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, April 22, 2010

Antibiotics, Gut Flora, Food Intolerance and Disease

Cattle Are Finished by Selective Killing of Gut Flora.  The Sickened Animals Store Fat that Grills Great.  People Get Metabolic Syndrome.
The likening of modern humans to potatoes sacked out on a couch is misleading.  The obesity epidemic linked to diets of processed foods more closely resembles the stumbling progression of cattle to abattoir.  Antibiotics and diet systematically lead in both feedlot and food court to gut dysbiosis, immune system failure, hormone disruption, rampant fat accumulation, physical inactivity, depression and the modern suite of chronic diseases.  Healthcare costs escalate, but vet bills, in contrast, are forestalled by a captive bolt pistol.
Background Observations
  • Antibiotics kill bacteria and not humans, because the bacteria have different machinery for making proteins, nucleic acids and cell walls.
  • Antibiotics kill bacterial pathogens and not viruses or fungi.
  • Antibiotics kill helpful bacteria in the gut (gut flora) even more readily than pathogens.
  • Antibiotics are used in meat production to alter gut flora to change animal metabolism;  e.g. cattle treated with antibiotics gain fat.  Protection from disease is secondary.
  • Simple diet means simple gut flora.  Processed foods are simplified foods that simplify gut flora.
  • Probiotics can replace only a small fraction of the gut flora diversity.
  • Gut bacteria control the immune system development in the lining of the gut.
  • Chronic antibiotic use permanently simplifies gut flora and compromises the immune system.
  • The appendix stores gut bacteria as a reserve to replenish gut flora following diarrhea.
  • Diseases based on inflammation and immune system intolerance result from gut dysbiosis (inadequate gut bacteria).
Antibiotics Kill Good Bacteria
This is a rant about antibiotics, not about humane actions.  Humane actions are not the point here, since I am talking about health care and not treatment of agricultural animals.  I am pleading for the rights of gut flora everywhere and antibiotics are the casual killers.  Compromised gut flora is collateral damage in attempting to eliminate bacteria characterized as pathogens.  Every time the pediatrician treats the mother by acceding to her pleas for an antibiotic prescription to silence a howling ear ache and get a good night’s sleep, or the dermatologist treats teen acne with antibiotics, billions and billions of domesticated bacteria die.
Constipation Is a Sign
Countless hours are wasted waiting, because antibiotic-depleted gut flora cannot hydrate and form normal stools.  Probiotics are gulped down, but they supply only a handful of the hundreds of bacterial species that are needed for health.  Yeasts and other fungi that are naturally resistant to antibiotics quickly replace the lost beneficial bacteria in the gut, vagina and on other body surfaces.  Surcease for simple sorrows leads to lingering and lasting laminations.  Don’t mess with mother nurture.
Damage of Antibiotic Use Is Slow
Most of the impact of antibiotic annihilation of bacteria normally present in humans is unobserved, because the deleterious effects lag months behind the initial treatment.  After all, cattle treated with antibiotics to restructure their gut flora to induce bovine obesity, appear to thrive as they rapidly gain weight and avoid symptoms of infectious diseases.  Humans on antibiotics also display fewer dental and incidental infections.  Constipation is not a high price to pay for a better mirror image.  
Antibiotics Compromise the Immune System
Unfortunately, allergies, autoimmune diseases, degenerative diseases and cancers are not usually linked to prior use of antibiotics.  There is no evidence that gut flora recovers  after antibiotic treatment, but constipation as a consequence of chronic antibiotic use is a common indicator of gut dysbiosis, collapse of normal gut flora bacterial communities.  The harbingers of inflammatory and degenerative diseases are present, but are usually discounted, because they are a common consequence of the Western diet.
Food Intolerance Reveals Inadequacies in Gut Flora
Food intolerance is a sign of depleted gut flora diversity.  Gut flora have hundreds of genes that can break down a huge diversity of polysaccharides derived from plant cell walls.  Gut flora of Japanese who routinely consume kelp have specialized enzymes to hydrolyze unusual algal sulfated polysaccharides.  Essentially all of the polysaccharides in plant fiber can be consumed by bacteria in the anaerobic environment of the colon.  Inability of individuals to digest particular food components usually results from a deficiency of the gut flora and an indication of a history of dietary simplification and antibiotic use.  Lactose intolerance, for example, results from depletion of lactose-degrading bacteria from the gut flora and can be remedied by simply eating lactose with probiotics for a couple of weeks.  Gut flora can adapt, but they need persistent exposure to diverse, i.e. non-processed, food.
Antibiotic Allergies Are Natural
Allergies develop from a combination of inflammation and compromised immunological tolerance.  Inflammation heightens processing of antigens for presentation to the immune systems, whereas loss of immunological tolerance means that aggressive immune responses are inadequately controlled.  Thus, innocuous environmental molecules are incorrectly recognized as pathogen components.  Allergies to antibiotics, such as penicillin, make sense, because the antibiotic is used to treat inflammatory infections and the antibiotic treatment eliminates the gut bacteria that are needed to develop gut lymphocytes (Tregs) to produce tolerance.  Antibiotics lay the foundation for immune system dysfunction that is central to many chronic diseases.
Healthy gut flora and a healthy immune system require:
  • avoidance of antibiotics
  • systematic (not simply eating yogurt) rebuilding of gut flora following diarrhea or antibiotic use; lack of an appendix means gut flora reservoir is gone
  • eating a variety of vegetables; avoiding processed food
  • using herbs and spices
  • don’t overdo hygiene; gut flora diversity derives from bacteria that you eat and those that rub off acquaintances
  • eat seasonally to increase diversity


Dr. Art Ayers said...

So, you can see that I take a dismal view of antibiotic use. The problem, as I see it, with a mitral valve replacement and infection, is gut bacteria or in this case bacteria of the dental biofilms introduced by trauma into the blood stream, migrating to sites of inflammation.

Since your replacement parts will provide chronic local inflammation, circulating bacteria or phagocytosed bacteria circulating in cells of the immune system, will end stick to the inflamed tissue and cause problems. The same is true for people with other sources of chronic inflammation as in arthritis or rosacea.

It seems that there are at least three targets for intervention:
Eliminate the bacteria (antibiotics)
Eliminate the local inflammation (lower inflammation)
Eliminate the source of the bacteria (leaky gut or dental hygiene)

As you can tell from my article, I am not so happy about the consequences of antibiotic use and I would guess that you never fully recover from your periodic antibiotic treatments. That suggests that your cardiologists approach will lead to some immunological consequences down the line and I would expect people with mitral valve replacements to have typical predispositions to chronic diseases.

That said, I don't see any way of getting around the antibiotic use.

In the best of all possible worlds, medicine would have realized that antibiotics are too dangerous to use without followup compensation and there would be a simple solution to the gut flora devastation. For example, prior to the replacement, an effort would be made to assess the health of the existing gut flora and after the flora has been repaired, store a sample of the flora. After the replacement and depletion of residual antibiotics, the stored flora could be used to reconstitute a healthy gut flora. The consequences of each subsequent use of antibiotics could be minimize with another replenishment.

Lacking gut flora transplants, you should be very aware that you are under constant threats of infections from leaky gut caused by NSAIDs or other compromisers of gut development. So, an anti-inflammatory would seem to me to be a very important defense for you. Gut integrity is vitally important. From this perspective, antibiotics are huge liabilities.

Keeping your immune system healthy is also of importance to minimize migration of intracellular bacteria. This falls back on gut function and healthy gut flora.

Perhaps your best approach is to minimize your need for teeth cleaning. I recommend that you become knowledgeable about dental health and start with Stephan Guyenet's articles on the subject:
You will find that D and K vitamins can go a long way toward eliminating numerous cleanings.

So my suggestion to you is to enjoy an anti-inflammatory diet and lifestyle consistent with my suggestions and look into ways to minimize the number of cleanings. The tough one is reconstituting your gut flora. I haven't been able to improve beyond probiotics, pectin/inulin and diverse veggies from local organic sources. Avoid processed foods, since you need the most complex diet possible -- get used to using lots of herbs, spices and diverse veggies.

Tell me how it works out.

Anonymous said...

Dr. Ayers,

The depth and speed of your response astonish me. Thank you. I had been anticipating the gist of your response, but I still find it difficult to trade the long-term, possibly devastating results of antibiotic use for the short-term prevention of acute infection. Until my doctor discovered my mitral valve problem (which she believes to be congenital) about 10 years ago, I had not taken antibiotics prior to dental cleanings, and had not had any problems. (I'm not sure whether I miscommunicated my case; I have mitral valve prolapse, but it is not yet severe enough to warrant valve replacement or surgical alteration of the valve). I'm no gambler, but this seems like a no-win situation. I am tempted to go to my dental cleaning without taking the antibiotics.

For the past three months I have been eating a diet very like the anti-inflammatory one you recommend. I have become youthfully lean (with no change in my weight 5'9" 124lbs). I have been reading Stephan Guyenet's articles and will revisit those on dental health. His blog is another of the excellent sources of information informing my shift in diet and lifestyle.

Do you recommend a particular type of Vitamin K supplementation, beyond what might be available in a wide variety of vegetables and aged artisanale cheeses? I am a true gourmand and frequenter of the farmer's markets. Spices and variety are things I incorporate into my meals almost by necessity.

I will take (and have taken) your advice on diet and dental health. I only wish you were able to tell me the prophylactic antibiotics were unnecessary, or at least the greater of two evils.

Thank you, Dr. Ayers.

I'll be reading.


sr said...

Even the mainstream sources say the evidence for prophylaxis for endocarditis during dental procedures is weak.
Here are the AHA guidelines:
(IE means infective endocarditis)
Although the absolute risk for IE from a dental procedure is impossible to measure precisely, the best available estimates are as follows: If dental treatment causes 1% of all cases of viridans group streptococcal IE annually in the United States, the overall risk in the general population is estimated to be as low as 1 case of IE per 14 million dental procedures.41,90,91 The estimated absolute risk rates for IE from a dental procedure in patients with underlying cardiac conditions are as follows: MVP, 1 per 1.1 million procedures; CHD, 1 per 475 000; RHD, 1 per 142 000; presence of a prosthetic cardiac valve, 1 per 114 000; and previous IE, 1 per 95 000 dental procedures.41,91 Although these calculations of risk are estimates, it is likely that the number of cases of IE that result from a dental procedure is exceedingly small. Therefore, the number of cases that could be prevented by antibiotic prophylaxis, even if 100% effective, is similarly small. One would not expect antibiotic prophylaxis to be near 100% effective, however, because of the nature of the organisms and choice of antibiotics.

Anonymous said...

Thank you, SR.
That makes the known vs. unknown risks much easier to weigh.


Garry said...

Shannon said,

"I only wish you were able to tell me the prophylactic antibiotics were unnecessary..."

It appears they may indeed be unnecessary:

Dr. Art Ayers said...

I am glad that I over interpreted your valve problem.

I think that an interesting aspect of heart action is the stretching of surfaces that are exposed to blood. There will normally be plenty of micro-traumas and the exposure of connective tissue that mimics wounds. This should mean that repair is a constant characteristic of the heart. That means that the level of chronic inflammation and the suppression of inflammation in heart tissue is very important.

In your situation, it doesn't matter if your valve is damaged by improper dynamics. What matter is the context of repair. If repair is robust, but constrained, i.e. appropriate localized inflammation, then all is well. There should be no long term effects. In the presence of chronic inflammation, in which it is likely that small defects will expand to involve more tissue, then the tissue becomes weakened, because the wound and scar tissue are not as strong. The valve would age.

In this context, all that is needed is to live in an anti-inflammatory state and the damage should heal. There might be some local inflammation, but it would not spread. It would seem that antibiotic treatments would be riskier than handling the odd bacterium that escapes. I would think that you would be best off reducing the need for dental cleaning so that you could reduce the treatments to once a year, and then make sure that your systemic inflammation and gut health are optimal.

So, if you asked me what I would do, I would not do the antibiotics and I would find a cardiologist that supported reducing risks with diet and lifestyle preparation.

Good luck and health.

Dr. Art Ayers said...

Thanks to my knowledgeable readers who can provide the facts.

I missed a couple posts and when I finished up the answer was posted most effectively by readers.

I love your input.

Nick said...

Hi Art,

Thank you for another great post. My girlfriend takes a low dose of antibiotics for, of all things, rosacea. She is under the impression that the low dose someone bypasses her GI because it treats the skin. I don't imagine you'll say it is okay, but I am hoping to find out what you think about the use of antibiotics for rosacea? Her diet is really quite good, though she won't give up on wheat and flour.

Thank you for your thoughts.


Anonymous said...

Dr. Ayers,

Your responses (and those of your knowledgeable readers) have relieved me of a huge burden. I am determined to live in an anti-inflammatory state as much as possible in the hopes that my mitral valve prolapse will not worsen, and may even lessen to some extent. To that end, you will be my virtual guru.

Thank you so much. I feel very optimistic.


p.s. Dr. Ayers, I must know...when you first responded to my initial inquiry on your previous post and you said it would just take "a few minutes" to write your article about antibiotics, gut flora, and disease, had you already been working on the article? I want to know whether I failed to interpret your dry sense of humour, or whether you are a genius of astonishing speed--or perhaps a little of both.

Unknown said...

Hi Dr. Ayers -
When dysbiosis is present in the gut and pathogenic bacteria significantly outnumber the beneficial (as was found to be the case with me), is it possible that supplementing with probiotics could agitate the existing gut bacteria in a way that inflammation actually occurs? I began taking L. acidophilus (150 billion cfu) daily but found myself developing extremely painful joint inflammation after 1 week of probiotic supplementation (all other areas of the diet remained the same as before the flare) and discontinued the probiotics. Could it be that the pathogenic bacteria is being crowded out or dying off and is thus creating a toxic overload that is promoting the inflammation? Does this resolve itself once the beneficial bacteria takes hold? Thanks.

Dr. Art Ayers said...

I hope that you have read my other posts on rosacea. My impression is that chronic oral antibiotic use for rosacea impacts the gut flora and gut predominantly and the effects seen on the face are ramifications of the immune system.

I would expect that your girl friend will show some problems with bowel movements and will gradually develop constipation and the need to use irritating laxatives. That would be typical for rosaceans and would reflect the attack on the gut flora.

I think that it would be wiser to try to get off the antibiotics and shift to an anti-inflammatory diet with increased vit.D. I would not be surprised if she shows flaring as the anti-inflammatory components start to work. I interpret that as die off of bacteria that are causing problems in the gut and face.

Good luck and let me know how it goes.

Dr. Art Ayers said...

There are reports of lactic acid bacteria causing overgrowth in the small intestines.

I wouldn't expect that just adding probiotics without modifying the diet that caused the dysbiosis would have a major impact on your gut flora.

If I was in your situation, I would just do a major shift in diet to destabilize the existing bacteria and move on to a healthier diet.

Did you get into the pathogenic gut flora as a result of antibiotic use or a hospital stay? Immobilization can also cause problems with gut flora.

Any disruption of the gut or gut flora can lead to release of inflammatory bacterial wall components, e.g. LPS leaking into the lining of the gut and contributing to inflammation. So, I agree with the possible scenario that you present.

You could use glutamine to help heal your gut and then shift to an anti-inflammatory diet. Under those condition probiotics with pectin/inulin should help to improve your gut flora.

Good luck and let me know what happens.

Dr. Art Ayers said...

I am glad to hear that you are feeling more optimistic. I think that it is important to feel like you have control of your own health.

Since connective tissue is a major part of the mitral valve composition and function, and inflammation undermines connective tissue/cartilage/extracellular matrix, I think that it follows that a consistent avoidance of inflammation should produce a healthier valve over time.

I am a quick writer once I understand the subject. I usually write in order to gain understanding, so sometimes the path is not very linear or even possible. In the case of the recent article, I had some strong opinions and had discussed aspects of the subject in comments to other posts. I was already planning to write the article and had essentially completed it when your comment arrived. That prompted me to finish it up and post it.

I really get pissed at how many people are poorly supported in their pursuit of health and it is upsetting to immerse myself in the biomedical literature and see an absence of interest in finding cures and understanding the causes of diseases. That is what spurs me on to apply some simple reason to diet and disease, and expose some areas in which the medical industry is undermining health.

