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 .

Monday, June 11, 2012

Dr. Oz on Gut Flora Repair

---  the other 200 posts  ---
Where is the hippo? Trying to repair a complex community of a couple of hundred different species of bacteria by just changing diet, is like a zoo trying to add hippos by building a new enclosure and supplying it with fodder. You can wait and wait, but you can't add new species without adding new species. Hippos don't appear by spontaneous generation and neither does E. coli or other gut bacteria. You have to ship in hippos from other zoos and after antibiotic-induced extinction of gut bacteria, you have to introduce or eat missing species of bacteria. Also just adding probiotics will not provide a lasting fix for damaged gut flora any better than adding more elephants or giraffes will improve the diversity of a zoo lacking hippos.

I am amazed that Dr. Oz and the medical industry can encounter symptoms of dysfunctional gut flora, e.g. constipation, food intolerance, autoimmunity, allergy, that are preceded by antibiotic treatment and not address the compromised species diversity of the gut. The involvement of gut bacteria in immune system function is documented in the biomedical literature. The lasting impact of antibiotics on gut bacteria is known. Then why do Dr. Oz and the rest of the medical industry just recommend probiotics, a half dozen different species of bacteria found in fermenting dairy products (think elephants and giraffes), to repair a decimated gut bacterial community? They seem to be perplexed and ask, "Where is the hippo?"

Generalizations about Gut Bacteria
Each healthy human maintains a subset of a couple of hundred of the couple of thousand different species of bacteria found in humans around the globe. The diverse community in each individual may differ in species, but has approximately the same complement of genes in people sharing the same diet.
  • 1-200 different species of bacteria per person
  • 1-2000 different species of human gut bacteria
  • 1 million different genes among the different bacteria
  • Most genes are involved in digesting plant carbohydrates, i.e. soluble fiber: inulin, pectin, fructans, algal sulfated polysaccharides, etc.
  • Diet diversity, e.g. the Modern American Diet, reduces the diversity of the gut bacterial community, presumably because the rapid change in foods permits survival of only generalist bacteria that can digest many different foods.
  • Simple diets produce gut flora diversity, but only if there is access to diverse bacteria.
  • Health may result from diverse gut flora developed from a simplified diet and ample bacterial resources.
  • Obesity and other diseases may result from simplified gut flora developed from a changing, complex diet and a sterile environment/isolation.
  • Vegan and paleo extremes can lead to healthy gut flora diversity, if the gut bacterial community is permitted to adjust to the diet composition by avoiding rapid changes and providing diverse bacterial sources.
  • Meat contains complex polysaccharides, e.g. glycosaminoglycans, such as chondroitin sulfate and heparan sulfate proteoglycans, which are bacterial fodder equivalent to soluble fiber.
  • Probiotics are unique bacterial species that do not persist in the gut of adults, but dominate the gut of milk eating babies and stimulate development of the gut and immune system.
  • Probiotic bacteria can temporarily provide developmental signals for immune system development that are normally provided by a healthy gut flora.
  • Antibiotics cripple gut flora needed for development of the immune system.
  • Common medicines have significant antibiotic activity and modify gut flora.

Damage to Gut Flora is Not Repaired by Diet Alone
There is little or no effort being made by the medical industry to develop approaches to repair gut flora damaged by disease, unhealthy diets or medical procedures. This is similar to a surgeon stepping away from removal of a diseased organ without closing the wound. Antibiotics leave a gut flora that will remain permanently damaged without systematic, monitored repair. It might also be suspected that disruption of gut flora by antibiotics and the introduction of large amounts of new foods, such as high fructose corn syrup and vegetable oils may contribute to or cause the modern prominence of obesity. After all, gain or loss of weight changes gut flora, obese individuals have damaged gut flora, and trading gut flora between fat and lean animals, trades weight gain/loss behaviors.

Sources of Bacteria to Repair Damaged Gut Flora
  • We must eat new bacteria in order to replace bacterial species lost by antibiotics or unhealthy diets.
  • Probiotics -- bacteria that aide gut function, commercially from dairy fermentation
  • Fresh vegetables -- bacteria are on the surfaces of plants unless the vegetables are cleaned or cooked
  • Fermented foods -- Bacterial growth leading to acid or alcohol production has beed used in the preparation and storage of many foods and provides a rich bacterial resource.
  • Environment -- Bacteria are transferred to our hands and face from other people, pets and surfaces, unless hands and the body are continually washed. Sanitizers and frequent washing of hands and surfaces eliminate acquisition of environmental bacteria to repair damaged gut flora. Social isolation and hygiene block repair of gut flora.
  • Replacement -- experimental replacement of damaged with healthy gut flora (fecal transplant) has been very effective in curing many diseases without significant risks, but is restricted by the medical industry.


Anonymous said...

how about eating the poop of a healthy person on a regular basis?

Anonymous said...

people can start eating wheat if they have the necessary bacteria/fungus to digest it i would suppose.

yogurt provides that. so i would guess people aren't eating enough yogurt to provide bacteria for proper wheat fermentation in the colon.

or is wheat inedible to begin with?

Anonymous said...

i'm glad that you are coming around to the vegetarian view point


Vasco Névoa said...

