced with chemicals called adjuvants. Proteins that don't produce antibodies aggressively themselves need stronger adjuvants to produce adequate antibody responses.

In any case, the vaccine components will not usually reach the gut, so they are not an issue for gut bacteria.

The problem with most vaccines, is that they don't work or they are very short term, and they pass little protection to offspring. Most people my age got mild cases of measles as kids and were already partially protected, because our mothers had measles. Now the vaccines provide partial protection to those vaccinated and little protection is passed on. That is only good for the vaccine industry, because the population is never fully protected even if fully vaccinated, and boosters will now be required continuously. Immunity for previously common diseases is declining.

I know how to make vaccines better, but no one is asking.

Thanks for the question.

Anonymous said...


What do you think the difference is between the vitamins one gets from a "pill" vs. the vitamins one gets in whole foods? Why would the pill be a problem, but not the food? Intuitively, it makes sense to me, but I'm curious what you think.


Richard said...

Hi Art,

I am not the Richard that you are thinking of, but would of course be happy to be considered a friend. I was not trying to catch you out or anything of the sort. I don't know much about biology and have learned what little I "know" in an attempt to deal with chronic fatigue, chronic migraine and all the issues that have come from living with them.

I asked about MK4 because: a) I'm taking it; b) I realise that even though I take it with lipids and bile salts, a large amount (from the perspective of the bacteria) will still make it into the colon unabsorbed; and c) I know that the menaquinones are produced by bacteria used to make cheese, natto and various fermented vegetables.

I could have as easily asked about the other vitamins and supplements that I am or have been taking. My thought was that if your gut contained large doses of quorum sensing molecules, or other molecules that are of a sufficiently similar structure to work as quorum sensing molecules, the noise would outstrip the signal and in consequence the bacteria that used those molecules would begin to act disadvantageously and their population would therefore decline. The concern was obviously about the large doses that we use when we a deficient (5-45mg for MK4 hundreds of milligrams for b1, b2, b3, b5, grams for vitamin c!) might cause dysbiosis and in particular a dysbiosis that could, by taking out the bacteria that produce that vitamin, be setting you up for a long term deficiency in that very vitamin.

Dr. Art Ayers said...

I guess all Richard are not interchangeable.

I think that your fears of vitamin induced dysbiosis are reasonable, since modern high dose vitamins are certainly something that gut flora and the human gut would not naturally experience.

Bacteria in biofilms along the whole length of the gut are probably the major source of vitamins and dietary plants are probably of no consequence. Vitamins may be in plants to inhibit plant pathogens from forming biofilms.

Thanks for the questions.

Old Road Primitives said...

Dr Ayers, I've read your postings on Probiotic 3 & Potato Starch for autoimmune disease & allergies but what are you thoughts on "leaky gut" (which seems to be the rage these days)? Also, I read that fermented foods raise homocysteine levels, do you have any thoughts on this? & Can I ask which Probiotic 3 you recommend? Thanks so much! I'm loving your Blog and appreciate the information that you are giving out! Kim

Dr. Art Ayers said...

I was talking about Probiotic-3, Advanced Orthomolecular Research, because it has Clostridium butyricum that grows on RS and produces butyrate. RS is just the most basic of the prebiotic soluble fibers and happens to be available by the tablespoon. It is probably more favorable to eat RS and other prebiotics in whole foods, but that is probably no big deal.

Fermented foods and homocysteine - no thoughts

Leaky gut seems to me to be the response of the gut to stressed gut bacteria. So the gut flushes away the local gut bacteria and takes in some bacterial LPS into the blood stream and produces inflammation and liver defense proteins, e.g. DNAse I. So it is a defense and should be just temporary and reset, just as inflammation is a healing cycle and leads back to a normal status.

Thanks for the questions.

Allison Hurst said...

Okay, I am asking. How do you make vaccines better?

Also, I read about your comments on metformin. I have taken in for a while to help with PCOS and the road towards menapause. My gut bacteria has probably already changed. Would it be better to just keep on taking it or stop?

Anonymous said...

Please elaborate low impact introduction of new bacteria?

List some vegetables that can be helpful in improving gut microbes and which ones to avoided.

Some veggies causes me problem like if i take spinach it comes out undigested as it is in stool.Any remedies for this

Can consuming colloidal silver improve ibs??

Thanks a lot.

Anonymous said...

Some studies says consuming alcohol in moderation
can help in decreasing symptoms of rheumatoid arthritis. How?? Whats your thoughts on this.


Anonymous said...

i think you wrote about PEG as a good thing, "PEG may end up being a general treatment for many diseases. It could be followed by a fecal transplant from a healthy individual. That may be the future of medicine, handling" did things changed?

Kay Dee said...