I am optimistic that simple cures will be soon available for many major diseases. A major change to a more sensible diet would be a good start.

Good luck and let me know of your progress.

marco said...

Hi Dr. Ayers.

My wife (38 y.o.) has no appendix since she was 12, because she suffered from gut pain in the lower right side of abdomen.
She has always been very constipated, but when she eats large quantities of fiber from vegs she obtain nothing but a bloated stomach. As I suppose bloating to be caused by bacterial fermentation, does this means that, in spite of the lack of her appendix, her gut flora is still there? What could she do to repair her gut flora, apart from eating forever home-made yoghurt or probiotics in capsules?

Thanks a lot for your help and sorry for my English...


Anonymous said...

Hey, is it possible that acne is related to a certain kind of gut dysbiosis? Antibiotics seem to help for some people. I tried all sorts of diets (low carb, no milk, no gluten, low PUFA) and nothing really works. No milk, no gluten and no sugar make it less, but it just doesn't want to go away (and i dont want to take meds). What would be the best approach to re establish a healthy gut flora?


Byron said...

Hello Dr. Ayers,
thanks for the interesting article and great comments. In my experience prebiotics like FOS and inulin works a lot better than probiotics in handling inflammation like asthma/eczema. Sure only with the right diet. I also discovered how great quercetin and vitamin c works in reducing histamine. Of course only high doses and a bioavailable form like buffered magnesium ascorbate. But in long term for sure better than antihistamines or corticosteroids. Have a great weekend.

Gluten Free Food Freak said...

David, have you tried a Paleo diet? I only ask as my wife suffered from acne to age 36, at which time she went 'Paleo' and exluded dairy and the result on her skin was miraculous. We suspect insulin may have been implicated as she was having blood sugar issues around the same time.

Dr Ayers, I have a question at the same time. In addition to being coeliac I have all sorts of problems with my gut. I have tested positive for IgA Candida and get unpleasant reactions from a range of foods.

So one might assume that my bacteria are not as happy as they might be.

Thankfully I have never had any major antibiotic treatment, but I can't tolerate probiotics as they trigger a nasty inflammatory reaction. I'm also allergic to yeasts and molds.

Is there anything you can recommend to help me get my internal army marching in time again?



John said...

"...lack of an appendix means gut flora reservoir is gone."

Are there additional/special steps to take for those that do not have an appendix?


Mike said...

Awesome post, once again, Dr Ayers.

Interesting comment on the appendix, or lack thereof; as far as I know, conventional medical training lists the point of the appendix as "unknown", but as a reservoir for GI flora, it makes perfect sense. Have there been any studies regarding the flora of those with an appendix vs. without?

Anonymous said...

.... Can you answer my questions...

i have added goat yogurt & goat milk kefir back in to help my bacteria critters... is this a good start? i just would like to be able to eat cheese, sour cream and stuff again(raw goat feta/cheddar)

cooling inflammation fan said...

Hi Dr. Ayers,

I think you've mentioned in the past that fecal transplants would be optimal for people suffering from gut dysbiosis, while also noting that it's not currently available as a treatment. Have you heard about fecal bacteriotherapy (a new method of fecal transfusion developed in Australia) and if you have, what do you think of its potential?

Thanks for all your hard work!

Anonymous said...

Dr, Ayers,

What about iodine supplements, such as Iodoral?
They are supposed to kill fungi and bacteria.
Would they also kill gut flora that we need to keep?

Thank you for the great information.

Anonymous said...

Dr. Ayers,

I wanted to send this message to you via e-mail but I didn't see a way to do that, hence this 'public' declaration.... :)

You have literally changed my life and I cannot thank you enough. I am a 34 y/o woman recently diagnosed with Mixed Connective Tissue Disease, but otherwise healthy. I've been active and a "healthy" (predominantly grain) eater my whole life. But slowly tearing down. Recent flare of MCTD means I went from running 30 miles a week to 4 miles the entire next month, needing 12 to 14 hours of sleep and STILL exhausted. But, otherwise, "healthy". Quite a puzzle for me and, it appears, for the various doctors I've seen.

Through all of my doctor visits and subsequent diagnosis, _not one_ doctor EVER mentioned diet modification. Instead I was given prescriptions for plaquenil and nifedipine. Only through slightly OCD research about MCTD did I come across your blog addressing grains and auto-immune diseases. You opened up the whole world to me; IMMEDIATELY I cut out all grains, boosted Omega 3, vit D and limited sugar.

From your blog, I discovered the Eades, PaNu and Mark's Daily Apple. While I am not focused on Paleo or Primal eating for weight management, they helped me see how I could put into practice zero grains, no added sugars, etc. My energy is back, I am sleeping 7 hours a night, I feel content (after being plagued with melancholia+ since I was about 8), my hair is already growing back, I FEEL GOOD.

I just want to tell you that I am so extremely grateful for your knowledge, research and desire to share information. I want to say this again: you have literally changed my life, and I'm a little choked up typing this right now THANK YOU. If you and your wife come to Vegas, I would feel honored if I could take you both to dinner.


Dr. Art Ayers said...

A missing appendix is not a cause for worry, but rather a need to remember the importance of continual maintenance of gut flora.

Constipation is not a sign of insufficient fiber in the diet, but rather lack of adequate gut bacteria. Bowel stools are made of bacteria, not undigested fiber.

It takes years to cultivate a fully functional gut flora. If you just feed fiber to someone who is chronically constipated and displaying a lack of gut flora, the result will be lots of poorly digested fiber bloating the gut.

Probiotic fermenting bacteria only work in the upper part of the gut, not in the colon. The anaerobic bacteria that work in the colon must be slowly acquired by persistent eating of diverse veggies to provide diverse polysaccharides and uncooked veggies to provide the bacteria.

The other alternative, would be a fecal transplant, which is starting to become available.

I suggest that you and your girlfriend eat small amounts of many different kinds of raw vegetables with each meal. She will also benefit from fruits/veggies with pectin and inulin.

Let me know if this gradually helps.

Dr. Art Ayers said...

Acne and antibiotics,
Antibiotic use for acne covers up the problem by eliminating immune cells that attack bacteria in the face. They also disrupt hormone balance that is contributing to facial symptoms.

For most people, antibiotic use guarantees future visits to the doctor. Pediatricians, for example, have three times as many office visits, if they actively prescribe antibiotics for ear infections.

Most people with acne are looking for triggering foods in their diets. That doesn't make sense or work, because the problem is multiple sources of inflammation. The answer is the approach that I recommend of eliminating all of the sources of inflammation. Since diet is the biggest problem, that requires the biggest change. Fish oil supplements can be used to compensate for minor sources of inflammation.

Your most likely problem is low vitamin D. Have it checked and then make sure that your supplements actually produce a high serum level (>80 ng/ml.)

Let me know how it works.

Dr. Art Ayers said...

I agree that prebiotics usually have more impact than probiotics. I prefer the pectin/inulin combo in apples and leeks, but each flora to its own.

I also find quercetin to be kind of magical. Mast cells are also favorites, because they secrete heparin to charge-neutralize histamine.

Thanks for your comments.

Dr. Art Ayers said...

Gluten Free Food Freak,
Celiac is a very big problem. I think that it is also problem several diseases with similar symptoms. This makes clinical trials less productive.

Among the other problems with celiac are messed up absorption of vitamins and minerals, because of changes in intestinal development/physiology, and the promotion of other autoimmune diseases via inflammation and self-antigen presentation. Thyroid problems are one common consequence. Leaky bowel complications are another problem.

Gut flora are an issue in celiac, because some of the normal gut flora can degrade some of the gluten peptides that trigger celiac.

A healthy gut requires a diverse diet supplied by lots of different veggies. That is difficult with a sensitive gut and compounds the problems.

All of your symptoms are consistent with immunological intolerance, a lack of T cell regulation and a deficiency of the Tregs that develop in the gut lining in response to gut flora.

The quick fix might be fecal transplants, but that has not be explored, though it is now available.

To achieve gut flora diversity: persistence, veggie diversity, ingested bacterial diversity. Persistence just means slow and steady. Veggie diversity could be a puree of every vegetable in an open market. Bacterial diversity is potentially dangerous and I don't have the answer. One candidate might be the results from composting all of the veggies left over from the farmers' market. That also might be dangerous for some people who have compromised immune systems to begin with.

There is probably a simple solution, but medicine is not looking for it. Most people are genetically predisposed to celiac, but function normally.

Good luck. I hope this is helpful.

Anonymous said...

Here's a letter to a journal, where antibiotics failed to ameliorate bacterial infection in the small intestine, but prebiotics did:

The prebiotic used was a synthetic disaccharide called lactulose. This is available by prescription only in the US, but over-the-counter in many other countries.

It is believed that lactulose alters the intestinal bacterial populations by selectively providing energy to acid-producing gut bacteria. Specifically, it increases the selection pressure for bacteria that produce acetic, butyric, and lactic acids.

That lactulose can be effective in the small intestine is not widely known. Most of the literature states that it passes, unaltered, through the small intestine, and is then metabolized by the much larger populations of bacteria in the colon.

The link, above, suggests that lactulose can be metabolized in the small intestine, especially when the small intestine is infected.

Dr. Art Ayers said...

John, Mike,
The appendix was linked to recovery from diarrhea and some diseases, e.g. MS, have been linked to a lack of appendix.

See my previous comments about maintaining gut flora without an appendix.

Thanks for your comments.

Dr. Art Ayers said...

I think that you can regain your ability to tolerate dairy by just going slow and being persistent. Your gut flora should adapt.

Thanks for your comments.

Dr. Art Ayers said...

I wouldn't expect iodine supplements to be bad for your gut flora, because the amounts of iodine are small and in the iodide form. I don't know much about this, but that is my understanding.

Thanks for your comments.

Dr. Art Ayers said...

Thank you so much for your generous comments.

Helping others is my reward and the impetus for my writing. It means a lot to me that others read my words and can find a path to health.

Thanks again for your comments and let me know if you have a subject that you would like me to ponder.

Dr. Art Ayers said...

Thank you for your heads up about lactulose. I read all around that article previously and didn't get it.

Lactulose is like a lot of the lactose-like oligosaccharides present in human milk that make up the bifidus factor that restricts bacterial growth in breastfed newborns. I guess that is why this synthetic disaccharide has such interesting properties.

It may be interesting to add lactulose to the list of recommendations for repairing damaged gut flora:
probiotics, lactulose, pectin, inulin.

I am trying to wrap my head around short chain fatty acid metabolism of gut flora and lactulose provides another piece.

Thanks for the lead.

Patty said...

Dr. Ayers,
My family is fighting lyme disease and coinfections such as babesia, erlichia, bartonella,and such. Most doctors want to treat chronic lyme with long term antibiotics.
My 22 yr. old daughter is very ill. She is in constant pain and her inflammatory tests are always off the charts. She is working on the anti-inflammatory diet, and taking tumeric. She is not on antibiotics. Most pain pills...even the strong stuff, don't touch her pain.

Can you please help us?
Thanks so much....Patty

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

The intestinal epithelium provides an essential barrier function to prevent proteins of food or food-hydrolyzing enzymes from entering the blood.

The enzyme treatments that are advertised on the site that you mention have no way of getting into a healthy intestinal lining. That is good, because they would be simply destructive. Uncontrolled proteases are unhealthy. None of the research articles (I checked the original abstracts) that are cited have anything to do with normal uptake of proteases in a healthy intestine.

The diagrams don't show how the enzymes would work and there is no explanation of how they would impact inflammation. It just looks like someone did a photoshop romp on an existing diagram of inflammation pathways.

If it worked, there would be some clinical studies or at least a straightforward explanation.

For your audience of advanced age, I think that the major point is that the symptoms that we attribute to aging are predominantly the consequence of poorly managed chronic inflammation. Most of their symptoms can be reversed with my suggested anti-inflammatory diet and exercise.

Thanks for your comments and questions.

Anonymous said...

Dr. Ayers, another wonderful post. I learn more from this site than many years of learning at my pharmacy school. I am glad you are carrying the water so to speak where so many others are merely content to call themselves Doctor and practice conventional medicine.

I have a question on fats in meat products. I don't have access to hormone free,antibiotic free, grass fed beef. As a substitute I have been thinking about buying the leanest conventional ground beef available, and then adding saturated fats in the form of butter or coconut oil. I hope this will minimize the toxicity of conventional feed-lot beef that I can get. Specifically I am trying to minimize hormones, anti-biotic remnants, and high omega-6 that feed-lot cattle produce. I would think that most of the "bad stuff" is stored in the fat and not the protein. Is this correct? Does adding my own fats to lean ground beef make sense?

spp said...

Dr Ayers,
Super post (along with the other posts in your blog). Do you have an opinion of how various fungi foods impact gut flora? For instance, Lions Mane mushroom appears to have benefits to the gut according to some asian cultures. (As well as heart protective effects).

Thanks, Steve

zach said...

Great post.

When I was 7-8 years old I had chronic strep throat. Antibiotics and penicillin shots for months at a time. Played havoc with my bowels. Giving up processed foods and enjoying fermented foods and raw dairy products has really restored my gut health. Antibiotics are very serious drugs that should be taken only as a last resort.

One thing that really worries me is the standard treatment of lyme's disease. It would seem to me that antibiotics would be the last thing you'd want to use to help such an inflammatory condition.

Gluten Free Food Freak said...

Hello Dr Ayers.

Many thanks for taking the time to respond to my question – I am amazed that you can find the time to help so many people. If I may, I'd like to ask your opinion on my thoughts about how to approach the problem.

1)My diet is paleo, but with a little added starch from yams and potatoes to keep my weight up. I eat no eggs or dairy as I don't tolerate either but try to get good nutrition using organ meats and varied seafood. The starches add up to around 70g carb per day. Do you think this is acceptable or is it possible I could benefit from lowering this?

2)I have had Enzyme Potentiated Desnsitisation in the past. I am not sure that it has helped, but then I am not sure that it has not. Do you have any opinion either way on EPD low dose immunotherapy?

3)In terms of bacterial replenishment, I am thinking a) low doses of probiotics that I can hopefully tolerate, particularly Bifido Bacterium which I have been OK with previously. As here on the west coast of Scotland I only have access to super-clean Tesco veggies, growing as many of my own as I can in good local horse poo :) And then trying things such as homemade sauerkraut and water kefir.

4)Considering Helminth therapy which you mentioned here:

I am not sure if I could get access to Helminths, but if I could, do you think it would be worth a try?

5)I couldn't find Lactulose here in the UK but would that be worth getting?

Thank you again for your generous help – if there is anything I can help you with, please let me know. I have some experience in websites and promoting them if that's of any use.

All the best


Dr. Art Ayers said...

Lyme disease, as you well know, is very complex. For some people it causes no problems. For others, it becomes a chronic disease with many complex and debilitating symptoms.

I hesitate to comment, because the treatment is so controversial and there are very powerful medical and insurance interests involved. Unfortunately the research on the disease has not provided clear answers on the treatments that work. There are not even clear diagnostics of which bacteria and viruses are involved.

Treatment of the bacteria using long term antibiotics produce many problems associated with the inflammatory die off of bacteria in tissues, and compromise of the gut flora.

I think that some combination of antibiotics with careful control of inflammation and eventual rehabilitation of gut flora, may permit recovery. Ultimately, I think that the answer may be gut flora transplants after the antibiotics.

The roles of all of the components of the anti-inflammatory diet that I recommend, may be paradoxical in many cases of Lyme disease, just as in rosacea.

All I can suggest in addition to finding a supportive physician, is to try some of the topical pain relievers that I recommend: menthol/Vicks, castor oil, vagal stimulation.

In the absence of antibiotic treatments, which anti-inflammatory diet suggestions have been tried? What is the impact of fish oil (only used after veg. oils are eliminated and saturated fat is increased)?

I wish I could be more helpful.

Dr. Art Ayers said...

I don't worry so much about the omega-6 fatty acids and fat soluble "toxins" in common beef. It would be better to eat grass fed, but I don't think that the whole equation is that sensitive.