Here's a question that's been on my mind for a long time:
Isn't gastric acid supposed to kill off any bacteria that enters the digestive tract?
If som how can eating bacteria restore the intestinal flora?

delic89enius said...

Fascinating. So more diet diversity leads to less robust gut flora ... could this also be why anyone on a weight-loss diet that cuts out a major food group (reduces diversity) loses weight at first? Perhaps subsequently eating novelty foods that are nonetheless within their diet strictures ("low fat" Snackwells from the 1990s or "low carb" Atkins products) are also part of what makes people regain weight ... not just because they are processed foods and added calories, but also because they are at first novel, thus reducing the gut flora.

Anonymous said...


But I wonder how this played out in the past. My understanding was that the diets in the past changed quite rapidly depending on what was available.

So people would not eat the same thing week to week since there were no grocery stores that always had eggs available. Mainly they would eat starch and then when they would catch something they would eat meat. It seems that the past would promote less stable diets than today.

organigal12 said...

What's a 27 yo Hashimotos, low thyroid, gluten intolerant, allergic to soy, corn, casein, chicken/beef, pcos, reactive to cephalasporins, EBV+, chronically constipated, overweight, extremely fatigued and totally depressed girl to do? I follow NO SUGAR. NO GRAIN. NO ALCOHOL. Yogurt, juices of unwashed thyroid replacement is compounded and NOT HELPING AT ALL!

Where can I go for a fecal replacement? I am truly desperate. My health care provider had me taking HUGE amounts of antibiotics, steroids, birth control pills, and round one of Gardasil. I moved back home and my mom has been trying to get me healthy again.

Now the joints in my fingers are killing me!

Anonymous said...

Gaps diet. Whats your view on this? Vegan is not good for brain development in the fetus and small child, and vegan soy consumption is endocrine disrupting.

Great blog! Regards from a fellow researcher

Steven Wright said...

"Simple diets produce gut flora diversity, but only if there is access to diverse bacteria."

Dr. Ayers - Is the term simple meaning a low variation of foods and preparation techniques (cooked/raw)? Or just foods? Any other factors that create a simple diet?

I want to invite you on our podcast... I'd love to speak with you about this article! Here's one we did with Dr. Allison Siebecker a SIBO researcher.

Please email me at scdlifestyle at gmail . com. Thanks.

Love your work!

Jorge said...

Dr. Ayers,

Thank you for your work.

Is there any way to completely wipe out the gut bacteria in someone suffering from dysbiosis (prolonged fasting plus antibiotics, for example)?

Since fecal transplants won’t be available anytime soon, repopulating the gut with proper flora from scratch strikes me as a viable option.

All the best,


Sarah said...

Have you seen the AP article. Looks like human flora is making it into mainstream news outlets.

Crap Stomach said...

Do you think that fecal transplantation could cure ailments like, SIBO, Lactose intolerance, Fructose Intolerance etc.???I have all 3 and can't eat anything without getting symptoms. I've suffered with IBS-D for 20 years!

I'm so fed up and depressed with it!

Javeux said...

Re: GAPS and restrictive diets

These things will destroy your metabolism if you're not careful. There's actually a growing market in counter-diets, since so many people have gained weight and developed problems following GAPS, v. low-carb paleo etc.

Surely the best way to kill pathogens is with a tanked up immune system. Following a diet that drains the life out of you isn't a great way to achieve that. SIBO is a tricky one though.

Steven Wright said...

@Javeux - that's just an unscientific argumentative statement that adds no value. GAPS, SCD and Paleo are healing people everywhere on the planet. I know because I talk with them everyday.

There is nothing about those diets that "destroys metabolism" only people who apply their principles incorrectly without the right support.

Actually in this article Dr Ayers makes a compelling argument to use SCD/GAPS/Paleo to heal the gut and reverse a messed up gut flora.

Chuck said...

NYT does flora!

delic89enius said...

Jeff Leach just did this column yesterday in the NYT:

Do you know about him? He's chronicling ridiculously exciting stuff over at his website, . Thought I'd point it out, in case you didn't know about it.

team JOB said...

I'm wondering about nut fats (almonds, brazil nuts, hazel nuts, pecans...). Are they high in omega 6? Do they fit in this diet?


Anonymous said...

Hey Doc, how about investigating Anatabine Citrate to cool chronic low level inflammation. Johns Hopkins is studying its effect on thyroiditis and the Roskamp Institute is studying it for Alzheimers and MS. Would love to get your thoughts.
BTW, great blog, good info. Thanks.

Anonymous said...

I'm treating my psoriasis with a systemic anti-inflammatory regimen that includes Anatabloc, curcuminoid complex, and ubiquinol with promising results after 30 days. I think I'm on to something. What do you think?

Anonymous said...

People you gotta look into ANATABLOC ! It is most effect supplement against chronic low level inflammation ever discovered. No BS. Look into it yourself. Wiki NFkB, anatabine citrate. Don't let big pharma poison you. Look at reviews all over the web at gnc ,amazon, fb, etc. Its too good to be true but it is 2012 after all.
Anatabloc contains anatabine citrate which has shown in vivo to be more effective than celebrex, lipitor, and other anti-inflammatory drugs. Its real. Look into it.

Anonymous said...