Dr. Ayers, just a few simple but important, for me, questions (sorry for the off topics):

MS, as autoimmune disease, can respond well to a Gut Flora Repair Plan / Anti-Inflammatory Diet Plain for life?

The integrations you recommend always are Omega3, Vit. D3, Vit. C, Acetylcisteine (glutathione)?
Are EPA-DHA particularly effective since they pass easily the Blood Brain Barrier?

The conventional MS treatment (I suppose Immunosuppressor) vanish the Plan or is it possible a sort of modulation or integration between your Plain and conventional treatment.
Thank you Dr. Ayers

Dr. Art Ayers said...

Kay Dee,
I see MS as an autoimmune disease that passes across the blood brain barrier. The BBB like the kidney/urine barrier is supported by heparan sulfate, but the HS is blocked by inflammation. Thus, chronic inflammation breeches the BBB and permits immune attack of the nerve sheath.

The Anti-Inflammatory Diet that I outline helps to avoid diet-based chronic inflammation and suppresses inflammation from other sources, so it helps to reestablish the BBB, which is good for MS.

The autoimmune part of MS requires continued disfunction of the tolerance part of the immune system. (Typical treatments tend to wipe out the remaining aggressive part of the immune system that is attacking the nervous system.) The root cause of MS is defective development of the suppressive part of the immune system in the gut in response to particular species of gut microbiota, e.g. Clostridia.

Repair of the gut microbiota should stop the progression and perhaps reverse the attack by the immune system by redeveloping immune tolerance of the nerve proteins. I discuss repair in several other posts. The important point that is missed in attempts to repair gut bacteria is that particular new bacterial species must be added to the gut, i.e. eaten. The cure is ultimately new bacteria plus prebiotic fiber to feed them.

It seems to me that the cure for MS is the Anti-inflammatory Diet plus repair of gut microbiota. I don't see this approach as in conflict with conventional attack on the aggressive immune system except that drugs used may be antibiotics that kill gut microbiota.

Thanks for the questions.

Dan Reese said...

I would image our gut flora would recover well in these occasional situations - cleanse/diarrhea/enema - However, the individuals doing cleanses likely already have some level of damaged flora to begin with since they are seeking digestive relief, weight-loss, etc.

glib said...

"Bacteria in biofilms along the whole length of the gut are probably the major source of vitamins and dietary plants are probably of no consequence. Vitamins may be in plants to inhibit plant pathogens from forming biofilms."

wow, this goes against anything that is taught in nutrition. but it is possible. why, for example, the Swiss high mountain people are healthy, in Weston Price's book, if they eat milk and other dairy, rye bread, plus some roots and meat, about six months a year?

Annoy said...

Hi Dr. Ayers

My Naturopath told me that studies show that introduced probiotics don't take up residence permantly and even the best ones only stay in the digestive tract for about 2 weeks. He told me that they don't yet understand why this is. I have been sick for some ten years and with gut issues, joint problems, weight loss and easy fatigue. The worst symptom is brain fog that comes on when I eat just about anything but worst with sweets. It comes on very quickly and cause blurry vision, balance problems and inability to think clearly and slurred speech like am drunk. It got so bad at one point I nearly had to quit working. Anyway to cut a long story short I stopped taking all the supplements and started on fermented foods and made the most improvements in years. I am going to start soil based probiotics next with prebiotics. Also my joint pain disappeared and I have been able to return to exercise which has made me so much happier. anyway thanks it was through your blog and Dr.Grace Lui's that I started to get my life back.



David Bird said...

Re alcohol.

I am pretty sure that straight spirits would effect the biome of the mouth and throat. Not sure if this matters but a good balance of healthy bacteria in the mouth is important to maintain healthy teeth and avoid colds. I think over chlorinated public swimming pools damage the immune system in the Ear, Nose Throat area. I got so many colds after swimming I gave up and only swim in lakes and rivers now.

Anonymous said...

Dr. Ayers,

You said, "I know how to make vaccines better, but no one is asking."

I'm asking.


TheKumaraKid said...

Hi Dr. Ayers,
I love your blog. After reading your blog I'm began taking soil based probiotics, that is until I learned about fermenting foods. I bought your friends' book. The results have been great, I finally had again the clarity of thought, healing of skin, and an easy time on the toilet that I last had as a child.

So naturally I have been printing out and sharing your blog with family who also have auto-immune disorders and food intolerances, however they stumble on the more technical terms and then give up reading the blog.

Could you please reproduce your 3 health diagrams or another summary in more simple English so that more people will benefit from the findings of your research? Or perhaps a publish a book?

Keep up the great work!!

Natasha said...

Dr. Ayers,

My husband has another auto-immune disease. First one, type one diabetes. Second one, sarcoidosis. It's been two years since his diagnosis and we have avoided steroids. He was doing better, now he is doing badly again,not able to work and barely functioning. The doctor says we will have to do steroids, or he won't qualify for disability pension.