I think that it is more important to worry about all of the major issues: vit.D, low carb, most calories from saturated fat, no veg. oil, plenty of greens, healthy gut flora. If you do those things and get plenty of exercise and avoid ticks, I don't think that where your beef comes from is a major issue.

I still grill my meat, so I guess I can't worry about antibiotics in the fat. I just sear it and enjoy the flavor, knowing that it is low carb and high in saturated fats. I eat veggies with the fatty meat to extract more vitamins.

Eating local and seasonal is a good secondary goal.

Thanks for the comments and questions.

Dr. Art Ayers said...

Fungi produce lots of novel chemicals, e.g. statins, antibiotics. They also produce some interesting polysaccharides. One of those is the beta-glucans, that are important in triggering inflammation. [I did some of the first work on plant response to those fungal polysaccharides, for my Ph.D.]

I think that eating some fungi may be good for health and it may take a little while for gut flora to adapt.

Thanks for the comments.

Dr. Art Ayers said...

I agree that antibiotics, especially long term, should be used very carefully and there should be aggressive compensation for the disruption of gut flora.

It is incredible to me that a child can be treated with a course of antibiotics for an ear infection and the only recommendation for regaining gut flora and normalizing the immune system is eating yogurt.

Lyme is so complex and debilitating that antibiotics seems to be the only solution, but the therapy could be improved with more care on reconstituting the gut flora and monitoring immune system function.

Thanks for your comments.

Dr. Art Ayers said...

Thanks for the meaty post.

1) I think that 70g of carbs per day is fine, but I would try to use lower starch sources.

2) My opinion on low dose desensitization is that it is an attempt to treat symptoms (a dysfunctiona immune system) as opposed to understanding the problem. Why do you have allergies? In your case the answer goes back to your celiac. Celiac causes aberrant display of self and other antigens in an inflammatory environment.

To solve the allergy problem, it seems to me that you need to avoid the celiac triggers, eliminate other sources of chronic inflammation and reconstitute the tolerance part of the immune system. The answer to all three is diet.

3) Replenishing your gut flora is a hard task with celiac, because celiac leads to intestinal restructuring. So you will have many deficiencies. Probiotics of some type will be only of limited use. The other components to try are glutamine, lactulose, pectin and inulin. Even starch may be helpful, and maybe that is why you already have more than I would normally recommend in your diet.

4) Helminth treatment works for an intrepid few. It just demonstrates that activating the tolerance system in the gut solves a lot of immunological problems, such as allergies. I think that the same result can come with a happy gut flora responding to diverse veggies. One of your problems is not tolerating enough different herbs and spices.

Most people with dietary problems think in terms of triggers, but the problem is that the diet is too narrow already and bacteria needed to stimulate tolerance are absent.

5) I think that lactulose is under exploited to enhance gut flora development. It would be good to give it a try.

You can help me, as you have been, by responding to my ideas and helping me to make sense of diseases so that we can come up with simple remedies.

Celiac shouldn't happen. Most people have genetic predispositions, but do not show symptoms. Many cultures are based on grains (even though there may be some severe health compromises.) I think that there is a simple answer, but I am missing something.

Thanks again.

suat said...

thank you Dr. Ayers for the very useful information;
Having had my appendix removed when i was kid and have used so much antibiotics. I have stopped taking antibiotics about 5 years ago unless it was really necessary. i believe I have destroyed much of my gut flora. I have been suffering constipation for years and all the doctors I have seen told me to eat more fiber drink more water and prescribed laxatives if it was very bad. I have never been considered about my gut flora; I will try to replenish my gut flora and see the results ! your approach to the diseases and underlying causes not just treating the symptomps is really inspiring

thanx again

B said...

Hi Art,

Over a year and a half ago I was diagnosed with ulcerative colitis. Since then I've been following a paleo/anti-inflammatory diet and things have definitely improved. Your blog has been a great help along the way! I have a couple of questions which I hope you can help me out on.

(1) Eating beef seems to upset my stomach and can lead to diarrhoea. Do you think that in addition to the recommendations you make in this post, that eating small portions of beef could help? I remember reading anecdotes on the Western Price site where eating raw meat seemed to help. Perhaps raw beef could help build the necessary gut bacteria?

(2) In previous posts you've mentioned supplementing with Vit C in increasing amounts to test for oxidative stress. I can tolerate about 1g. Can you clarify what this means? Is it good or bad?


Cristian said...

Interesting abstract, I hope:

Abolition of Biofilm Formation in Urinary Tract Escherichia coli and Klebsiella Isolates by Metal Interference - Competition for Fur.
Hancock V, Dahl M, Klemm P.

Microbial Adhesion Group, DTU Food, Technical University of Denmark, Lyngby, Denmark.
Bacterial biofilms are associated with a large number of persistent and chronic infections. Biofilm-dwelling bacteria are particularly resistant to antibiotics and immune defences, which makes it hard if not impossible to eradicate biofilm-associated infections. In the urinary tract free iron is strictly limited but is critical for bacterial growth. Biofilm-associated E. coli are particularly desperate for iron. An attractive way of inhibiting biofilm formation is to fool the bacterial regulatory system for iron uptake. Here we demonstrate that biofilm formation can be impaired by addition of divalent metal ions, such as Zn(II) and Co(II), which inhibit iron uptake by virtue of their higher-than-iron affinity for the master controller protein of iron-uptake, Fur. Reduced biofilm formation of urinary tract infectious E. coli strains in the presence of Zn(II) was observed in microtitre plates and in flow chambers, as well as on urinary catheters. These results further support that iron uptake indeed is crucial for biofilm formation and thereby, targeting these uptake systems might be an effective way to eradicate biofilms caused by infectious strains.

PMID: 20418434 [PubMed - as supplied by publisher]

Dr. Art Ayers said...

As I admit, I am not much better at growing new gut flora than most GI specialists. My best guess is probiotics, lactulose, pectin and inulin, with diverse veggies.

Starch is usually a problem, because it is hyperglycemic, but it may be useful in a crude veggie form to kick start some colonic bacterial growth.

Good luck and let me know how you progress.

Dr. Art Ayers said...

Red meat and vit.C
Cooked red meat should not be a problem, unless some of your problem bacteria are starved for iron -- see the adjacent post by Cristian.

That would suggest that some zinc supplements might be helpful.

I mentioned vitamin C as an anti-oxidant. I think that some people are also deficient in vit.C and have incipient scurvy symptoms with weakened connective tissue. Vit.C gets depleted under condition of chronic inflammation with associated production of ROS. Even lots of sun exposure can deplete vit.C. Under those conditions it may take more vit.C supplement than a gram a day. That can be checked by gradually increasing the vit.C supplement until the excess spills over into the gut and causes diarrhea.

So, if you can't take more than a gram a day without diarrhea, that could mean that you aren't consuming extra vit.C due to extra oxidative stress.

Thanks for the questions and comments.

Dr. Art Ayers said...

Thanks for another interesting abstract.

Starvation of pathogens for limited nutrients, such as iron and biotin, are typical strategies used throughout nature. Common examples are bacterial siderophores to chelate iron, milk lactoferrin to bind iron, and biotin bound to egg white avidin.

It is interesting that a strategy to enhance the starvation of bacterial pathogens for food iron, is to include metal ions, such as zinc, that can bind to the bacterial metal sensing system a turn off iron acquisition. That is another suggestion for adequate minerals in our food and another explanation for why processed foods are a health problem.

Thanks again.

Unknown said...

Hey Dr. Art,
I have searched the blog but can't find anything on IBS/SIBO.

I have been dealing with some SIBO symtoms for about 2 years. Bloating, gas, borborygmi, gas and cramps. Bowel movements are fine though. Lactose and fructose make things worse.

I think it is likely that they are a result of using one antibiotic or another every day for about 2 years. Followed by a couple of months of Roaccutane. If I could go back in time I would gladly endure the acne.

Do you think it is possible that antibiotics caused the SIBO?

Am I wrong in assuming that you would be against using Rifaximin or another antibiotic to treat it?

Would your methods for removing biofilms be effective?

Thanks for your time,

Becks said...

Dear Dr. Ayers,

I had been on antibiotics for teenage acne for many months and my health has never been the same ever since. I am trying my best to recover by changing my diet, taking supplements and probiotics.

'There is no evidence that gut flora recovers after antibiotic treatment.'

Does this mean there is no hope for me? Any advice would be really helpful. Thank you.

Dr. Art Ayers said...

Usually there are small numbers of bacteria like those used in probiotics, e.g. lactobacillus, bifidus, in the small intestines. When the small intestines gets damaged by inflammatory bowel disease, then more of these bacteria that grow in the presence of low amounts of oxygen can overgrow the lower part of the small intestines, i.e. SIBO.

Two things that should help IBD and SIBO are peppermint oil and lactulose. The lactulose should favor the anaerobes in your lower gut after the peppermint oil helps with the IBD. As I recall, the peppermint oil works better than drug treatments for IBD.

In both cases, moving toward an anti-inflammatory diet would be helpful and improving general gut flora with the diet I recommend at the top of the blog should be helpful.

Let me know what works.

Dr. Art Ayers said...

I kind of paint with broad strokes to make a point. Antibiotics are used casually without thought of consequences. One of those consequences is the extinction of some species of gut flora. Since most adjustments to gut flora in response to diet are just increasing or decreasing bacterial species relative to each other, then the absence of critical species can have essentially permanent consequences.

The assumes that there is no intervention to specifically introduce and cultivate diversity in antibiotic-damaged flora. I think that gut flora can be altered by diet and by eating veggies that are not too clean or sterilized by cooking. Making an effort to eat lots of diverse fresh, local veggies and avoiding antibiotics should improve gut flora.

Gut flora can recover, but it takes work. For dramatic changes, you can also look into fecal transplants.

Let me know how your efforts work out.

Mike said...

Dr Ayers,

Another question: You've mentioned glutamine to stimulate healing; would conventional, OTC l-glutamine be appropriate for someone attempting to recover from chronic damage from gluten intolerance? And if so, in what oral dosages?

Dr. Art Ayers said...

I would suggest 1-2 grams of OTC glutamine with each meal to help heal damages intestines.

Shelly Fox said...

Hello. I was wondering about your thoughts on my situation. I am 36 years-old and have been on countless regimens of antibiotics since childhood for various reasons (ear aches, acne, respiratory infections etc) I have also had problems with constipation since childhood. Three years ago I was diagnosed with asthma and since then I have been on a downward spiral. I now have GERD and have trouble swallowing on a regular basis. I don't have to tell you my quality of life is lacking. A couple of years ago I had a fecal analysis done for problems with chronic constipation. Testing showed I wasn't digesting protein and there were not even traces of good bacteria in my gut. The chiropractor put me on Betaine HCl (stomach acid pills). My mother-in-law insists this is why I now have GERD.
As all medical professionals I have consulted have not been able to help, I was wondering if you think my problems could be related to the gut flora. I'm sure that starting a regimen of probiotics will be helpful after reading your article. But I cannot eat herbs and spices or even citric acid (Vitamin C) because of the GERD.
Is it possible to gain health again with no existing beneficial gut flora?


Shelly F.

Tanya said...

I might offer the suggestion to Roger to look into LDN low dose naltrexone to help heal the celiac damage. I don't have any references to offer but I know I've read about it several times in various alternative health newsletters I receive.

I am intrigued by the iron/copper/zinc idea. My last tests showed high iron sat, and I have had some succes with zinc supplements in the past. I have a cousin who almost died from a zinc deficiency (horrible rash to start with) who has to take lots of zinc daily, so zinc has often been in my mind. I may add it back in again.

Last time I tried fish oil I was burping it off and on all day. It seems to be a specific brand that bothers, but I never really got to a high enough dose to make a shift in my symptoms. I have been taking more and more vitamin C, both because of the antioxidant help and the connective tissue ...perhaps will help with the muscle aches etc.

Post and comments are all good food for thought as usual.


Bob said...

Dr. Ayers, Thanks for your helpful blog and for taking the time to answer people's questions. I think you are onto something that the entire medical world needs to explore in more detail.

You mention the following for rebuilding gut flora: probiotics, lactulose, pectin and inulin. What would be a sample program and dosing of these on a day to day basis and what is the best way to take them? What type of Pectin should I use (powdered canning Pectin, apple pectin pills, other)?

Unfortunately, I am currently on a regimen of Cipro to clear an overgrowth of Entrobacter Colace in my gut (found through stool test). I have zero Lactobacillus spp. and zero Bifdobacterium spp.. I also have elevated Lactoferrin level in my stool, Celiac disease, a number of food allergies and pain/aching in my gut a lot of the time. I want to rebuild as best that I can after I clear the bad (and a lot of good) bacteria out.

Anyhow, any information you could provide on a suggested routine/procedure for incorporating probiotics, lactulose, pectin and inulin would be helpful.

Thank you!

Deluth Stool said...

There is a clinic in Deluth, MN that is performing stool transplants, mostly for C. Diff patients. I looked into this because my wife had multiple bouts with C. Diff after being hospitalized for a serious Staph infection.

We never ended up going through with the stool transplant, but we DID use heavy probiotics immediately after she stopped her antibiotice regimen. The antibiotics (Vancomycin) helped with the C. Diff, but probiotics have kept it away for good.

Dr. Art Ayers said...

GERD is caused by acid from the stomach passing back up into the esophagus. About half of people with GERD also have infection of the stomach with Helicobacter pylori. Hp is the cause of ulcers and stomach cancer. It is interesting that Hp also lowers stomach acid production.

Closure of the valve between the stomach and esophagus is triggered by build up of stomach acid. It makes sense that Hp lowering of stomach acid leaves the stomach full, but without sufficient stomach acidity to close the valve properly.

Eating large meals and obesity contribute to GERD, because the large meals increase the time the stomach is distended without valve-closing acidity and extra fat puts pressure on stomach contents.

Basic treatments for GERD are elevating the head and weight reduction. Changes in diet don't make much difference. This says that a major problem is that people with GERD go to bed with a full stomach and stomach acid leaks by gravity and belly pressure back up into the esophagus.

All of the drugs that are used to treat GERD don't make a lot of sense, because they focus on stomach acid production, which isn't the problem. The only benefit is making the stomach more susceptible to Hp and thereby increasing the amount of infected stomach tissue that can no longer produce stomach acid. This will actually exacerbate GERD until the stomach is so compromised it can't raise acidity of the esophagus.

The cure for GERD seems to me to be:
1) Eat fewer meals.
2) Only eat early in the day with a long fast of 2-3 hours before bedtime. It's OK to be hungry, since you know that it is healing your esophagus.
3) Switch to low carb/high fat diet -- the Anti-inflammatory diet recommended at the top of this blog.
4) Check your serum vit.D. Supplement with vit.D3. Check to see that serum vit.D is over 80ng/ml.
5) Gradually increase your dietary saturated fats until most of your calories are from saturated fats. Then, start to increase fish oil until other symptoms of inflammation (aching joints, acne, depression) are relieved.
6) Increase physical exercise until walking 3 miles per day is possible.

Let me know if this helps.

Dr. Art Ayers said...

Hi Tanya.
Nice to hear from you.
I don't understand the fish oil burps, since it has only happened to me once in over five years of taking the capsules.

Thanks for your observations. As always, they are helpful.

Dr. Art Ayers said...

I am the wrong person to ask about specific dosages of supplements to help build gut flora. Basically, I think that there is too much variation from person to person and very high tolerances, so the amounts are not very important.

Readers: Please make recommendations for use of probiotics, lactulose (availability?), pectin & inulin (supplements, foods, recipes) and other prebiotics. Most of you are better at this than I am. Please post with what you have found to be useful.

Dr. Art Ayers said...

Deluth Stool,
Thanks for your info on fecal transplants. I have seen numerous reports that gut flora are being exchanged. That is a good beginning.

I have also seen a report of a DIY transplant procedure. Does anyone have a link to this step-by-step how to do it?

There are botox parties and other places where people readily exchange bodily fluids in very unhealthy ways, so why not share some healthy gut flora?

dextery said...

I certainly do not have any of the problems that some of your posters have and I do not want any of the problems with my gut flora.

But I have been reading about GI track problems and how to heal. And Lord knows, I have abused my GI track in the past years.