I have many of your same problems. I just finished BREAKING THE VICIOUS CYCLE (Intestinal Health Through Diet) by Elain Gottschall B.A., M.Sc.
Excellent book and also very interesting.

Anonymous said...


Or just eat real food and get some sun.

Tanya said...

Just read this linking fibromyalgia to SIBO.

Susie Cassens said...

So if our problems arise from the gut...What if the some of epithelial cells which make up the lining of the gut are genetically damaged and are sending chemical information to the vagus nerve to make insufficient acids?Then you would need to supplement just about everything depending upon the amount of damage.

Christie said...

How would organic produce versus non-organic produce effect gut flora?

I ask this because I recently left a bag of organic potatoes and a bag of non-organic potatoes in the RV. The organic bag rotted quickly compared to the non organic. The non organic potatoes had been in there about 4 times as long and there was no sign of decomposure what so ever, nor were there any eyes growing on the potatoes. Yikes.

TedHutchinson said...

Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity
Nice hypothesis here linking food processing to inflammatory gut flora and obesity and diseases of western civilization.

Unknown said...

I love this, i am always Pushing probiotics! I have question n two different topics, 1st my son is 1week shy of 1 yr and has had reflux since birth and then zantac and then 2 back to back rounds of antibiotics all before 5 months. He has been very sensitive (affecting his bowel movements and inreasing reflux/spit up) to foods through my breastmilk, he also has FPIES to rice and oats and sweet potato and ige allergy to oats and peanuts (found through blood work) he used to have diahrrea when reacting to foods, however he now has a difficult time and gets stoped up and even wakes up multi times crying (a littlt) and straining when we feed him anthing other than avocado and russet potatoes, (I'm talking broccoli, speghetti squash, plums, peaches, lentils). We have a gi dr, allergist, and pediatrician he sees, but not much help honestly. I have tried multiple probiotics for babies for him and they all increase his reflux, he is no longer on meds for reflux since he gets congested on constipated on them, so i do not want to irritate his esophogus. He also has sandpaper bumps on abd. When add the other foods. What is you opinion on this? Are there any good guides that would inform me as to which straines of probiotics function for certain groups of food? I am aware he is a baby and you may not want to advise since he is, but I fully understand any reply is just your opinion. I've left off a lot im sure but i also have so much that ill stop there for that one.
The next is, I always have been a carb fool, I went gluten free for my son and upon reintroducing wheat (or any grain really, but wheat is the worst) i discovered it was the wheat that always made me sleepy immediately and makes my face feel bloated (may sound wierd), get a headache and I get congested (i get more congested with other grains such as oats when I could eat them), do you believe this is a gut flora issue or might i be lacking certain enzymes since the reaction is so fast? (blood work 5 years ago showed no ige allergy) i apologize if i rambled, and for any grammer errors and i truly appreaciated your time. Thank you so very much!

Dr. Art Ayers said...

Hi Ted,
I much appreciate your comments and input.

It is very interesting that food processing may alter gut flora. Diversity of soluble fiber may also be a problem, because it limits genetic adaptation of gut flora to diet. Abundance of bacterial diversity contaminating food may also be needed for gut flora adaptation and reduction of gut inflammation.

Dr. Art Ayers said...

Sorry about all of the problems and poor support.

The star of all of this is your gluten intolerance. This is not simply a gut flora issue and cannot be treated the same way as other food intolerances. Start by staying away from grains. They certainly aren't needed in a healthy diet.

I think that all of your son's problems are reversible.

Your son's problem is absence of gut bacteria. Probiotics are a stopgap, a quick fix, but not a permanent solution. How is your son being exposed to the thousands of other species of bacteria that could help him construct a functional gut flora? His immune system development is dependent on species of bacteria that are not present.

You need to follow the suggestions on my blog to fix your own gut flora, so that you can pass on healthy gut flora to your son. It also sounds like you have too much hygiene in your household. Does your son play in the grass and have dirty pets? Those are good sources of needed gut bacteria.

You haven't mentioned the major parts of your son's diet that should be meat/fish/eggs/dairy, veggies and bacteria. The diet sounds very deficient in saturated fats and omega 3 oils. I expect that your son has a vitD deficiency. Has he been tested for serum vitD?

You and your son have a ways to go to be healthy, but this is a start. Let me know how you do and I can help with the next steps.

Jamie said...

I was diagnosed with bacterial colitis and given two strong antibiotics. Now, 3 months later, my gut feels inflamed at all times and my eyes and nose burn AND I have diarrhea at every bowel movement. I don't know how to fix it. My doctors just want me taking PPIs. Help!

Shawn said...

Dr. Ayers

Could fecal transplants be a potential cure for Crohn's? I feel like my Crohn's has been caused by overuse of antibiotics, and theoretically the transplant would get to the root of the problem.

Alexs said...

Are you advocating raw food diets in support of this? in most really depleted cases this is untenable and exacerbates things rather than assists. The fermented raw is an exception, of course.
just asking. thanks great blog!

-liz- said...

My daughter (11 months) contracted MRSA in May. She was treated with heavy antibiotics and they had to surgically remove the MRSA. Since then she has developed food intolerance to TONS of things...fruits & berries (everything except pears and bananas) oats, and possibly gluten. I fear what is next.