My husband hates saurkraut, always has. Things all the fermented stuffis awful. He was willing to do potato starch, but withe all the in-fighting over RS2 and RS3, I have not given him any. He was raised on canned milk, never breastfed. I see the steroids as a slippery slope to complete dysfunction. He is only 50 years old.


Anonymous said...

Dr. A,
Love the blog!

Wondering if you consider doing an entry (or share your thoughts) on beans.

Again, love the blog...thanks so much for all your time and effort.


Dr. Art Ayers said...

All I can say about beans:
I eat them.
They provide a glucan prebiotic that is good for gut flora.
People have problems with beans, because they are lacking the bacteria to digest the prebiotic. I have several posts on repairing gut bacteria.

Thanks for the comments.

Dr. Art Ayers said...

I cannot understand how people will refuse to change eating habits. If they just persist for three weeks, their tastes will change. It is that simple. That is why they have kids eat one bite each day.

The RS2/3 quarrel is silly. The point is that potato starch is easy and useful for many people. Some people lack the bacteria to digest RS2, so they can just take Probiotic-3 with C. butyricum. In all cases, it is better to eat whole vegetables with several different prebiotic fibers. So, don't get distracted by arguments and feed your microbiota with prebiotics.

Thanks for the questions.

Marianne said...

Hi Dr,
Thank you for all the amazing information. My question is regarding pathogens...I just had a slew of tests done with a DC, I have hashi's, elevated a1c & cholesterol,trashed adrenals and sex hormones, chronic constipation, like never remember having a normal bowl movement, except when pregnant?? My stool test revealed low bacterial diversity (shocking, I know!) and high levels of klebsiella pneuomoniae, eosinophil protein x and prevotella. After all that my question is do you believe it's necessary to kill pathogens with herbals etc or to move right into ferments.. I started fermenting and using resistant starch and was having no measurable improvement. Thanks! Marianne

glib said...

under the influence of this blog I have started adding pieces of ACV mother to my smoothies about once a week, with excellent results. I don't think I ever had such a long run of apparently good gut health.

I have found that 4-days beans (2 days soaked, 2 days germinated) are much lighter than regular beans or potatoes for that matter. Next I have to try 2-days fermented grains. all little but not insignificant improvements to one's health.

Natasha said...

Dear Dr. Ayers,

Hi! Thanks for the feedback. Sorry to have an irritating post. I didn't know my husband was so limited in his food selection until after we got married.

There is a story behind each refusal. Among other issues, he is sensitive to smell and texture of food. Perhaps a little on the Autism Spectrum... and a fair bit of stubbornness.

Over the years, working within the limitations and never tricking him, I have introduced some new foods. Raised the quality too. He used to eat at McDonald's daily and now he has declared himself "alllergic".

I will keep working on him. Perhaps starting with pills and fibers. Maybe someday ferments. If I had my way we would have a kitchen full of crocks bubbling away, and a shaggy dog at my feet.

I enjoy your research and writings. Thanks again. N.

Dr. Art Ayers said...

Fermented veggies provide three things:
1. Lactobacilli, like dairy probiotics that do not grow in the gut, but provide immune system development as they pass through, i.e. temporary function
2. Veggies are converted into prebiotic fiber to feed gut bacteria in the colon that convert fiber into short chain fatty acids that feed other bacteria that make up half of normal stools and prevent constipation.
3. Some of the normal gut bacteria that will repair your damaged gut flora.

Resistant starch is just the food for some of the essential gut bacteria needed for development of the immune system. Eating RS will increase the population of healthy gut bacteria in the colon, but only if the bacteria are already present in small numbers. In your case, your constipation indicates that most of the essential species of gut bacteria have been killed off. Some probiotics, e.g. Probiotic-3 and soil based, may be sources of a small number of the types of bacteria that you are missing.

An indication that you are starting to establish bacteria in your colon will be normal bowel stools in response to eating RS or apples and other prebiotic fiber.

Let me know of your progress.

Anonymous said...

Do you consider Fermented Cod Liver Oil/High Vitamin Butter Oil a supplement? I've been taking a teaspoon of it for years; now I wonder if this might be a mistake? Thanks!

herve said...

Thanks for your stance on colon cleanse. We see them everywhere in the alternative health industry, i've always thought it was a bunch of baloney but nevery really knew the reasons behind why they are wrong.

Anonymous said...

I thought of you and your gut work when I saw this video on Autism being connected to gut bacteria...clostridium Suppress the bacteria and the kid does much better but if antibiotic is withheld the ASD behavior returns. Our microwaved society is triggering the clostridium to explode...cell phones, ipads, iphones, wifi, televisions all emitting blue light frequency.

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Andy B. said...

Dear Dr. Ayers,

First of all, thank you so much for your generous efforts in making this world a healthier place!