After reading Cooling Inflamation and reading Stephan's

I have been eating fresh burdock root along some dried burdock root with chickory root. I do add to this dry mix a teaspoon of canning pectin. Plus jicama I eat each day with some lemon juice and a little iodized salt. Delicious.

Still looking for jerusalem artichokes. Regular artichokes are fine also.

Each of these will ferment in the gut and will foster good GI track flora.

The dried burdock root and chickory are avail from

I purchased the fresh burdock root from my local speciality store. Just chew and swollow fresh.

I can say I feel somewhat better with this regime...but it may be just a placebo. It certainly isn't hurting anything.

The diseases of civilization that we are all having problems with all originate with food that travels through our gut. So it seems to me that eating anything
that our ancestors did not eat can bring about problems.

Get outside and walk around with shorts and no shirt or a sports bra for your D3 and lift heavy objects and get out and sprint-rest-sprint a few times.
And in the winter, do supplement with D3. I am always amazed when I see the map of colon cancer showing a concentration of patients primarily in the northeast. Think there might be a relationship between urban living in a cold area and low sunlight in the wintertime? And no d3 supplementation in the winter?

Heal your gut naturally as best you can and most of your problems will abate...those problems are only symptoms of unhealthy gut flora.

Dr Ayers seems to correct. Cooling inflammation is the key to an excellent quality of life.

Dr. Art Ayers said...

Thanks for the tips on building healthy gut flora.

Anonymous said...

Recently in the states I found sheeps milk yoghurt, which is my favorite anyhow, from It has L. bulgaricus, S. thermophilus, L. acidophilus and Bifidus, and boy were my guts happy. So far I’ve only found cows milk yoghurt with all but the L. bulgaricus, which hopefully shouldn’t make too much difference, and it seems to be fine.

My dietician recommended that I try to incorporate resistant starch, but a lot of forms are just too much for me right now (Or contain gluten which I don’t eat), having malabsorption issues with fructose/fructans, but I’m going to try reintroducing more slowly once I get things working a bit better. Whole buckwheat groats, which I believe are a good source of RS, don’t cause problems. Legumes are iffy, lentils, chick peas and black eyed peas make me very ill.

I was researching sources of pectin and found that citrus peels contain a lot, and oddly enough have been craving/adding lemon zest to a lot of things. Makes an amazing marinade, along with the juice, a bit of salt, tarragon and olive oil, for salmon. Also good in almond meal muffins.

As for triggers and acne, just a personal anecdote, diet is absolutely essential, I have hidradenitis suppurativa, sometimes called acne inverse, which is believed to be an auto-immune disorder and mine stays in remission as long as I stay low carb, but will flare up if I fall off the diet and is especially sensitive to fructose. A couple months ago I made the mistake of eating some mango sorbet, especially high in fructose, and after a very small bowl of it it was back. Back down now after accepting that I just can’t do that. I ate a small apple yesterday without problem, which makes me happy as fructose generally causes a pretty immediate (within two hours) reaction, chills, fatigue, joint pain.

Anonymous said...

Re: Lactulose Dosing

This is new territory for me. Studies show people taking 20 gm - 40 gm per day, divided into two doses.

So far, I've been unable to handle more than 10 gram/day, divided into two doses. Subjectively, I think it might be providing some benefit. The only way to test that is to stop. And I don't want to stop just yet.

By the way, the on-label use of lactulose is as a laxative. Do not let that concern you. My problem is I tend towards diarrhea. And that is what the lactulose appears to be helping me with.

Dr. Art Ayers said...

Rainarana and anon,
Thanks for your personal observations on improving gut flora.

Gluten Free Food Freak said...

Hi again Dr Ayers

Apologies for the time it has taken me to reply. I wanted to do your thoughtful post justice.

Before I dive in, does anyone reading this have a source of lactulose? I'd love to give it a go but can't find it here in the UK. If you do, I'd be most grateful if you could contact me through my website

Firstly, regarding starch. Interestingly, a lot of that starch comes from yam (true yam, not sweet potato) which I understand is a source of inulin?

"To solve the allergy problem, it seems to me that you need to avoid the celiac triggers, eliminate other sources of chronic inflammation and reconstitute the tolerance part of the immune system. The answer to all three is diet."

Thankfully, my coeliac is well controlled – I have had a totally gluten free kitchen for over 5 years, and a careful diet for 15. The rare occasions I get glutened is when eating out, and that is very rare. I eat no sugar (not even fructose) and all starches are taken with lots of sat fat. (Hmm... I just read this in your anti-inflammatory diet page:

"Saturated fats appear to be problematical primarily if chronic inflammation is established. Saturated fats are healthy in the absence of inflammation."

I have been 'paleo' for around 6 months, and although I feel much better (probably mostly due to steady energy supply with free-flowing FFA's), I have gut pain that is worse than I have ever had. I wonder if the sat fat is causing those problems. If so, I'm stuffed, I can't go back to low fat! ;)

Last time I checked, my 3:6 ratio was 1:4, and it should be even better now (all from fish, I don't take fish oil). Next to no veg oil (although I have a bit of a weakness for potato chips – a bag a day but working on that!)

I do regular muscle building exercise, and am building in more walking, plus sprinting.

And I was reading your stuff on vagus nerve stimulation – as I understand it, cold showers and relaxation can help use this pathway – am I right there? (I happen to be in the hypnosis business so the relaxation part holds some interest. Not that I don't love the idea of cold showers of course!;) )

Daily supplements are 6000iu Vit D, 1000mg Vit C, 5g glutamine, 2 tsp topical magnesium oil.

"The other components to try are glutamine, lactulose, pectin and inulin. Even starch may be helpful, and maybe that is why you already have more than I would normally recommend in your diet."

As mentioned above, the glutamine is already in there. I've now added more inulin with veggies and will get some pectin (I'd rather do that and avoid the fructose in apples and potential yeasts on the skin, which my system strongly disagrees with.)

"One of your problems is not tolerating enough different herbs and spices."

"Most people with dietary problems think in terms of triggers, but the problem is that the diet is too narrow already and bacteria needed to stimulate tolerance are absent."

That is an interesting angle, and it makes sense to me. I'm definitely guilty of narrowing the range to aim to stay well. I'll start working on pushing back the boundaries again while avoiding the inflammatories. I'm pretty good on herbs and now summer's here will consume lots in pestos and salads. The spices can be more problematic (I think perhaps due to mold/yeast in them?) but I will continue to test, especially the turmeric.

"I think that lactulose is under exploited to enhance gut flora development. It would be good to give it a try."

Again, if anyone knows of a source in the UK, or would be willing to send me some from overseas, I'd love to give it a go. From a gut bacterial profile I had done, I've got a good range of bacteria, they're just not in the right proportions.

Off for a cold shower ;-)

Thanks again for your generous help Dr Ayers,


dextery said...

GlutenFreeFreak, This is a wholesale lactulose company and they say that they do package small amounts in retail sizes but they do not name the private label. Perhaps an email to them might reveal the private label.
They have a lactulose syrup in retail packages.

And here is another:

Lactulose appears to be a stool use with caution.

Anonymous said...

Hey Roger, a quick bit of googling brought up this link: No idea about the company but their site looks legit.

As for pectin, citrus peels have a really high amount and I've been adding lemon zest to everything I can think of. It's particularly nice in yoghurt.

I do have problems with inflammation but the fats don't seems to be bothering me. It's more the starches and sugars when I get into them. Turmeric works well for me and is especially good if you're prone to acne outbreaks. Some people either make a poultice or salve out of it and apply directly, although I've not tried it.

I too reduced a lot of the variety in my diet due to malabsorption but am adding things back in. I just bought herbs and some greens for the garden this weekend and will be buying more this week. I like to add fresh basils, thymes, lemon balm, oregano and tarragon to an assortment of leafy greens.

Dr. Art Ayers said...

Thanks everyone for providing lactulose info.

I just wanted to add my observation on lemon products to your zest.

A bottle of lemon all purpose cleaner spilled unobserved on the corner of our cloth washer. The lemonene (the terpene that provides the lemon odor) in the all natural cleaner stripped the enamel paint finish off of the metal surface. It may be natural, but it is powerful stuff.

You might go easy on the zest. I think that most of the pectin is in the pulp under the oily, anti-microbial zest.

Thanks for your comments.

Dr. Art Ayers said...

I think that your gut will continue to feel better as you cultivate gut flora that can grow on the new parts of your diet.

In order to absorb fats, you have to produce bile salts that are also derived from prior fat in your diet. The problem is that you aren't absorbing fats very well, because your small intestines are still probably damaged from celiac. I think that the result will be potential discomfort in your lower bowel, until your new gut flora are established.

The glutamine can also sometimes be a problem instead of a cure.

I am still skeptical about your response to fungi. I can't imagine that there are enough on an apple to cause a reaction. I think that your response is to the pectin, because you still don't have any gut flora established in your colon.

I think that it will take time and presistence to get your gut flora back. Each new food addition will be upsetting. Perhaps the approach would be to use less each time until the symptoms are minimal and then build back up.

I hope that your symptoms gradually decline in severity. Let me know how it goes.

Gluten Free Food Freak said...

Thanks for the lactulose sources folks - heck knows why I couldn't find those! Anyway, I've got some on order now.

If anyone has any experience using lactulose, I'd be glad to hear of any suggestions for use.

Dr Ayers, thanks again for your thoughtful help. I'm persuaded by your suggestions about widening the diet and will persevere. Yeast/fungi/mold are the only things that give me a classic allergic reaction - that is, hives on the hand plus gut pain.

So I'll avoid those and attempt to get as much as I can in the way of veggies - home grown ones too judging by the thriving seedlings in the polytunnel.

Now one thing I haven't been able to tolerate for a while is alcohol. So I'm off to persevere with that. (Only kidding ;-)

Dr. Art Ayers said...

When you mention that you can't tolerate alcohol, do you mean that you respond to it with facial flushing, or do you mean that you would rather not indulge?

If alcohol causes some of the same symptoms, then you may be stirring up H. pylori in the stomach. I suggest that, because dietary alcohol can be used to enhance antibiotic treatment to eradicate H. pylori.

Just a thought.

Vicki said...

Hi Dr. Art,
Just found your blog and have been reading many of the posts. I have major digestive issues and have been diagnosed as fructose and lactose malabsorbtion. I am told to avoid apples and inulin. Most of my pain is up high in the abdomen particularly on the left side. I have been feeling better on low fructose/fructan diet but still having some really bad days. I will follow your suggestions for the diet. Will try yoghurt and daily sunshine exposure. Any other suggestions?
Thanks, Vicki

Dr. Art Ayers said...

The major digestive issues is a bit vague. I would assume that you are antibiotic damaged and constipated. That means your colon is lacking bacteria.

I don't know what fructose and lactose malabsorbtion is, but I presume that it means that your gut flora can digest those sugars. Unless you also have gluten intolerance, I think you probably just have an over simplified gut flora. You have seen the suggestions. I would recommend avoiding sugar and dairy for a while and increasing the leafy veggies and moving toward the low carb, anti-inflammatory diet as suggested. Then try some apple and leeks to gradually build up your lower gut flora. After you get some normal bowel movements, you should be able to start some dairy and get rid of the lactose intolerance.

Let me know how it works out.

Vicki said...

Thanks Dr Art. I will let you know how I go.

Martin E said...

Dr Ayers,

I have an auto-immune disease called Hashimoto with TPO antibodies.

I have been eating an anti-inflammatory diet for over a year now in order to cure my thyroid disorder, but I seem to get no results. In fact, my antibodies keep rising all the time, despite my efforts.

My diet is low in carbohydrates and free from both grains and milk products. Since I ruled them out I have been experiencing joint pain to a lesser degree although it hasn´t disappeared. I have a chronically sore throat and I am always dry in my mouth.

I have done som testing against IgE antibodies, but I don't have any. Which is what I expected since I don't get that kind of quick responses that IgE antibodies have.

I have however heard of slower allergic reactions involving IgG antibodies. In your opinion, would it meaningful to do such a test, and if I do, are the result reliable?

Now back to diet. If I have some kind of allergic reaction with IgG antibodies, I suppose I should avoid the food that I´m allergic to in order to heal my gut and body? I think I know the answer, but I had to ask.

Martin E

Dr. Art Ayers said...

Hashimoto's thyroiditis is caused by either celiac or a viral infection (I wrote a post on it.) Until you get the immune attack on your thyroid under control and regain normal thyroid function, you will have symptoms of thyroid hormone deficiency.

To stop the attack on your thyroid, you need to regain normal immune tolerance. From my perspective, that means to regain normal gut flora and stop your ongoing celiac. You must eliminate grain very systematically (as you are doing) and then focus on gut health. You can read the other posts. There are a lot of suggestions.

Make sure that your anti-inflammatory diet includes:
1) checking your serum vit.D and adjusting to 70ng/ml
2) eliminate veg. oils, use only olive oil/butter; supplement with fish oil
3) low carb/most calories from saturated fat; eat meat/fish/eggs/dairy/veggies

Help your gut and gut flora by supplementing your diet with:
glutamine, probiotics/live yogurt, lactulose, pectin, inulin

You should have normal bowel movement as a goal and avoid antibiotics.

The antibody info should just confirm the diagnosis. I can't make medical suggestions, so I just comment on the diet choices that should help.

Good luck and stop back with questions or comments on your progress.

Martin E said...

Thank you for your quick response.

A little further information on my diet. Except for a beer on christmas I havent eaten any grains since july. I have eliminated all veg. oils. I use lard and other animal fats. And I eat meat/fish/eggs/veggies only.

Are you sure about the viral/celiac connection? I have been tested twice for IgE gluten antibodies with negative result twice. The thing is that I got in contact with a woman throgh the internet who had the same diagnosis that I have. She got rid of her TPO antibodies by eliminating all food she has allergic reactions to, i.e. IgG antibodies.

I'll however try the things you suggest. Can you give som good sources of glutamin, lactulose, inulin and pectin?

Martin E

Anonymous said...

Sorry if this has been asked already, I don't really feel like digging through all those comments. If it has been posted, a quick referral to the specific comment would totally suffice:

My question is, are those bacteria that live on the pants really only on I'm askign this because I am washing most of my vegetables with water and soap a)because most of them aren't organic and b)even if they were there still would be some toxins and pollutants on this. (Dr. Eades once blogged about that, but that does not really matter now anyways) But I never thought about the bacteria. Most or even all of them would get washed/soaped away, wouldn't they? Or are they also living deeper within the plants?

Gluten Free Food Freak said...

HI Dr Ayers

When I say I can't tolerate alcohol, I mean that I just feel horrendous the next day (yes, yes I know it does that to everyone ;-)

I mean that one dram of whisky or a gin and tonic will leave me feeling like I've had an all night session the next day. So I have abstained for a couple of years now.

While I'm here, I should update you that (ahem) my stools have greatly improved in the time since my first post here when I started getting lots more salad and veggies. I'm not sure whether this is due to the extra fibre, or a bacterial boost, but the result is a good one.

My gut pain is greatly reduced, so maybe we're onto something here :-)



crapartist said...

Joseph Pizzorno, ND (et al;) writes (on controlling rosacea)

Go Easy on Meat. Limit your consumption of meat and poultry to one serving a week...
All animal products contain an acid that your body converts to inflammation-promoting substances.

What do you make of this Dr. Ayers?

Dr. Art Ayers said...

You can expect your Ig levels for particular antigens to drop if you do not encounter the antigens. If you remove gluten from your diet, then your Ig for gluten will drop. Avoiding the triggering antigen is the standard approach for allergies or autoimmunity, but it doesn't provide anything but relief from symptoms and doesn't address the causes.

The active link between your current Hashimoto's and the celiac cause could have been years ago. It starts with antibodies against antigens shared between the gut and thyroid and then the attack on the thyroid spreads antibody production to other thyroid-specific autoantigens.

It's wise to eliminate foods that are causing allergic reactions while you try to restore your gut flora and regain some immunological tolerance. Food allergies are very common with celiac.

Keep me posted.

Dr. Art Ayers said...

Your sensitivity to alcohol is an important symptom and indicates another damaged part of your physiology. Were you ever sensitive to fish oil?