My sister recently told me she thought it was due to the medicines messing up her gut flora. You said in your article these flora can not be balanced by diet alone....what can we do to ensure our daughter does not suffer this craziness her entire life?

Also relevant, our son has anaphylaxis to egg and thus that is not in our home at all - we eat mainly turkey meat (he is also allergic to chicken and intolerant to pork) and beef a few times a month.

Aside from what hurts her and eggs, she eats a great variety of foods eating bananas and pears/veggies (all kinds)/meats/tuna and shrimp....she eats organic baby foods

We have pets (dirtier than I'd like!) and she is beginning to play outside now that she is walking.

So I can...
1. switch our veggies to fresh since she eats many of our table foods now.
2. diversify her omega-3 sources?
3. increase her yogurt....

what else?

I've been told fatty foods (olive oil, butter, and milk) will help cool the gut inflammation... I know you are probably bombarded with questions. Any advice would be greatly appreciated!!! Thank you!


Anonymous said...

Hi Dr. Ayers,

Very interesting site, thank you for the interesting dialogue.

I have a question relating to skin staph infections. I am a chronic sufferer for about 3 years now, off and on chephalosporin antibitocs for treatment. My staph is MRSA negative, so always responds to that antibiotic.

Anyway. I need help because the infections keep coming back. I have a known skin barrier issue (genetic I am told) and must diligently manage the exterior of my skin to maintain moisture and prevent bacteria and allergens from entering and causing havoc.

Lately I am on and off antibiotics constantly. I finish a course and then get an infected hair follicle--small little bump--and it just body rarely beats these things and they turn into giant boils, so painful and dangerous if they start streaking into my lymphatic system. I think the longest break I have had from antibiotics in three years has been 5 weeks. Most of the time I get a reinfection after about 3 weeks.

So lately I have been really focused on anti-inflammatory diet to help manage my skin, which is why I found your blog.

I am 32 year old female, healthy weight, regular exercise and no other ailments other than managing my skin.

I supplement Omega 3s, and evening primrose for GLAs. Also Vitamin D daily, probiotics and enzymes if I feel like it.

I rarely seem to have digestive distress, but this last round of antibiotics I was very bloated and uncomfortable. I suppose it was inevitable.

What I would like to know and understand is--is there a way to be more preventative when it comes to management of skin staph? Infection is not necessarily the result of scratching, it appears it can move in if a hair is pulled out on my leg and then all of a sudden, infection. I have been dabbling with topical antibiotics mixed in with my emollients to see if I can keep it at bay topically rather than having to treat orally.

Any help or advice appreciated. My diet is pretty good--I avoid wheat, alcohol, processed foods. Eating lot's of veggies, and meat. I am allergic to eggs and most tree nuts so a bit limiting with respect to protein. I also have been juicing lately--any opinion of fresh vegetable juice and the gut?

I really want to stop the antibiotics but I am afraid I am in some cycle that I cannot get out of.

Your insights are appreciated.


Tom said...

Dr Ayers,
Thanks for another great article. A question about lactulose; as this presumably counts as a soluble fibre, given that it is not absorbed and requires gut flora for digestion, is lactulose for the relief of constipation effectively just a prebiotic? Has the medical industry got this one right?

And also, given that soluble fibre is a good thing for gut flora, but glucose and fructose are bad for us - why not sweeten things with lactulose?!

Nina K. said...

Hiya Doc,

have you seen this review yet? Very interessting read about fatty acids, gut and their antimicrobial activity, inflammation etc...

Be well!

Nina K.

Anonymous said...

Where you at Dr. Ayers?

Unknown said...

I left a comment just yesterday on a blog you had (2008) re: glucosamine, Please read! I truly feel now after reading this blog I Am the only one with my condition. I was born with my intestinal flora out of balance. My only hope is the fecal transplant. At least there are the researchers like yourself out there that care/know! I will, nonetheless, continue to follow your blogs.

Unknown said...

Had to come back and leave additional comment, even though Dr.Ayers may never see it. (He answers very few here). Nonetheless, all the diet talk Again, and I just Had to come back and say the ONLY DIET ANYONE needs to be on is not a 'diet' at all - it is simply Just The Right Way to eat and what is that? BLOOD TYPE EATING. I Am alive Mainly due to Dr.Peter d'Adamo, his father's 40yr research and his continued work. It is SIMPLE Common sense to eat according to what is COMPATIBLE with your blood-what carries all the nutrition everywhere in your body. I, unlike anyone I've run into yet, was Born with my 'gut flora' out of balance. This wasn't diagnosed, as I said in above comment, until 2008, so if I hadn't have already been eating via blood type,(2yrs),I would be dead. It's SOooo simple, but Noone either/and/or wants to listen, believe, try to find out this is the TRUTH. The one and ONLY truth when it comes to what you put in that GUT. I AM THE living proof. I am also gluten and frutose intolerant. But guess what? Blood type A And O are not supposed to have much gluten, O's more so. So, gee guess That's why so many are out & out Celiac. I became borderline. BLOOD TYPE EATING - THAT IS YOUR STARTING LINE FOR ANY AILMENT. On the off chance Dr.Ayers may see and read this, maybe This month lol my email:

Anonymous said...

Good afternoon Professor Ayers, before I ask my question I'd first like to say thank you for taking the time to publish this blog, it's very much appreciated.