I've been struggling with an inflammation in the great saphenous vein (left leg), for which I was repeatedly wrongly advised by various doctors based on a venous reflux in the echo-doppler test;—result: they all said to operate, INSTEAD of looking into the root problem!

Had I listened, I wouldn’t have found out so much (Michael Pollan's books, Sandor Katz's fermentations, Weston Price, etc.) about what is wrong with my nutrition;—although plenty of fruit & veggies, mom taught us margarine, low fat, carbs etc.
Only recently, after months of reading did I realize that my nutrition had excessive Omega 6 intake!

For the past 9 months, I've been almost sofa-ridden trying to get control of the veins associated to the great saphenous vein, that are not really varicose or twisted but are swollen and blue, until I realized I was eating too much fruit and not taking enough Omega 3 in conjunction with saturated fat.
I had followed the classic organic apple cider vinegar remedy with a bit of sodium bicarbonate (2 soupspoons vinegar with 1/8 of sodium bicarbonate to alkalize in a glass of water, twice daily), which resulted in loosing excessively weight (20Kg.) and I was a thin but strong runner of 75Kg/height: 1.80m, but I got much better, —though only very, very slowly!

I am sticking to the anti-inflammatory diet: so no starch&carbs, by eating a variety of veggies/leafy greens with fish and seafood, and only 1 piece of fruit after dinner.

I also take with breakfast Seven Seas high strength cod liver oil which contains about 4000mg EPA&DHA and 2000i.u. Vit. A (Retinol), about 10microgr. Vit. D, and 15microgr. of Vit. E, together with some 10% fat greek yogurt and some veggies with butter to stimulate bile activity as you mention.

At lunch: seafood or fish with veggies and 500mg of Vit. C and an overall supplement that contains the following in small amounts: Glucosamine sulphate, Magnesium, Silicium, Calcium, Pantothenic acid, Fluor and Vit. B1, B2, B3, B6, B12.

And for dinner again: big mixed salad or steamed veggies with fish or seafood, occasionally an egg and 1 x Daflon 500mg tablet (Hesperidin, Isorhoifolin, Linarin and Diosmetin) so that I can have one fruit, since the flavonoids seem to control also blood sugar or insulin spike. In the afternoon I take a short sun-bath of about 35min, to get some more Vit. D, although my fat deposits are so depleted that I am struggling probably to synthesize it properly. Curcumin with a bit of black pepper diluted in some water, also helped when I was experiencing burning and stinging in the vein in the past, within 30-45min everything would calm down and I am now only applying some organic apple cider vinegar wraps around the leg, which seems to help tighten the veins, stimulate circulation and provide a host of enzymes and minerals to the surface veins in treatment.

Based on your anti-inflammatory regime, I saw drastic results within less than a week, in what has become an ordeal of over 9 months in which various other veins became blue, spider veins appeared around my ankles and larger veins swelling up. temporarily when standing for too long, and then starting to disappear again with prolonged days of rest and plenty of vinegar.
(Compression socks made it worse, so I skipped them.)

I am indebted to you, and express my gratitude for teaching me the potential inflammatory impact of sugars in fruit (and not only), which I was eating in excess 6-8 pieces per day, to keep an adequate vitamin intake and energy level since I skipped completely on starch and carbohydrates of any kind, but did not see the improvement I saw in the last week.

If you have the time, and it's not too much to ask, could you perhaps be so kind to have a look... if there is any improvement to be made in what I am already successfully applying?

With tremendous respect and gratitude,


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Hi -

Just wondering if you have any thoughts on the big controversy brewing over Cod Liver Oil vs. Fermented Cod Liver Oil? You say most vitamins are made by our gut bacteria, but why do so many in the Ancestral Health Movement, those who believe strongly in eating fermented foods to create a healthy gut micro biome, still feel taking CLO is beneficial? Can you comment on this? Thanks!


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There doesn't seem to be much of a controversy and several authorities have commented. There doesn't seem to be much of a difference. I don't understand why fermentation has been brought into the mix. Fermented cod liver oil, doesn't seem to me to be related to fermented veggies, i.e. essentially dairy probiotics plus prebiotic fiber. There doesn't seem to me to be an obvious relationship between CLO and a healthy gut microbiome. Omega-3s are good and beneficial in the context of inflammation. So, CLO or FCLO may be helpful therapeutically, but they shouldn't be of much benefit to healthy people/healthy guts.

Fermented veggies are beneficial because they provide lactic acid related bacteria that are surrogates for a healthy gut microbiota with respect to immune system development. Homemade ferments provide the extra benefit of stray bacteria that can actually contribute to the gut microbiome. FCLO would presumably be of minimal benefit in this context, because the bacteria present are from commercial starter cultures.

Thanks for the questions.

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