I am glad you are feeling better.

Dr. Art Ayers said...

Sorry, I don't understand the low meat suggestions and I don't know what acid is involved.

Dr. Art Ayers said...

I think that it is more important to get the essential parts of the diet right before fine tuning the minor parts. That means to me getting healthy ratios of fat, carbs and proteins; greatly reducing omega-6 oils; increasing saturated fats and omega-3 oils; and correcting vit.D deficiencies; before worrying about toxic contaminants on my veggies. To me, it is more important to get my immune system functioning through a healthy gut flora, than to worry about pesticides. Current studies show that eating organic vs. typical produce has no detectable impact on health. Changing to the diet I recommend has a huge impact on health.

If you already have a diverse gut flora, then you can just feed it lots of different veggies and all is good. If your health is currently compromised by a simplified gut flora, then you have to find a source for some new bacteria.

I hope this helps.

Anonymous said...

Interesting about the alcohol intolerance, as for years one drink would make me feel like I was hit by a truck. This past winter, after being off of gluten for a few months, I was actually able to have a few drinks and feel fine. Having to eat gluten for the biopsy screwed that up though, so I think I'll wait before giving it another go.

Anonymous said...

Dr Ayers (is it ok to say Art?),
Alright, this has been helpful already, thanks. However two questions still remain:

To me, it is more important to get my immune system functioning through a healthy gut flora, than to worry about pesticides
Does that also mean that the benefits of not washing veggies (the bacteria) outweigh the downside of ingesting small amounts of pesticides?

...then you have to find a source for some new bacteria
Additional to probiotic foods, this does also include raw vegetables/fruits, doesn't it?

Dr. Art Ayers said...

Gut flora is a new subject to medicine and so little research has been done to learn how to increase the complexity of gut flora.

Probiotics are OK as a source for a small minority of the gut flora. These bacteria also reside in the ileum of the small intestines, where most of the immunological action is. So probiotics can be powerful, even though they may not remain in the gut.

I can't tell people to not wash their veggies, because many people have such dysfunctional immune systems that they will have problems with every new bacterium they experience. Because of these immune system defects, these people will also be sensitive to a variety of minor compounds in their environment. So I would tell these people to wash everything until they have restored their immune system with a proper diet.

Where did they get their new gut bacteria? If they were in the hospital, they would have picked up antibiotic resistant hospital strains from the hospital staff. If they were at home in a healthy community, they would have picked up healthy gut bacteria from the people they encountered and from pets and garden vegetables. Sedentary people will end up with different bacteria than physically active people, so immobile people in a hospital (especially babies -- that's one of the reasons that homebirths are paradoxically safer) are in double jeopardy.

I wash veggies from the supermarket, but just rinse veggies from the garden or farmers market. I make sure to wash after talking to physicians, but don't worry about farm animals or pets.

It would be very interesting to analyze the gut flora from hospital staff compared to organic farmers.

Good luck.

Alisa said...

Dr. Ayers, my husband is undergoing high -antibiotic treatment for Lyme Disease. Though he is taking ample probiotics, the gut inflammation is hard to mitigate. In this case, we haven't been able to find an alternative to the antibiotic use. Can you recommend how to best keep his gut healthy during this treatment?

Dr. Art Ayers said...

Lyme disease is certainly very complex and the treatment is very problematical. Several species of bacteria are probably involved and they can exist is tissues in forms that make them very refractory to antibiotics.

As you acknowledge, even the successful use of antibiotics releases inflammatory bacterial wall components from body tissues and from the gut.

It is a serious problem to develop a functioning gut flora while using antibiotics, but you don't have much choice but to try, because your husband needs to re-establish his immune system.

I don't know of any other treatments, but to use the probiotics with prebiotics (pectin and inulin) to try to keep the bacteria in the ileum functional. Lactulose and lactoferrin may also be considered. The antibiotics will wipe out his gut flora and it will be very difficult for him to re-establish it. You might consider a fecal transplant, as is used for Clostridium treatment, after the antibiotics.

There are many support groups for Lyme patients. Hopefully this will not convert to chronic lyme.

Let me know how you are doing.

Gluten Free Food Freak said...

Dr Ayers, that's interesting to hear. I stopped taking fish oil some time back in favour of eating lots of fish, so I'm not sure about a sensitivity there. (Oily fish agrees with me very well).

What could be the problem do you think?



torunafter said...

Here's a protocol from 2005 for doing a fecal transplant at home, from Thomas Barody at the Center for Digestive Diseases.



The human bowel contains a complex population of bacteria containing several hundred different species. The colon itself is densely populated with around 500 species and more than 30,000 subspecies of various normal bacteria. These organisms and the chemicals they produce affect the body and these effects can have both positive and negative impacts on health. The human flora protects us from pathogenic or “bad” bacteria, however if a bad bacterium does implant itself into the population of normal healthy “good” bacteria, it can have a debilitating and sometimes toxic affect on our health. Due to the nature of the bacteria which are able to produce spores, it is difficult to remove the infection which can remain for many years, even a lifetime.

The use of healthy human flora appears to be the most complete probiotic treatment available today. It acts as a broad-spectrum antibiotic capable of eradicating “bad” bacteria and spores, and supplies the “good” bacteria for recolonization.

This therapy involves the infusion of healthy human donor faeces via enema into the bowel, which is prepared prior to the procedure. This infusion process is repeated for at least five days, depending on the severity of the condition.

The treatment is expected to improve symptoms of Irritable Bowel Syndrome and potentially cure the cause of the problem. This however is not guaranteed. The treatment has demonstrated success in treating some of the most difficult cases of Irritable Bowel Syndrome.


You will need to go on a LOW FIBRE DIET at least TWO WEEKS before beginning the antibiotics and during the course of the antibiotics. The following list gives you an idea of low fibre foods:

Refined cereals – white bread, pasta, rice cakes and pastries made from white flour
Milk (all forms)
Butter, margarine, oils
Chicken and fish
Egg dishes
Jellies, custards, mousses
Fruit and vegetables (cut down the amount you eat and discard the peel) – the following are relatively low in fibre:

Apples Pears Melon Peaches Cherries Plums Grapes
Pumpkin Zucchini Marrow Lettuce Capsicum Cucumber Potato

Foods to AVOID:

Processed meats: sausages, ham, salami
Citrus Fruits
Nuts and seeds
Berries and dried fruit

Your diet must change to a HIGH FIBRE DIET after your first probiotic infusion and we recommend you maintain this high fibre diet to enable the new flora to be strong enough to survive and implant. You are able to eat the following:

Anything “wholemeal” – bread, pasta, brown rice, pulses (lentils, beans, chickpeas), muesli, fibre enriched cereals.
All fresh fruit and vegetables, including juices
All meat, fish and chicken

AVOID the following foods:

Oysters, shellfish, prawns
Processed meats


Equipment to be purchased through the Probiotic Therapy Research Centre

This equipment is essential for the infusion. Price on request.

Enema bags
Rectal tips

Equipment to be purchased locally

Bottles or bags of normal saline.
Latex gloves
Psyllium husks
Imodium tablets (Loperamide)

You will also need the following

Somewhere to hang the enema bag from, ie nail in the wall.
Stool collection device (disposable ‘takeaway’ container or a potty!)


You need to purchase medication for a COLONIC LAVAGE. – Usually this is available from a chemist without prescription. This is the same bowel prep you would use if you were undergoing a colonoscopy.

torunafter said...




You will need to take one or two of the following antibiotics as per the schedule below for a minimum of 10 day. You will be advised accordingly.

Morning 1 capsule (150mg) 2 capsules (250mg) 1 tablet (400mg)
Night 1 capsule (150mg) 2 capsules (250mg) 1 tablet (400mg)

Your last dose of antibiotics will be taken
the night before your bowel washout

You should still be maintaining your low fibre diet at this point. Please refer to diet requirements section.

Bowel wash out. ( day before the first probiotic infusion )


On waking in the morning:

DO NOT EAT any solid foods.

DRINK CLEAR FLUIDS ONLY – eg. clear soups, clear fruit juices, tea, coffee , Bonox, soft drinks.

Follow the instructions on the back of the packet of the colonic prep starting at 10 am approximately (rather than the time mentioned on the packet).

Drink the colonic prep throughout the day as per instructions on packet.

IMPORTANT – please ensure you maintain your fluid intake to prevent dehydration..

Be prepared to visit the toilet regularly throughout the day


On Rising

In the morning, on rising, take 2 IMODIUM tablets. You only take these on the first morning of the infusion.


You will need to start your high fibre diet today as per instructions. You may have a light breakfast before commencing your daily infusions..

Infusion procedure

Collect donor stool in appropriate container. Place immediately into the blender with half teaspoon of the psyllium husks and between 100 – 400mls of normal saline (the volume of saline needed to make mixture ‘pourable’).

This should be blended for approximately 15 seconds.

Ensure the white ball in the bag is removed and the white clip is closed on the tubing. Pour this mixture into the enema bag via the red cap. Eliminate as much air as possible and close the red cap.

Once preparation is complete, recipient will lie on their LEFT side in the foetal position with lower half of body elevated.

Lubricate the rectal tip and gently insert the tip into the anus until you reach halfway of the blue tip.. Slowly unclamp the enema bag after hanging the bag up which will to commence the infusion. Allow 5-10 minutes for infusion.

Once infusion has been completed, clamp the tubing and gently remove the rectal tip (still attached to the tubing and bag). Discard the enema bag and tip and ‘double bag’ for disposal.

You then remain on your left side, massaging your abdomen for approximately 10 mins. Repeat this massage, lying on back, stomach and completing on your right side.

This procedure is repeated each day for 5 - 10 days approximately.

If you difficulty retaining the enema you can take Imodium or codeine as required.


Blood work and stool testing for patients and donors

A) HEP A > IgG, IgM







Donors are selected by the recipient on the following criteria:

The potential donor must have a healthy bowel motion every day.
No history of bowel problems (eg no constipation, diarrhoea, colitis etc)
Is not on any medications that may interfere with stool viability (eg antibiotics).

As a potential donor you will be fully screened to ensure that you are free from infection. This involves a blood sample and stool tests as per the enclosed protocol.

torunafter said...



The person receiving your stool (recipient) will be relying on the donor to pass a bowel motion every day. We highly recommend that you start the following changes at least one week prior to the commencement of the infusion. These changes include :

Avoiding foods at risk of contamination

Avoid shellfish, prawns, oysters and processed meats such as salami, ham and sausages.
Avoid all antibiotics.

You must commence a high fibre diet to improve the quality of your flora

All breads, cereals and grain should be wholemeal. This includes bread, pasta, rice and breakfast cereals.

Eat plenty of fresh vegetables (with the exception of corn).

Include beans and pulses in your diet (lentils, chickpeas, beans, hommos)

Eat at least two pieces of fruit per day

Drink at least 1 litre of water per day.



At breakfast have wholemeal toast, muesli or a high fibre cereal. Maybe include some yoghurt.


Salad sandwich with wholemeal bread and whatever filling you wish and a piece of fruit.
Pasta with vegies
Noodles with vegies


Pasta with meat, sauce and vegies
Meat, fish or chicken with two types of vegies or salad and potatoes.
Stir fried vegies (with or without meat) with noodles or brown rice.
Brown rice with beans or lentils.


As a donor it is vitally important that you understand the instructions mentioned. There are two major points:

You need to make sufficient dietary and lifestyle changes for the duration of the recipient’s treatment to ensure that you will pass a bowel motion every day.

If you experience any of the following, please withdraw from donating:

Cold / flu
Any antibiotic usage


This is the biggest concern of the donor. By following the dietary recommendations above ,you should have no problem passing a bowel motion every day.


If there are any questions please contact Sharyn Leis (SRN)

Probiotic Therapy Research Centre (PTRC) on 612 – 9712 7255
Centre for Digestive Diseases on 612 – 9713 4011


1. When did you last use antibiotics ?

2. Have you experienced ‘travellers diarrhoea’ ?

3. Do you or have you worked within a hospital, health care facility or child care facility ?

4. Please describe your stool quality ie is it soft, hard or runny ?

5. How frequently do you go to the toilet in a day ie once per day, twice per day or more, or once every two to three days ?

6. Do you currently have or have you recently experienced any type of abdominal discomfort ie pain / cramping or swelling / bloating ?

7. Do you currently suffer from excessive flatulence ( gas ) ?

8. Do you currently experience nausea or heartburn ?

9. Have you ever noticed blood in your stool ?

Tanya said...

Re: Grilling your meat...making it healthy...better yet don't cook it at all...(ICK! I know where my meat comes from --my back yard so to speak--but ICK! I can't even chew steak that is anything less than med-well without choking on it...)

Does give even more credence to using/consuming spices with your meals etc.

Alisa said...

Thanks Dr. Ayers,

Unfortunately, what he is treating is chronic Lyme. He actually thinks he contraced it in his early teens, and he is now in his late 30's. I wasn't even aware that he was dealing with joint pain (which apparently he had been for decades, but never said a word), and he didn't start working with his doctor until he noticed quite a bit of memory loss.

The treatment seems to be going very well, and he is following a protocol that involves antibiotics (his gut wasn't actually doing that badly until he started the IV antibiotics), supplements, etc. (our MD is also an alternative practitioner). but, as mentioned, his gut has been suffering, even with the probiotics. He isn't really a believer that diet will have a big difference (he doesn't eat fast food, and he eats better than average, but he is very low in the produce department), so this is something I have stopped pushing. It turns into an argument and more stress for him (not good either).

I guess we will just hope for the best!

Dr. Art Ayers said...

Thanks for the DIY fecal transplant protocol. There are a lot of precautions needed to take this approach safely, but it seems less intrusive than many other medical procedures.

Dr. Art Ayers said...

There is a fair amount of focus on the production of carcinogens and advanced glycation endproducts(AGEs) by cooking at hight temp., e.g. grilling. I don't think that browning carbs, caramelization, is as big a deal as chemically reacting protein amino groups with carbs, glycation. Glycations may contribute to production of the carcinogen acrylamide.

AGEs are highly inflammatory and bind to a special AGE receptor. AGEs are also produced when the blood sugar rises and is responsible for the symptoms of diabetes. High blood sugar is detected by measuring the AGE produced when glucose glycates hemoglobin, HbA1c.

Blocking this process may be the point of the transglutaminase that is involved in processing of gluten/gliadin in celiac.

Frucose is particularly nasty, because it doesn't contribute to blood sugar, but it is very active in glycation. HFCS is not healthy for anyone, including diabetics.

Thanks for the meaty comments.

Dr. Art Ayers said...

Chronic Lyme is hard to treat. Let me know if you think I can be of any help.

Gluten Free Food Freak said...

I'm sure you've seen this Dr Ayers:

It would be nice to see the full abstract to see dosing and levels of response, but basically it seems like taking Bifidobacterium might be a particularly good thing for us inflammatory coeliacs.

Cristian said...

Dr. Ayers, any comment on the following news?

"It was previously thought that the inflammation in the blood vessels
arises when the T cells react to oxidised LDL particles located in the
atherosclerotic plaque. Now, however, the team at Karolinska
Institutet has found that the opposite is true, namely that the T
cells react to components in the normal LDL particles, and that they
no longer recognise LDL once it has been oxidised."

Dr. Art Ayers said...

That is a complex article, but the bottom line is astounding. I have always felt that the inflammation precedes the lipid deposition in atherosclerosis, so saying that inflammation is not caused by oxidized lipids, but rather just LDL at the site, isn't as surprising.

The absence of a role for oxidized LDL also explains why anti-oxidants don't prevent athersclerosis.

Remember that the LDL receptor uses heparan sulfates to bind to LDL.

I don't know enough about atherosclerosis, so I will continue to ponder the article.

Anonymous said...