On to my question, although it doesn't relate to this article in particular, do you have any knowledge of keratosis pilaris aka "chicken skin". If so, do you have an explanation for how this disease manifests itself? And also, are you aware of any effective treatments?

Here's the wiki article if you are unfamiliar with the condition

Thank you

JEAN said...

Hi Dr. Ayres,
You helped me two years ago with candida, and the program you suggested worked very nicely. Unfortunately, this last year, I had surgery and radiation therapy for cervical cancer, twenty five treatments, all aimed at the center of my gut, I am assuming that disrupted my intestinal flora, a major burn in my body. I had no major events, diarrhea or constipation, but I did have very stubborn nausea that the radiation oncology docs thought was excessive, I failed all the anti nausea drugs and acupuncture, I finally just toughed it out. But, I can't find that you've ever addressed radiation, although your blog is huge and I might have missed it. So, is there anything other than the loss of my intestinal flora, does the radiation, however 'directed' as they assured me it was, cause any long lasting issues? Thanks, and I'm glad to see you posting again. This is my favorite blog.

Puddleg said...

Dr Ayers, you say
"Diet diversity, e.g. the Modern American Diet, reduces the diversity of the gut bacterial community, presumably because the rapid change in foods permits survival of only generalist bacteria that can digest many different foods."

This makes sense; is there a reference for it?
It may be mentioned in here:
But I haven't had time to read all 27 pages yet.

Anonymous said...

dr ayers or others,

looking into starting "prescript assist" probiotic to help shift my gut bacteria in the right direction. dealing with crohns, likely as a result of years of antibiotics for acne. this probiotic contains a number of soil-based organisms. most of the bugs have limited info avail on the web, which is concerning to me.

any thoughts on the safety of:
Arthrobacter agilis, Arthrobacter citreus, Arthrobacter globiformis, Arthrobacter luteus, Arthrobacter simplex, Acinetobacter calcoaceticus, Azotobacter chroococcum, Azotobacter paspali, Azospirillum brasiliense, Azospirillum lipoferum, Bacillus brevis, Bacillus marcerans, Bacillus pumilus, Bacillus polymyxa, Bacillus subtilis, Bacteroides lipolyticum, Bacteriodes succinogenes, Brevibacterium lipolyticum, Brevibacterium stationis, Kurthia zopfii, Myrothecium verrucaria, Pseudomonas calcis, Pseudomonas dentrificans, Pseudomonas fluorescens, Pseudomonas glathei, Phanerochaete chrysosporium, Streptomyces fradiae, Streptomyces cellulosae, Streptomyces griseoflavus

citrin said...

Healthy and useful information.Probiotic bacteria help us digest our food, kill harmful microorganisms and keep our bodies functioning propertly in a number of ways

Anonymous said...

I am also interested in your opinion on the "Prescript Assist" probiotics.

Sandra Leidelmeijer said...

@whitney penton
Have you ever looked into Japanese natto? It's fermented soybeans. I have found tremendous improvement since I started eating natto. Maybe you're cautious about giving your son soy beans, but with natto, the bacteria are actually in the slime covering the beans, so maybe you could put the beans in a bit of water and give the liquid with the healthy bacteria to your son?

Anonymous said...

I'd like to ask a question and here is the only place I can find.

Is having a Colonoscopy routinely bad for the gut flora? Ie a complete bowel clean out? Or is it not bad, or even good? I think I have really good gut flora at the moment so I don't want to mess it up, but I have a terrible family history with bowel cancer.

Unknown said...

Hi Dr. Ayers,

In your post, you said that probiotics are not enough to recover from antibiotic usage, and that a monitored, systematic approach is necessary to restore gut flora.

After ten years of committedly avoiding antibiotics, I recently had to take a course of them, and am researching how to rebuild my gut microbiota. This is how I came across your blog.

Can you offer more information on the protocol to which you referred in your post and/or resources for further information or help?

Thank you,


Unknown said...

Hi Dr. Ayers,

In your post, you said that probiotics are not enough to recover from antibiotic usage, and that a monitored, systematic approach is necessary to restore gut flora.

After ten years of committedly avoiding antibiotics, I recently had to take a course of them, and am researching how to rebuild my gut microbiota. This is how I came across your blog.

Can you offer more information on the protocol to which you referred in your post and/or resources for further information or help?

Thank you,


Anonymous said...

Dr. Ayers,
The gadget that shows the latest comments posted is not working.
I hope you can rectify.
Appreciating your information, as always.
Best regards,

jgold said...

Dr. Ayers,

Regarding cultivating gut bacteria, could raw, local organic bee pollen be a kind of rosetta stone?

Andrew Jackson said...

Dr Ayers what is a good email address to use to contact you?

Anonymous said...

start eating Whole Foods, as many fruits and veggies in their organic raw state as you can, fermented foods,and read "The Makers Diet" plus exercise will also help, it takes time to restore you cells back to health, so be patient.There is a product out there called Juice Plus it can help you get what you won't , can't or don't do day in and day out...There is Gold standard science behind JP+ that no other company can boost of....Be your own advocate.....Research not antidotes Best Wishes

Ac repair said...
This comment has been removed by the author.
Anonymous said...