Thanks for your time and dedication. Dr, I would like to know if you have seen Lactobacillus and Bifidobacterias recover after probiotic intake shown in a CDSA. Human Probiotic Infusion looks like the only way to recover the friendly flora lost after antibiotic therapies. Colonics and Enemas with fecal matter only reach the colon and I doubt the small bowel can be repopulated using this way. Using a nasogastric tube the infusion go straight to the stomach and can reach the small bowel. Since I don't have this type of facility at home, I am prepared to drink the mix by mouth. I will take the PPI to neutralize the stomach acid before to do it. Dr, I am sorry to say you this crude way, but I am tired of been sick and need to try anything. My case is an intestinal candidiasis after antibiotics which relapse everytime I stop the antifungals. I see no way to recover Lactobacilus colonies using probiotics, kefir, fermented food or any other way. How you said in one of your previous answer ...Probably, there is a simple way, but the medical field isn't looking for that. I see very simple for today technology to do fecal implant at hospitals and to return the health to many sufferers.

Dr. Art Ayers said...

The tolerance of your yeast infection to anti-fungal drugs suggests that it is present in the intestines in a biofilm. That would suggest that treatment with biofilm destabilizers (EDTA, PEG, enzymes) may make anti-fungal treatments more effective. Lactoferrin may also be useful.

I would say that it would be difficult to replace an existing yeast biofilm with probiotics. You might want to look as my article on biofilm stripping for ideas on disrupting the biofilms and then starting to reestablish your gut flora with pro- and pre-biotics (pectin, inulin).

I hope this is useful. Let me know what happens.

Dr. Art Ayers said...

Another point about candidiasis is that the yeast converts omega-3 fatty acids into resolvins that inhibit the action of neutrophils needed to kill the yeast. This suggests that it may be wise to modify the anti-inflammatory diet to just high saturated fat, low carbs and plenty of herbs,spices and veggies. I think that alcohol also stimulates yeast biofilm production. I don't think that vit.D3 supplements make a difference in yeast infections.

This also suggests that some people who exhibit inflammation in response to fish oil may be observing symptoms of stimulated yeast infections.

Anonymous said...

Dr, I will research your article about biofilm. Dr, IMO, the biggest problem is most oral antifungals are fungistatic, so they never kill the fungus at all. This is happening with the azole drugs, even more, when the therapy is short. It looks like a drug combination can become fungicidal in short therapies. Dr, I understand all antifungals are fungicidal in vitro but unfortunately we can not take high doses of them to get this effect in vivo. So, my plan is to combine them to get fungicidal action. It looks like Terbinafine plus any triazole become fungicidal to many candida strains. I will also take a polyene (Nystatin Powder) to get direct effect in the gut. My biggest concern is I have seen many people who their Comprehensive Digestive Stool Analyses don't show lactobacillus and bifidobactiriums growth even after heavy probiotic intake. This make me think probiotics only implant the gut temporary and when you stop the intake, they dissapear from feces. Probably, science need better technology to see if they really implant or not. Since the intestine can not be seen totally, recovery from feces and top small bowel biosies are the only way to verify if new probiotic colonies are implanted. I still think Human Probiotic infusion or implant is probably the best way to recover the benefical flora.
Thanks for your quick answer.

Mrs. Ed said...

This is interesting because I have had severe GI reactions to several antibiotics. I was put on "preventative" anitbiotics as a child because I couldn't seem to keep strep throat away. There are several I can no longer take. Tetracycline bloats me up so severely that I look pregnant, sulpha drugs make me vomit so severly I had to go to the emergency room and was only able to digest fluids for 3 weeks after(lost 21 pounds and weighted 79 lbs afterwards), etc, you get the picture. I have never heard anyone address this before though.

Dr. Art Ayers said...

Mrs. Ed,
I think that routine use of antibiotics produces a gut flora and gut which is unhealthy. Unfortunately, I think that it is also probably contagious. That means that those around people with antibiotic gut will probably pick up the abnormal gut flora and their gut and immune system will also be modified. This will give the appearance of familial or genetic predisposition, but is just bad gut flora. I think that this is the reason that ASD kids can see symptom improvement after replacement of their gut flora, but when they return to their home flora they will relapse.

It would seem reasonable to me for the family members of kids with ASD to be treated first to repair their gut flora, before the kids are treated. It may even be important for health care workers who treat families with ASD to have their gut flora routinely monitored. I would predict that a test of the complete gut flora of these health care workers would be indicative of contamination with bacterial species dominating in ASD families.

Mrs. Ed, I have looked over your site and see what I am doing as closely related. If you can find a way that I might be helpful, just let me know.

Mrs. Ed said...

Dr. Ayers,
Yes, we are on the same page about diet and gi flora. I have really found your site to be a treasure trove and will probably be spending my lunch breaks reading your post for awhile. However, I have no science background. I just happened upon this by chance and had no one to ask so I would dig in medical journals to see how this could actually work and then look words like "Paneth Cell" etc up on Wikepedia to see what they mean. I'm just an average she-Joe that stumbled upon some life changing information.

Yogurt commercials aside, the average person will never get exposed to enough of this info to make a difference in their lives. They're not going to hear it from their doctor, collegues and will hear about the oppsite of what they need to know from the media. The autism community is told this is Voodoo and even describes it as "Cult" thinking. We're not genetically screwed, more like informationally screwed. If any drug could work the miracle that diet, good tummy bugs and a few supplements have done you would here about it on every street corner. I can't commend you enough for the information you have put forth here. I am also compelled to do so but I'm better at recipes than any other advice.

I have found this subject fascinating and have tons of questions to try to understand it better. So beware, I will probably be asking alot.

Thanks again for the great info!!

Dr. Art Ayers said...

Mrs. Ed,
Thanks for the encouragement.

Go ahead and keep asking questions until I tell you to stop. Persist until I make sense. Unfortunately, I am a dyed-in-the-wool professor, so I have the occupational disability of stating the points and expecting others (until recently primarily students) to fill in the blanks. That used to be the way that recipes were provided, i.e. just a list of ingredients without amounts. It is not as popular today.

Ask away.

judiblue said...

Hello Dr Ayers

I get raw milk weekly and make buttermilk, yogurt, butter, sour cream, farmer cheese...Everything being cultured to some degree.

I read something Ray Peat said about stress causing lactic acid build up (not just physical stess), and wondered if i was doing harm by consuming mostly cultured dairy rather than just straight milk.
My understanding is that lactic acid is the by product of milk digestion anyway.

He said something to the effect that since physical/emotional stress causes lactic acid build up that it was not in my best interest to be consuming milk in this manner.
In other words, why add fuel to the fire.

Here's another bit; Proponents of the Specific Carb Diet state that bifidus can over colonize and it should not be consumed. Acidophilus and Strep(?) are the best.

What are your thoughts?


Dr. Art Ayers said...

I don't think that lactic acid is a big deal. Every time I do squats, I get a burn in my quads that I associate with the buildup of lactic acid as my inadequately trained muscles go anaerobic and start to produce lactic acid. My liver is quite capable of using the lactic acid, just as it uses the short chain fatty acids from my gut flora.

I don't think that it makes sense to avoid milk to avoid lactic acid.

I think that people following the specific carbohydrate diet are trying to reconstruct damaged gut flora and may be cautious of overgrowth of bacteria in the small intestines. This may be an issue for some people with damaged GI tracts.

I think that a more balanced gut flora can be produced under overgrowth conditions by treatment with lactulose. Soluble fiber, pectin/inulin may also be helpful. It would make sense to use diverse sources of probiotics.

Thanks for your questions/comments.

Anonymous said...

New reader here, and enjoying the blog very much.

I've since lost the exact quote, but I seem to remember Dr. Art mentioning that antibiotics used for acne are not working primarily against the bacteria in the face, but the antibiotics are altering the gut flora, which....then suppresses the immune system?

If so, is this also true in the use of antibiotics for arthritis & scleroderma, and Lyme?

If anyone has time, I'd appreciate some clarification. I don't think I get it, or might be misunderstanding.

Dr. Art Ayers said...

The use of antibiotics to do anything but kill bacteria at the site of an infection is controversial. At the same time it is assumed that antibiotics do only minimal damage to gut flora that is readily reversible by probiotics. I think that this perspective is simply wrong.

I think that the body has low levels of micro-organisms residing in it and many of the various forms are not readily cultured, i.e. they are cryptic. These bacteria are protected from circulating antibiotics, because of their intimate relationship with host cells, perhaps even within host cells or in biofilms. Thus, simple antibiotic treatment may not kill the bacteria, even if the bacteria would be susceptible to the antibiotics in vitro.

At the same time, antibiotic treatment, even IV, has an impact on the 100+ species of bacteria in the gut that influences the GALT (gut associated lymphatic tissue.) I would contend that antibiotics always impact the immune system, because they impact the gut flora.

Thus, any type of antibiotic treatment, e.g. for acne, rosacea, arthritis, etc. impact the immune system. I also contend that in most cases a decrease in disease symptoms is not due to killing of cryptic bacteria at the site of symptoms, but rather an attack on the immune system. The crippled immune system can no longer produce the symptoms and an apparent remission is observed.

To get around these false remissions that may hide progress of the disease, the cryptic bacteria must be attacked with a protocol that exposes the bacteria and kills them and then the gut flora is comprehensively reconstituteded. I don't know of any medical procedures that currently satisfy these requirements, but some of the procedures are at least apparently attacking the cryptic bacteria.

Thanks for your questions.

Connie Hopper said...

My daughter has 6 ulcers. She was prescribed prev pac. 2 weeks at 3000 mg per day. then 6 weeks taking prevacid before each meal. She is 37. She is sicker now than she was before. Her quality of life is suffering. She went from a vibrant active person to chronic fatigue and stomach pain. She is nauseated a lot. Seems to cycle. Her stomach feels weird to her. We have both been researching damage caused by antibiotics. Should she try to eat organic? Should she try to introduce probiotics into her system? What can be done? The doc advised another round of antibiotics. She says no for now.

Dr. Art Ayers said...

As far as I know, stomach ulcers are caused by either Helicobacter pylori or NSAIDS. The Hp is usually treated with antibiotics and the NSAID damage is harder to treat.

The healthcare industry makes billions of dollars selling acid reducing drugs to people with Hp infections or acid reflux, even though reducing acid aggravates those conditions -- Hp grows better in lower acid and acid reflux is caused by low stomach acid that is insufficient to close the stomach valve.

Elimination of Hp infections is, I think, becoming controversial. It seems that the problem is not the Hp by itself, which can either cause ulcers and cancer, or stimulate the immune system to reduce autoimmune diseases and allergies. The problem may be producing a gut flora that properly controls the action of the Hp.

In your daughters case, the antibiotics may not have killed the Hp, or Hp was not the source of the ulcers. In either case, it would seem best to rebuild her gut flora and support a healthy gut. That to me means using the anti-inflammatory diet I outline on this blog, supplementing with glutamine, using probiotics and developing the rest of the gut flora with pectin and inulin. The goal is to eliminate all food intolerances with a diverse gut flora supported by diverse veggies.

Eating organic meat and veggies has been found in clinical studies to provide very minimal impact on health. The major contributors to health are getting most calories from saturated fats rather than starch (reduce or eliminate grains to avoid gluten intolerance), eliminating vegetable oils and developing a diverse gut flora.

In your daughter's case, I would check for vit.D deficiency and inadequate saturated fat in her diet.

I hope that this is a start. Let me know how you do.

Anonymous said...

Hi Dr Art,
Thanks for all the great info. As a pharmD, I appreciate your depth of insight and ability to see past the main problem to the cause (which is really what we all care about). I was recently diagnosed with crohn's disease after years of diarrha and more recently weight loss. for close to a decade, I was on antibiotics for acne (into my early 20s) and now in my early 30s I find myself with crohn's--i'm sure this is no fluke. based on a capsule endoscopy, my small bowel is full of ulcers, but my colon looks pretty good. i'm wondering if you could direct me to a resource that might address a systematic approach to healing my gut. i've been moving things more in line with your suggestions, but wonder what you might suggest for a situation like this? Any type of raw fruit/veggies is hard for me to handle, so incorporating more into my diet has been tough. one thing i've been toying with is using a wide spectrum antibiotic (rifaximin) to essentially wipe the slate of my gut clean, followed with intesive probiotics thru diet and pills to reseed the gut. any thoughts on this approach? Thanks in advance.

Dr. Art Ayers said...

If you have damaged gut flora, due to antibiotic treatment, then you will also probably have some immune system dysfunction, since the proper function of the immune system is dependent on interactions with the gut flora in the gut near the appendix.

The healthy gut has about 150 different species of bacteria (people with Crohn's typically have only 100) and probiotics can supply a half dozen temporary gut residents. So trying to kill off the remaining bacteria and replace them with probiotics is probably not helpful.

Antibiotic use typically results in yeast replacing the lost bacterial species.

Loss of the gut immune function results in a tendency for autoimmune diseases, since the immune functions lost involve blocking immune attack on self or common bacteria.

Your inflammatory bowel disease would benefit from switching to the anti-inflammatory diet that I recommend and then starting to reconstruct your gut flora. Other issues would be serum vit.D, omega3 vs. 6 ratio, grain, yeast infection. Also consider pectin and inulin to build gut flora and lactulose to avoid overgrowth of the probiotics.

I would expect that you are constipated with bouts of diarrhea triggered by particular foods. This is not a dehydration cycle, but rather loss of the gut flora that hydrate stools. The lost bacteria normally use soluble fiber as a food source.

I hope that this is a start. Let me know about your progress.

Anonymous said...

there have been some small studies with n-acetylglucosamine in crohn's.

what effect would this have on shifting the atomosphere of the gut microbiota vs plain glucosamine sulfate?

Dr. Art Ayers said...

N-acetylglucosamine, NAG, is made from glucose by most human cells and also bacteria. It is a component of glycosylaminoglycans, GAGs, the major constituent of connective tissue matrices and also the bacterial cell wall. Eating meat should provide lots of NAG as the gut flora hydrolyze the connective polysaccharides.

I am surprised that NAG or glucosamine has any impact, but perhaps it acts on bacteria residing in the small intestines. I would expect that the response is just a matter of what gut flora are present.

I have also speculated that glucosamine may interact with the transaminase enzymes in the gut. Tissue transglutaminase is involved in celiac.

Cronh's is suspected to be linked to Klebsiella infection and Klebsiella trives on undigested starch.

I hope this answers some of your questions.

Unknown said...

Dr. Art. I posted to you about my daughter on June 16th, 2010. She is worse I think. Vomiting 8-10 times a day. Stomach very tender and hurts to move.
She is on her 5th day of a 7 day colon cleanse so the probiotics can be absorbed. She plans on seeing a doctor and getting a saliva test and a few others. I am trying to find a doctor who also practices natural medicine. I am feeling helpless. Is there a list of doctors? How do I find out which one is reputable?

Dr. Art Ayers said...

Sorry I have taken so long.

I am out of the loop for suggesting physicians. Maybe some readers could provide suggestions on how to find more holistic healers.

I am perplexed as to why your daughter would be doing a colon cleanse. It should have no impact on probiotics, that work higher up toward the end of the small intestines. I would not expect her to have any gut bacteria left after the antibiotic treatment. She needs probiotics and soluble fiber. I would also expect your physician to be recommending glutamine and perhaps lactulose (if overgrowth of the probiotics is suspected.)

The antibiotics would be expected to produce the symptoms of food intolerances until the gut flora is re-established.

Let me know what happens.

lightcan said...

Dear Dr. Ayers,

other things being equal and while following an anti-inflammatory diet with reasonable amounts of different vegetables, would it be possible to explain a relatively serious outbreak of acne (even cystic) because of taking lactulose (with galactose, lactose and fructose) and S. Boulardii with L. rhamnosus and L. acidophilus?

Dr. Art Ayers said...

Hi Lightcan,
I think that in serious cases of gut flora decline, e.g. by antibiotics, the gut flora needs a lot of help reestablishing. The process will be very slow unless adequate new bacterial diversity is provided. That means essentially what would be typically considered as poor food hygiene. Most people are too careful to avoid pathogens and throw out the baby (gut flora candidates) with the vegetable wash water.

The point here is that antibiotics are used to treat acne, by wiping out all of the gut bacteria that support immune system development in the gut. That eliminates both the aggressive immune cells that aggravate the skin and the regulatory cells that keep the aggressive cells in check. Recovery of normal immune function requires the return of both types. Unfortunately, the aggressive, Th17, cells typically recover first and the system is still sensitive to attacks until the Tregs recover.

I think that you are half recovered and your gut flora still has a ways to go. I think that you mentioned that you still have some problems with constipation and the lactulose is normally taken for problems with gut flora. The probiotics are just a start. You have another hundred species of bacteria to find homes for in your gut. Your response to lactulose, I would interpret as just a food intolerance, i.e. an indication that your gut flora diversity is not sufficient to digest the new oligosaccharide.

More local, dirty veggies, herbs and spices are needed. Taking up gardening would be a good idea. As you say, it takes a lot of persistence.

Keep me updated.

lightcan said...

Dear Dr. Ayers,

thank you for your reply. I get very disheartened by setbacks like this especially as I don't understand the cause. Yes, I do struggle with constipation, although while in Romania for 3 weeks I did well without any kind of laxatives. However, after coming back my haemorrhoids prolapsed and I decided to take lactulose (to allow them to shrink) as it is a prebiotic and an osmotic laxative. It is disgustingly sweet, I don't know if it is because of the added sugars or the lactulose itself is like that.
I suppose you know this already:,,10320-2-0,00.htm
I do eat unwashed organic root veg as you suggested and try to take different types of probiotics while consuming pectin and inulin.
After a week or so the acne has calmed down a bit but still have numerous inflamed areas.
I will continue taking Laxose for another 10 days. (another bottle)

restall999 said...

thank you for a very informative site, have not managed to review all the info, but will get there in the end. without the addigion of a search bar do you have any views on colonics? see like many my appendix was removed when younger and i sometimes wonder whether the hydro therapy could aid in removing or neutralising unwanted bacteria.

Jack said...

Hi Dr Ayers,

Been reading many articles on your blog but this is my first comment. Your in depth analytical work is incredible. Thank you so much for your diligence.

My wife was recently bit by some sort of bug (we assume it was a spider). It was on her shoulder and is spreading toward her armpit. Her bodily reaction has been rather mild, with no pain, no itching, but a curiously wiggly line of red irritation down to her armpit area. Her doc says it needs to be stopped before it goes systemic and into her lymph nodes or something.

So antibiotics to the rescue! She comes home and tells me this the same day that I had found your input on antibiotics.

Under most other circumstances, she would not so quickly take antibiotics, but due to this odd situation, she began taking them yesterday and is supposed to take 3 per day for 3 weeks.

Here's my question(s): Is there an alternative? Is antibiotics the right thing to take to combat a spreading bug bite reaction?

Again, thanks so much!!

Dr. Art Ayers said...

I think that "bug bites" are all potentially problematic. My first aid treatment is Vicks VapoRub applied liberally to the site of the bite. That should act as a penetrating, broad spectrum antimicrobial. It is also anti-inflammatory.

In your case, the infection seems to have progressed. I think that under those circumstances antibiotics would make sense. They will disrupt your wife's gut flora, but if she previously had a functional gut flora, it might bounce back. She could probably help out by continuing to eat a varied diet and using probiotics during and after the antibiotic treatment. The bacteria that she has in biofilms will be resistant to the antibiotics and may survive anyway.

Let me know how it progresses.

Jack said...

Dr Ayers,

Thanks so much for the reply. My wife and I both eat a diet based on whole, nutrient dense foods. I've been actively studying healthy eating lately, frequenting a host of sources including WAPF, Whole Health Source, and many others, including your blog here. We both take probiotics so it's nice to here that these things can play some sort of role even while taking antibiotics. Oh and she told me that's it's actually for 10 days, not 3 weeks like I had put. So I'm sure that she will handle it just fine then.

Thanks for the reassurance.

lightcan said...

Hello Dr. Ayers,
I see you mention in your replies many times gum disease as a major disease that needs to be avoided and I totally agree. However, what can you recommend for somebody who is suffering from it? I asked a question a few weeks ago, regarding IL6, I don't know if you could answer it as I don't remember where I posted it.
I have a gum infection that doesn't want to go away. (it's the third day that I'm in pain, because I didn't want to take an NSAID) I am worried that I will have to take antibiotics.
I don't totally agree with your emphasis on dental hygiene or diet regarding professional cleanings in gum disease. I had treatment for gum disease 3 years ago (involving antibiotics and deep debridement) and I've never had gum infections before and after until a month ago and now. My cleaning regime hasn't changed, I took vit D and K2, I eat a low carb, high fat diet but my gum disease doesn't seem to improve. There must be something else at work.
The last time I had an infection I used hot salty water and it subsided after 2 days, now it doesn't work, maybe because I have a cold that might influence the immune response.
Is there anything else that you could recommend for reducing inflammation/swelling and pain in this case and for avoiding the complications that come from having gum disease?
Thank you very much.

Dr. Art Ayers said...

Hi Lightcan,
I think that you are doing all of the right things and can understand your frustration at still suffering from gum disease.

My focus on trying to avoid gum inflammation with hygiene is based on the observed success of lowering overall inflammation and some inflammation based diseases with flossing.

After gum disease has developed, then the approach is more complex, because I think that gum disease is autoimmune. My impression is that gum disease autoimmunity is based on antibodies against peroxyreductase, an enzyme produced in abundance at sites of inflammation, for the hydrogen peroxide produced in defense. This may be parallel to the spreading autoimmunity of celiac to Hashimoto's thyroiditis based on tissue transglutaminase.

The point here is that an autoimmune disease has both the lasting impact of antibody production against self antigens, but also defective tolerance, usually in the form of compromised Tregs due to dysfunctional gut associated lymphoid tissue.

The autoimmune component would suggest that removal of inflamed gum tissue would usually not provide a permanent cure, unless some persistent infection provided a unique source of inflammation that could be removed. It would seem that the only cure would be elimination of sources of inflammation, gradual loss of autoantibody producing B cells by attrition, and reestablishment of protective Tregs by diet/gut flora/gut remediation.

Reading back over your previous posts, the persistence of inflammatory symptoms, such as acne in response to food triggers, indicates that your gut has previously been damaged and provided the basis for the gum autoimmune attacks. It seems that you still have not recovered normal gut/immune function. Food triggered symptoms should be eliminated by a healthy GALT.

You need short term and long term solutions. The short term is inflammation/pain control. The long term is fixing your gut.

Gums are almost approachable by topical applications. Unfortunately, the gums are not wired like the skin below the neck, so there are lots of unique features related to the face/brain proximity with nerves and vascular systems. The things that I would try for relief would be hot/cold applied to the gums, e.g. hot tea vs. ice. These responses could be related to menthol, capsaicin, castor oil. Oil of cloves, would be another obvious one. Aspirin applied to the gum instead of ingested may give the anti-inflammatory benefit without the gut leak problem. The broad area response to cold and heat sensors may mean that you should try all of these also on the skin of the neck and face to see if that provides relief.

Let me now how you are doing.

Anonymous said...


I suffered from bleeding gums for years until about a year ago I started to clean up my act. Besides the regular bleeding when brushing, I would get a somewhat painful infection about once a year where a wisdom tooth is lying on its side.

One of the things I've been doing to keep plaque to a minimum is oil pulling (google it). I produce a lot of plaque and I can see that oil pulling keeps it to a minimum. By chance I happened upon a video by a professor who has done some research on what happens to oil swished in the mouth, so I have heard some scientific backing to the idea that oil attracts bacteria which leave the body when you spit out the oil. Unfortunately, the video is not in English.
The last time an infection in my wisdom tooth started up, I oil pulled with coconut oil and it disappeared right away, never to come back. It may give you immediate relief for your infection. I suggest coconut oil for this one. Other oils didn't have the same effect.

Good luck,

lightcan said...

Thank you dr. Ayers and Glither

I kind of thought that my gut flora has not recovered yet.
My frustration changes into resignation and fatalism, but with your help I see that all is not lost. I have already lost a lot of bone, so I really have to be careful. These 2 infections have surprised and saddened me, as I said I've never had one before. I'll try to implement your suggestions. I definitely felt that the pain was shooting up and down to the extent that I wasn't sure, at the beginning, without touching, where was the 'epicenter'. The proximity of the tonsil might have something to do too as I have had since more symptoms due to my cold.
I tried the coconut oil, rinsed with hot salty water for two days and applied corsodyl gel to the area. The area where a tooth is missing was totally swollen, now it's gone smaller and the pain is gone but it doesn't look good. Maybe it's a part of the healing process. It's scary, I don't want the infection to spread. My mother had an infection and she had to have all her teeth removed, she is only 67.
I really appreciate the information even if I don't really understand. I'm going to look into it and maybe take it to my hygienist to give him something to think about. I heard of cloves, but wasn't sure what form.
Paul Jaminet also suggested cranberries against the biofilms.
Could it be really working if you only apply something on the face in that area, instead of locally, under that gum, it's counterintuitive, maybe you're referring to the pain relief, and it involves nerves or the lymph circulation but what about the actual infection and inflammation site? We just let it take its course? I also had mackerel for resolvins.
Just curious. Thanks again.

Dr. Art Ayers said...

My suggestions treat the pain quickly, by relieving the inflammation.

Look at my other articles on capsaicin, menthol and castor oil. They are very potent. I have successfully applied them to my wrist and stopped in seconds the pain and inflammation from a burn on my fingers. They act via the nervous system to resolve inflammation/pain. I would think it quite possible that eating hot peppers would reduce the pain and swelling. Applying menthol, e.g. Vick's Vaporub to your jaw and neck might also be helpful. Hot tea or ice might also reduce inflammation. Mouth washes are effective at removing biofilms, because their ingredients are anti-microbial and also destabilize the matrix. They also typically contain menthol as an anti-inflammatory. Clove oil is an anesthetic an probably works in the same way. It would be applied directly to the gum. It is also used for teething babies.

Inflammation is the source of most of the pain in gum disease and can be reduced temporarily by the approaches that I have suggested. The underlying problem is poor circulation adjacent to the established infections. It is parallel to toe nail infections, or sinus infections, in which the difficulty is getting the blood-based immune system to the site of the infection. Surgery just cuts to the chase, as it were and makes the whole area a wound and eliminates the pockets of infection. It doesn't get to the cause any more than treating toe nails with a fungicide or taking antibiotics for an infection.

The long term solution is repairing your gut/flora.

I hope that my suggestions provide some relief, even if you still need professional help.

Anonymous said...

i took antibiotics for a throat infection i apparently didn't have and since then i have been having loose stools. i tried to take probiotics but i get diarrhea and red eyes from taking them. you said appendix is a reservoir for gut flora then how do i go about re balancing my gut. i just want to go back to having normal stools.

Anonymous said...

I have struggled with a bloated gut for 10 years now. I did a stool analysis and it showed that I had alot of pathogens in my gut and and not alot of the good bacteria. I tried herbs to kill off the bad bacteria and took stool test nothing much happened so they put me on a broad spectrum antibiotic and after 10 days on it I had to get off. The doc did not mention that I needed to change my diet. He is a natural IBS doc and he also told me not to take pre biotics like I have seen u mention as he said that they feed the bad bacteria as well. No FOS either..At one time he gave me ultra clear sustain by metogenics and it helped the constipation but caused even more gas and bloat so he told me to stop taking it as it has inulin in it which he thought to be the cause. Another doc said not to take it either if I had candida as it has rice protein in it shich can feed candida which I also struggle with..any thoughts on this? All so confusing at times..thanks

Anonymous said...

The link above should show the ingredients in Ultra Clear Sustain..

Anonymous said...

Hi Dr Ayers,

After perusing the GJ journals at the med library were I work today, I was amazed at the number of articles discussing the gut microbiota--you're definitely ahead of the curve with regards to your insights. i've been dx with crohn's and am trying to rebuild by microbiome. one of the articles from this months "gastroenterology" showed increased amts of lactobacilli in crohnies. do you think this would suggest that an avoidance of fermented foods would be advisable?

Ken D Berry MD said...

Good information. Have you written your complete thoughts and a plan for rebuilding a robust, natural gut flora in detail somewhere?

Anna said...

Dr. Berry,

Dr Ayers has a link at the top of every page of his blog that directs to his basic anti-inflammatory diet recommendations.


All health care starts with diet. My recommendations for a healthy diet are here:

Anti-Inflammatory Diet and Lifestyle.
There are over 160 articles on diet, inflammation and disease here (find topics using search [upper left] or index [lower right]), and more articles by Prof. Ayers on Suite101 ."

debbie said...

Dr. Ayers I am so happy to have found this blog... like many others on this site I suffer from painful stiff joints . 3 years ago i came down with flu like symptoms and a rash that was on one side of my body the back of my leg lichen planus and wieghtloss which they first thought was lupus... i have had every test imaginable done. I have been pegged with undifferentiated connective tissue disorder. I am taking plaqunil and methotraxate. I have slowly started weening my self off the plaqunil and would like to get off the methotraxate. would you still recommend fish oil the inflammation diet. would love to hear from other people who have had success. I really want to get to the root of the problem and am sick treating the symptoms

Dr. Art Ayers said...

If you are suffering from some type of autoimmune attack on your connective tissue, then your problem is based on the tolerance system provided by the immune system that develops in your colon in response to gut bacteria, e.g. Clostridium spp. That means that you should reduce inflammation by following the recommended anti-inflammatory diet and reestablish your colon gut flora with dirty veggies and soluble fiber.

The point is that you are missing dozens of species of bacteria from your gut and you need to ingest these bacteria and feed them on diverse plant polysaccharides, i.e. veggies. It is that simple, but it takes patience and persistence. Of course you could always take the fast track with a fecal transplant.

Thanks for the comments/questions.

debbie said...

Thank you for getting back to me... Can I reestablish my gut flora while still taking methotraxate. I am increasing my intake of fish oil with hopes of getting my inflammation down. i have a low vitiamin D level. I am taking 4000ui. Should I be taking more than that?

Dr. Art Ayers said...

Methotrexate is a drug that kills off rapidly dividing cells, such as cancers, the lining of the gut and cells of the immune system. Since the aggressive cells of your immune system are attacking your joints, killing those cells using methotrexate relieves symptoms, although it also ruins your immune system. This is similar to using antibiotics to treat acne, in which the gut bacteria needed for the development of the aggressive immune cells in the gut are killed.

What is actually missing in your case, is the second half of the immune system that suppresses and controls the aggressive half, i.e. regulatory T cells or Tregs. Tregs develop in your colon in response to gut bacteria, e.g. Clostridium spp. You are apparently missing the required bacteria from your gut flora, probably because of prior antibiotic treatment. The Tregs prevent autoimmune diseases and allergies. Another common indicator of inadequate colon bacteria is constipation.

Omega-3 fish oil can be used to suppress some forms of inflammation, but it makes more sense in the long run to eliminate the inflammation. Please review all of the recommendations on an anti-inflammatory diet that I make on this blog. Since you have symptoms of profound inflammation, I suspect that your diet is the major source.

Most people who test low and supplement for vitamin D deficiency do not take enough vit. D3 to overcome the inflammation produced by their deficiency and remain deficient even when getting adequate sunshine. The only way to tell if your supplementation is enough is by retesting. I would suspect that you are still deficient and that is an ongoing source of inflammation.

You can start to correct your gut flora even while taking methotrexate, but remember that this drug is an immunosuppressant.

Thanks for your comments/questions. Let me know how you progress.

Anonymous said...

Is it possible after years of medications to re-establish your gut flora. Does it just take more time and patience?

Dr. Art Ayers said...

I is always possible to reestablish gut flora, regardless of your medication history. It may take more time, persistence and exposure to new sources of bacteria that are carried into your gut clinging to the food that you eat, but it is still just a matter of persistence.

Cooking food and other processing also kills needed bacteria. Thus, if you have used lots of antibiotics for extended periods of time and/or have had your appendix removed, then you may need to replace dozens or perhaps a hundred different species of bacteria that should be present for a healthy gut/immune system.

The bacteria that are needed in the colon use soluble fiber from vegetables as their major nutrients. So, supporting a diverse gut flora requires eating a diverse diet rich in vegetables. Saturated fats appear to be much healthier for gut flora than starch and sugars. That is another reason why I recommend a low carb/high saturated fat diet with ample protein and veggies. That is also why the paleo diets are healthier than vegetarian diets rich in carbs. [Grain fiber is not recommended, because it does not support healthy gut flora and has the problems of gluten, lectins and phytic acid.]