Why do people think they need the medical establishment to do this for them? It would be easy to do a fecal transplant at home. Take some poop from a healthy person (preferably screened for harmful parasites), add to a cup of water at core body temp, give it a good shake and administer into the proper orifice (not the mouth!) with a turkey baster.

Tanya said...

Sad to see no posts since last summer. Hope all is well with you, Dr Ayers. This was in a newsletter I received:

Consider skipping breakfast eat lunch and dinner and make sure you stop eating three hours before you go to sleep, so you’re eating within an 8-hour time frame every day. In the 6-8 hours that you do eat, you want to have healthy protein, minimize your carbs like pasta and bread and potatoes and exchange them for HEALTHY fats like butter, eggs, avocado, coconut oil, olive oil and nuts. The type of fats the media and “experts" tell you to avoid.

This will help shift you to fat burning mode from carb burning mode. Remember it takes a few weeks, and you have to do it gradually, but once you succeed to switch to fat burning mode, you will be easily able to fast for 18 hours and not feel hungry. Your cravings for sugar will magically disappear and it will be much easier to achieve your ideal weight.

The other “magical” benefit that occurs is that you will radically improve the beneficial bacteria in your gut. Why is this a good thing? Because supporting healthy gut bacteria, which actually outnumber your cells 10 to one—is one of the most important things you can do to improve your immune system so you won’t get sick, or get coughs, colds and flus. You will sleep better, have more energy, have increased mental clarity and concentrate better. Essentially every aspect of your health will improve.

Gillian said...

Since this is a post on gut flora... I have heard of the dangers of starches to gut flora. Yet, what about those who are extremly low weight? While much of the Paleo world is directed toward weight loss, there are a few of us who are looking to it as a hope for help from gut dybiosis and other illnesses that have caused us to lose weight. Thus, we are looking for healthy weight gain, recovery from malnourishment, and intestinal health (i.e, no yeast infections, bacterial overgrowth, etc.). We have all heard testimonies of colon-health recovery via the paleo-world.

Yet, for someone of extremely, extremely low body-weight, the low-carb can present a concern. Yet, there are certain aspects that make a lot of sense to go low-carb, ie., the reduction of inflammation, starches/sugars feeding infections, anti-body attack against starches/grains, etc.

My general question is—what would you suggest for healthy weight gain for those of us with extremely low body weight?

What is a good macronutrient ratio? I.e., I have heard a 50% fat, 30% carb, and 20% protein; or a 60-20-20 or a 40-30-30 respectively ratio. Is there one that is better to gain weight?

More specific questions that pertain to us all follow:
The paleo-world talks about the body being able to make all its glucose needs from fats and proteins. What about someone who has no body fat to lose? Will it all come from the fat consumption in the diet without endangering further loss of body fat or eating muscles? I.e., I have heard that 100g of glucose forming carbs will raise insulin sufficient to shut down ketone production --is ketone production bad or good for a person trying to gain weight? Or something that may potentially bring health to the intestinal system?

If one was trying to eliminate sugars that feed bacteria, yet ensure enough calories and weight gain, should “safe” starches be included (white potatoes, taro, yucca, sweet potatoes, squash, white rice)? Or should a greater number of sugary vegetables (beets, carrots, tomatoes, squash) be included? Is one type better than another then, i.e. if a carrot has glucose is it better than a glucose molecule from a starch?

Related, will a cup of salsa that has a lot of the sugary vegetables (onions and tomatoes) raise blood sugar just as much as one of the maligned starches, i.e., potato?

Is the sugar in beets better than starch to not feed unhealthy bacteria? The GAPS diet advocates the elimination of starch because they feed the bad bacteria--but would a non-ketogenic diet that has a lot of squash and beets and the "sugary" vegetables feed it just as much?

Depression and serotonin deficiency often accompanies a low body weight and malnutrition. I have heard concerns of low serotonin and cortisol levels on a low-carb diet (but it is not defined what "low" is). How grams of carbs, or ratio of calorie consumption, does one need to CREATE good serotonin and cortisol levels?

Thank you so much!

Dr. Art Ayers said...

Gaining weight is so easy for me, that your question is difficult. I think that it comes down to eating enough calories (appetite), uptake of digested food (gut health), health of gut flora and avoiding inflammation.

Since you don't mention diversity of gut flora, I get the impression that you missed the major point of the hippo article: You are sick because you are avoiding environmental bacteria required for your health.

You need to eat starch to easily gain weight, but you must avoid fructose and finely ground starch/wheat, which are toxic to most people. To lose weight, 20g starch per meal is max, so to gain weight you probably should target more than 50 g/meal.

I think that you are overthinking the whole process, by focusing on developing a universal answer. AlI you need is something that works for you. Approximately, 50-30-20 is OK, but not magic. Avoid vegetable oils and use butter, coconut and olive oils. Make it delicious with herbs and spices. Don't worry about saturated fats. They are your friends. The polyunsaturated fats are the problem.

It sounds like you are starting from scratch without gut bacteria. That means that you lack gut bacteria of two key types, those that produce in your gut the two halves of your immune system: aggressive and suppressive. The aggressive part attacks pathogens and the suppressive part prevents the aggressive part from attacking your body. You are trying to restart both halves without letting one half clobber the other and make you sick.