Thanks for the question.

Anonymous said...

You said that "Saturated fats appear to be much healthier for gut flora than starch and sugars. " I am curious how does saturated fat affects gut flora. I thought gut bacterias only consume carb or protein. I am trying to increase my saturated fat intake but it gives me stomach upset. I am trying to increase intake slowly. Is fat easier to digest than carb or protein?
Rashed Hasan

Anonymous said...

Hi Dr. Ayers,

My father turns 85 next week and just went into today to have dye put through his veins to check the blockage as his feet are red and swollen finds it hard to walk any distance ,very painful at night. He has suffered his adult life with Arthritis and has had a heart bypass and knee replacement. The doctor told him that his veins have dried up from the knee down. When it gets to this point are there still things he can try. He has been very active even with all his health problems . He really needs to get the circulation to his feet. Any thoughts would be appreciated...

Anonymous said...

{Sigh} You recommend: "vit.D, low carb, most calories from saturated fat, no veg. oil, plenty of greens, healthy gut flora." I do low carb and vit. D and sat fat... but I have never, starting as a baby in a high chair, been willing or able to eat vegetables. I HATE the taste, I literally gag. (I write that as an editor -- not someone using an exaggeration. I almost spit out a new food (lychee) in a restaurant once, barely managed to stop!)

At age 33 I learned to eat (small) amounts of green pepper. At 45 my husband taught me to be able to eat small amounts of lettuce, but only with Thous. Isl. dressing. I think the veg aisles in the store look magnificent -- any veg I try tastes repulsive. I'm reading your site and WANTING to improve my gut flora -- heck, I'd even prefer to eat DIRT than dirty veg!!

Is it hopeless? Do I have to force myself to eat veg (which I've tried for many years and can't succeed at) or is there a way to build healthy flora without eating "lots of greens"? (I take vitamins, just bought some L-glutamine as you recommend, avoid grains and legumes... but I just can't seem to face eating horrible horrid veg.)

Dr. Art Ayers said...

I am focusing here on the cultivation of gut flora needed for normal development of the immune system. That usually means eating diverse plant soluble fiber needed as the nutrients for diverse species of bacteria. It also means introducing hundreds of different species of bacteria that cling to uncooked food.
Most people can readily change food preference simply by eating a new food for three weeks. It simply takes the nervous system and gut flora a while to adjust.
The gut flora and particularly biofilms can also evolve new bacterial species, if diet is abnormally constrained.
In your case, your gut will not have access to normal nutrient diversity and will have to evolve new bacteria. Those bacteria can only evolve if they can pick up needed genes from other bacteria that have them. Since you can't get the needed bacteria/genes from dirty veggies, then you will have to pick them up from dirty people, pets, etc. I would suggest that you learn to enjoy gardening and kissing children and pets. Hygiene is your enemy.
Do you have symptoms that suggest that you suffer from inflammation or other defects of your immune system?

Anonymous said...

Thanks for the quick answer!
>> "I would suggest that you learn to enjoy gardening and kissing children and pets. Hygiene is your enemy.

I do enjoy gardening, but I've found I need to wear double surgical gloves and, even so, afterwards wash around and under my nails with alcohol to prevent "felons" -- infections under the nail that end up needing treatment with antibiotics and antifungals. {eye roll} (I'm working on my blood sugar, as felons are often a symptom of pre-diabetes, which I am.)

I'm not a nut with alcohol hand-cleaner except on cruise ships, where Noro is all-to-common. I wear footwear in the Y lockerroom (CA-MRSA is 'in the wild' here in GA), but share the big pool with adults and kids alike (I do not believe that "swim diapers" are sufficient prevention / protection, so I keep my face out of the pool water).

>> Do you have symptoms that suggest that you suffer from inflammation or other defects of your immune system?"

Way overweight for decades (280#, 5'6"). The felons (which I have not had since starting the alcohol post-gardening). Been treating my adrenals (very successfully) and my thyroid (somewhat successfully) (both as per Stop the Thyroid Madness, which site/forum was eye-opening beyond belief!). Semi-successful at low-carb (down 60 pounds, then back up 30 while I was taking (physiologic doses of) hydrocortisone for my poor adrenals). Still taking T3-only (75 mcg a day), plus one Iodoral, having had reverse T3 problems when on desiccated thyroid.

Right now, I'm fighting the residual coughing after a medium-bad cold, generously shared by my 15-yr-old (Type 1 dm) nephew. (I always end colds with a month of coughing-with-wheezing; I *feel* perfectly normal, except for the coughing.)

I just ordered a "Ninja" food processor, and am hoping, by pureeing the heck out of veg and maybe mixing it with stuff I will eat, I can 'sneak' some veg in...

Oh -- and I believe I lost my entire gut flora and fauna this past xmas. I swig the occasional 'probiotic' and -- having read someone recommend using different brands to get different species of bugs -- I tried a somewhat expensive pill-form (just two pills over two days -- and then I had to stop). I have never been so completely sick in my life! I lost 16 pounds in 7 days -- I had continual liquid diarrhea and essentially (believe I) threw off everything in my gut!

Over the past couple months, I have seemingly 'put myself back together' -- starting with home-made chicken broth, first without, then with, a small amount of rice. (Interestingly, my stomach seemed unaffected, just my intestines were ... non-functional.) I didn’t allow myself to get dehydrated too far, so didn't add that to the loss of flora and fauna. (No answer ever from the pill company about contamination...)

I'm back to my "normal-abnormal" diet. Mostly meat and cheese, occasional protein drink, occasional carbs in the form of a cup or less of rice, and the weekly salad at our japanese restaurant (where I have the rice).

Anonymous said...

Permit to add, that after I raised my Vitamin D levels to the high 60s, I have not had a cold for several years. Then, we visited CA, and our nephew, a few weeks ago. Strange bugs with a lack of sleep, stress dealing with family, and bad diet for ten days out there seem to have opened the door to the cold!

Hope renewed said...

Dr. Ayers,

This is another "you've changed my life" post.

After a trip abroad last year, my previously energetic healthy 6yo daughter was given two rounds of antibiotics for intestinal parasites (first round was unsuccessful). Our doctor suggested eating yogurt for the duration of the antibiotics to protect her gut. However, in the last year she's suffered from frequent stomach aches, nosebleeds, bedwetting, long daily naps, leg cramps, sinus congestion, dark bags under her eyes, and constipation. We've endured numerous medications but symptoms persisted with new ones added.

I've read most of your posts, and those on other blogs you linked to, and in the last two months I've changed our family's diet to follow your anti-inflammatory diet recommendations. Most notably, replacing omega-6 fats with saturated fats and cutting out sugar and grains.

I'm literally crying with gratitude as I write this because I'm watching my child come back to life--her energy is returning and many of her symptoms are lessening. I wish I had found your blog sooner.

There's still more we need to do as per your recommendations for rebuilding gut flora, but you've had such a positive effect on our family's quality of life already. Wish us luck for the rest of her journey back to health. I'm not asking for personalized advice but if any specific recommendations come to mind ...

Anonymous said...

New York Times article re gut flora research:

Anglin said...

Hi Dr. Ayers,
I was prescribed antibiotics 4 months ago for a sinus infection. The antibiotics cleared up my sinuses but have completely messed up my gut. At first I suffered with weeks of daily (yellow) diarrhea. I seemed to be especially intolerant of dairy so I cut out all milk products 8 weeks ago. I still continue to have daily diarrhea, although the frequency has reduced somewhat. I now seem to have developed low blood sugar because I am eating simple carbs (ie. white rice, toast, etc.) in an effort to try not to upset my stomach. I wake every morning very sweaty, shaky and trembling.

How can I get out of this horrible nightmare? I haven't been eating yougurt (since no dairy). Do I need to start with a probiotic? At this point I am nervous to ingest anything. But I would greatly appreciate any suggestions you may have.


Unknown said...

Hi again Dr Ayers

It has been a while since I posted on this thread. I'm still struggling with sensitisation to foods and working out what is going on.

However, just under a year ago you said:

" Your sensitivity to alcohol is an important symptom and indicates another damaged part of your physiology. Were you ever sensitive to fish oil?"

I have recently tried to suppplement with 2g of high-DHA fish oil per day which has given me a major reaction.

Can you tell me what this might tell us about a potentially damaged part of my physiology, as you mentioned?



Anonymous said...

Dr. Ayers have you ever hear of large does of fish oil 6-9 pills elevating ones liver enzymes

JEAN said...

Hi Dr. Ayers,
I've been thinking of you lately. I had a laparoscopic hysterectomy recently and the surgeon offered me a "free" appendectomy, because, as she said, 2% of people over sixty, (I am) get appendicitis. I refused and she was quite derisive about it. But there was no question in my mind. A very smart doctor, in her field, women's surgery, but disappointing in her knowledge of the body.
She was never able to acknowledge any of my arguments. But I still have my appendix.
I get Science News and the last two issues have focused on the gut, they've even mentioned fecal transplants (with great distaste). I want to write and chastise them about being behind the times. But they are at least getting the information out to the public. Most of it seems accurate. The best stuff is here, though. Thanks for the many posts. I'm in much better health because of them.

Anonymous said...

Great article in the New York Times re bacterial genome sequencing:

Anonymous said...

That antibiotics "can't be avoided," is absurd most of the time. Oh sure, with some horrible infection, perhaps they are needed. But in our informed times, there is no excuse for their use most of the time, and certainly not as an "only recourse." Our daughter--after we decided antibiotics not only weren't helping but were dangerous--had no antibiotics for 17 or 18 years. How? We built up her immune system with nutrition. We took her off cow's milk and most milk in general. No sugar, except rarely (it depresses the immune system), and we treated any colds (and they were rare) with high-potency herbs, vitamin C or enzyme formulas. High-wattage protease enzymes, for example, will quickly knock any bacterial infection AND NOT CREATE SUPER BUGS and we ALWAYS used things like the Chinese herb (the Chinese understand working with, not against, the body) Yin Chaio to knock an infection, although even good old EmergenC or Airborne is not to be underestimated. But do the natural nutritional support to "charge" the immune system first, and I assert you'll almost never need antibiotics, especially if you also use common sense and REST!

Niko said...

Hello Dr. Ayers!
Thank you for this post and so many others, they are so interesting, to the point and very helpful. I am particularly interested in your articles concerning inflammation and gut flora. It's been six months now since I started drinking kombucha about 2-3 times a week, and it has helped with the bloating and other digestion problems (but I also cut gluten and dairy from my diet). I am just wondering what you have to say about Kombucha? There are so many mixed opinions and studies on it, I am kind of confused. Is it really as beneficial to digestion as they say? How much is too much? Thanks so much for your time. -Nico

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Anonymous said...

After no antibiotics for 15 years- 3 years ago I took an antibiotic and got C.Diff. Which was treated with another antibiotic. Since then, I've had fairly mild bloating and constipation.

A month ago, I had to take another antibiotic. My stomach is swollen like I'm 6 months pregnant and constipation is worsening. I tried taking some probiotics but I imagine the ones I got at KMart aren't good enough. I can't find any actual recommendations of what brands to get. Can anyone send a link for good pre and probiotics?

I wish I could just get flora from my 7 year old daughter- breastfed for 2 years and has never taken antibiotics...

I'm just over the swelling and constipation for something that happened 3 years ago! Thanks...

Anonymous said...

Hi Dr. Ayers,

Hoping you'll see this, as it's been a while since your last post. My daughter is currently on a round of amoxicillin to knock out a tooth abcess prior to what will probably end up being an extraction of a baby tooth with a very large cavity. I was told that due to the acidity in an infected area, local anesthetic would be metabolized, thus leaving her essentially unanesthetized for the procedure. We've successfully avoided antibiotics for her and me for years, although she did take a round or two when she was 1 to 3 years old. I was still exclusively breastfeeding at least the first time, so I hope that will have mitigated it some. I'm not comfortable with the fact that she has to take this course, but the dental issues have to be taken care of. I'm sure the question of why she's having so many cavities is a whole 'nother can of worms. I've seen some of your recommendations, short of fecal implant, for trying to recover from antibiotics: variety of raw veggies and hopefully some dirt on them. We'll be having wild dewberries soon, so I can have her eat some of those, but otherwise, it's hard to see how to get much dirt into her. Would a little bentonite clay in water help any with this? How bad would it be if I just went out to the field behind our house (I'm sure our lot is mostly builder's sand with chemicals in it) and grabbed a few teaspoons and sprinkled a tiny amount in her drink or food? Is that crazy? We live on Texas gumbo soil. Of course we will do yogurt, and kefir, and I can also get her to eat fermented carrots. Would raw cream help as well? I know you're not too keen on milk, whether raw or not. Any other suggestions for helping her get through this as healthy as possible? I'd really appreciate it, as I'm praying every time I dose her that it won't do any long-term damage.

On a totally different topic, I first found your blog because I'm looking into a gluten-hypothyroidism connection. I've been hypoT for 18 years, and it's getting a little old, ya know? I know celiac is strongly connected with Hashi's and I've seen some of what you have to say about that, about tTG being the target for both. I'm interested to know more about how tTG is a target in hypoT because I was under the impression it was thyroid peroxidase and thyroglobulin? After 17 years, I was finally tested for those, just to make sure it was Hashi's and not another type of hypoT (at my request, having been told 90% of cases are Hashi's and it the etiology wouldn't change the treatment anyway). When they both came back normal, my endo said there were lots of other antibodies we hadn't tested for and that my immune system could be having fluctuations and we just caught it on a good day. But I never see any other antibodies mentioned. Are there?

I know of one study of celiacs where total gluten avoidance failed to reduce thyroid antibodies over a 6-month period. I've read you say that Hashi's could result from a disease event in the past in the presence of an environmental trigger that was most likely gluten. Do you have reason to believe a gluten-free diet would help improve Hashimoto's symptoms now that the Hashi's has been in progress this long? I have been tested for celiac (IgA EMA, tTG, and AGA) which came back within normal limits. I have found a lot of discussion in the research of non-celiac gluten sensitivity as a condition distinct from celiac, but I haven't yet read you refer to gluten sensitivity in any context other than in the classic sense of equating it with celiac. I'd love to hear your opinions on that as well.

Anonymous said...

Just a thought. Though this may be far fetched..
I work in the 2nd G EtOH business part of development of enzymes that will digest different types of lignocellulosic biomass.. to hydrolyse these "wood type" materials into single sugars.. One application is to also degrade yeast (from 1st G EtOH production where there are e.g. wheat husk etc still present) to also make use of these nutrients. But yeast is hard to degrade and it is difficult to design a enzyme production host that produce the correct enzymes to hydrolyze yeast. The production systems used is fungal or bicterial. The fungal though (which we use) do code for enzymes that will degrade certain components in other fungals (their defense system..). One trick in the industry to achieve production of the correct enzymes are to add deactivated yeast (just the cell walls) to the fermentation this will program our enzyme production host to produce also enzymes capable of hydrolyzing this new "food source". The same is done some times for cellulose type materials, to program the expression system to produce cellulases..
My thought: Supplementing with nutritional yeast, maybe that could help arm out gut flora with more tools to fight candida infections..?

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Steve said...

Dr. Ayers,
I just started keflex AGAIN. I really tried to let my issue heal on it's own but it took a turn for the worse and I don't want more disfigurement.
You said

"Antibiotic use typically results in yeast replacing the lost bacterial species."

What are you thoughts on taking Florastor. It is a yeast to crowd out or eat C. diff while on antibiotics?

After this course of drugs I think I must set my gut flora right because my immune system is over0reacting. Do you do consultations?

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Anonymous said...


I read and understand the terribly damaging effects of long-term antibiotic use on the gut.

I am 27 years old and have been on long-term (6months) antibiotics for a serious deep tissue infection. I am constipated, bloated and have severe stomach reactions to food, that I never did once before.

What I don't understand is how to counteract or improve my gastrointestinal health. I HAVE to be on these antibiotics for another 3 months. There is no way around it.

I'm thinking of seeing a gastro to discuss what to do about the cramping, pain and constipation but I would love to hear your thoughts.