This makes you like a newborn lacking gut flora and an immune system. You need the equivalent of mother's milk, which permits development of the immune system by permitting the growth of only a few species of bacteria and killing all of the rest. Breast milk is a selective antibiotic and dairy products are the only dietary component that mimics. Unsweetened, live, whole fat yogurts contain some of the needed bacteria, probiotics, that can provide temporary development of the immune system. Note that bariatric surgery is followed by whey (a high concentration of the antibiotic proteins in milk) shakes.

Another quick fix before you rebuild your gut flora is to suppress inflammation by fixing your vitamin D deficiency (test serum levels, supplement and retest) and supplementing with omega-3 fish oil.

GAPS, when it works, is just a formalized version of guidelines in my Anti-Inflammatory Diet. The problem with GAPS is that it fails to provide a way to introduce new types of bacteria and avoid the contributing problem of excess hygiene. One good point of GAPS is that it avoids the problem of too much variety in fruits and vegetables. You need to let your gut flora adjust to the types of soluble fiber and phytochemicals (which are also anti-bacterial) you are providing. Variety kills gut flora.

Thanks for the hard questions. Feel free to follow up on my brief answers. Let me know how it works for you.

Anonymous said...

Hi, and thank you for the information that you freely provide.
I am writing to you because I am really desperate.
I am a 23 years old male, 177cm and around 60kg. I have really bad cystic acne since 4 years now. I didn't have when I was teen and “suddenly” around 19 I started getting big cysts on my face. I took lots of antibiotics and have done 2 rounds of accutane (6 months each). Acne was always coming back. Then I tried lots of diets: vegetarian, fruitarian, raw foodist. Nothing helped!
So for 3 months now follow the gut diet ( which I think agrees with what you support in your articles.
Although I follow it strictly I haven't seen any improvements, on the contrary I have 2 active cysts on my face.
I don't know what to do.
Here is my daily menu plan:
1) when I wake up take the daily recommended probiotic supplement (dr. mercola)
half hour later i drink my kefir (around 400-500ml) with 2 raw egg yolk (not always)

3-4 hours later I make a big salad (2-3 cucumbers, 3 lettuce's leaves, a medium-large carrot, avocado, parsley, lemon, dried oregano or basil, coriander (sometimes), 6 tablespoons of extra virgin olive oil.

3-4 times per week: 4-5 hours later I eat 300gr of meat (beef/lamb/chicken). If I eat less I eat also some beef's or chicken's liver. For cooking  I add parsley, mix and black dried pepper, celery, some Himalayan salt, garlic, lemon, oregano and some other herbs. + a small salad (4 tablespoons of virgin olive oil)
3-4 times per week: sardines in the oven. For cooking  I add parsley, mix and black dried pepper, celery, some Himalayan salt, garlic, lemon, oregano and ginger. + a small salad (4 tablespoons of virgin olive oil)

If  I am still hungry (which recently I am not, my appetite is less) I eat or an avocado or a small salad.

I eat daily sauerkraut and some cooked onions and garlic (for prebiotics)

I consume 99% organic foods

I wash my face only with water

I am experiencing serious digestive problems (since I never have had before...I started to experience little before starting this diet) and I have an abdominal pain on my right upper side, under the rib. Also, I have less appetite than before.

I do a workout at home 3 times per week (mostly squats, push up, dips, pull ups)

What I am doing wrong?
Is it the omega3-6 ratio? Is it the workout? The pepper (spices) that I use in cooking?
Is there anything else that could help? Any remedy: salt baths, aerobic exercise, water lemon in the morning, something to do with oral health?

I am sorry for this huge post, but I am really disappointed and that affects my psychology and my social life...
Thank you in advance,

Dr. Art Ayers said...


You can fix your problems, but it will take a little persistence and uncommon sense.

Your problem is chronic inflammation, gut dysbiosis and vitamin D deficiency. The cause is antibiotics (that killed your gut flora) and Accutane (that killed your skin stem cells).

Your diet is fine and should support healthy gut flora, but you are prevented from healing, because of a continuing vitamin D deficiency and not introducing any new gut flora. You missed the point of the hippo post.

Probiotics, e.g. lactobacilli from dairy, are TEMPORARY fixes for missing species of gut bacteria and they do not survive in adults. So, keep taking probiotics for their first aid capacity, but introduce the hundred of missing species of bacteria that are needed to digest the soluble fiber in your food and stop your digestive discomfort. You need a pound of gut bacteria (trillions of 200 species) to be healthy and you are trying to replace those with a couple of capsules containing billions of a half dozen species. You need to essentially eat dirt, but you need to avoid the rare parasites and pathogens. Dirt has thousand of different species of bacteria and some of those could replace those missing from your gut community. Read my other posts.

There are a couple of hundred articles on my blog and dozens are directly applicable to your health problems. I have already spent hundreds of hours to help you and you haven't spent more than minutes reading that help.

You can't repair your gut and still take antibiotics that kill your gut flora.

Vitamin D supplements and sunlight do not fix vitamin D deficiencies. Measure your serum level, supplement at high doses, and then measure again to make sure you have 60ng/ml. Most people under doctor's supervision for vitamin D deficiency remain vitamin D deficient. Check up on the doctors, because they frequently do not know what they are doing and they don't read and make sense of the biomedical literature.

Please do your homework and let me know how you are doing.

Anonymous said...

Thanks for the response.
You are right about the homework I should do. So, I will do it and I will post some questions that probably I will have...

For now, I am looking to find a test-lab to have my vitamin D levels checked. Also, search for a good vitamin d supplement.

I have to read more on dirt and fecal transplant. Although I have already some questions, I will do my homework before posting anything.

I really appreciate your help. Thanks again.

Anonymous said...

Hi again,
the last 2 days I read many of your articles including the comments.

As you told me in the previous comment, gut flora can't be restored with few species of bacteria that come from kefir, probiotic supplement and sauerkraut because a healthy one needs 100+ different species.
I am not sure if I understood the reason that I am vitamin D deficient ( Maybe because of this: quote from an article of yours: “People exposed to daily sunlight for hours in San Diego, for example, may still be deficient in vitamin D, if their production of vitamin D has been shut down by chronic inflammation.”)

As I understand I must introduce new bacterias from: coming in contract with healthy people and pets, eating a variety of minimally washed organic vegetables, eating dirt, doing a fecal transplant, not being obsessed with hygiene.

I have some questions on how I will do it:

I don't have a garden (I am also living abroad) and usually organic vegetables are washed. I will stop washing them (or should just wash them as little as possible?). Although, is this enough?

Eating dirt: how I can do this? Pick some soil and eat it? Put some in water? In an article you said that you don't suggest this because it can be containing parasites and pathogens. Is there any method to eliminate those parasites and pathogens, so you can eat the soil?

Contract with healthy people: Is there a method to help the procedure of getting some new bacteria? (I know that this sounds stupid, but I am really desperate). Also, you say that they have to be healthy. This is even more difficult but surely most of them are healthier than me.

About peeling the vegetables: I always peel them (cucumber, carrot). Should I stop?

Variety of vegetables: I suppose I should slowly introduce new vegetables to avoid big reactions. For example: raw garlic, raw onions, raw leeks, raw bell pepper, drill, (other herbs). Is it ok to start eating them, introducing one by one in my salads? What about mushrooms, is it ok to eat them? Raw or cooked? Is there any vegetable that I should avoid or pay attention? I understood that food allergies/intolerances depend on the presence or absence of the right bacteria in the gut, but may exist some vegetables that is better to be introduced after restoring the gut flora.

Probiotic supplement: I should buy another supplement that contains other species of bacteria than the one I have, and taking both? Or it will make no difference?
Different pickled vegetables have different species of bacteria? I will make some fermented carrot, broccoli and cauliflower.
I will try to get some water kefir and kombucha. Is gonna be too much or it's ok?

Vitamin D supplement: Is anything that I should consider before buying one?

Fats Omega 3-6 ratio: I read that the ratio matters and not the consumption. Although my consumption of omega 3 is high, the ratio is still very bad (1:9). Should I supplement?

Hygiene: I will use only water to wash my hands. I already don't use anything for my face, not even water. (Just wanted to experiment but I think it is not working since my acne is getting worse). I use a organic soap and shampoo in bath. Any other suggestions on this? When I must wash my hands using soap? (when touching raw meet for example? Going to toilet?)

about fecal transplant: It is really fascinating. I read in a comment about Tom Borody's protocol. But I didn't search it more, since it is impossible doing it now. Surely in the near future I will give it a shot, if I find a good donor...

Food combination for better digestion: I don't know If this is true. I read that every meal should have some raw food(veggies for example) and some protein.

I am planning to read all of your articles but since I am so desperate, I want to start making some changes as soon as possible.
So, I hope to excuse for any questions that you have already answered in other articles.

Thanks again,

Dr. Art Ayers said...

I only mentioned the excessive idea of eating soil to indicate how much work a person with antibiotic induced gut bacteria damage needs to do. Eating soil is impractical, and not recommended. Persistently eating live, fermented or raw non-sanitized vegetables are the best choices.

Cultures have not adjusted to the recent introduction of antibiotics, so there are not traditional or medical solutions to systematic destruction of gut flora. That is also why there are no medical solutions to lost gut flora in the form of constipation. Laxatives are cynical medical exploitation.

To benefit from fish oil omega-3 oils, you must eliminate the inflammatory omega-6 oils, i.e. vegetable oils. Get rid of all of your vegetable oils. Coconut, olive and palm oils, and butter are healthy mono-unsaturated/saturated fats.

Typical social customs increase the exchange of bacteria and that is one of the major reasons for picking a healthy mate and exchanging body fluids. That is also why everyone kisses babies and even pets.

I assumed that you were vitamin D deficient, because most people are deficient and chronic inflammation leads to vitamin D deficiency. I would expect that you would see improvement with 10,000 IU per day of D3, but you still need to get it measured and fixed under supervision.

Fecal transplants should be low tech, non-medical procedures, but they displace very expensive medical procedures that are very profitable. Medical procedures that disrupt gut flora should not be permitted without an effort to repair gut flora. Treating acne with antibiotics, without repairing the damage to gut flora is abusive and typically leads to more severe illness, e.g. autoimmune disease.

Food poisoning usually results from a person with a compromised immune system eating common bacteria. The problem is usually the susceptibility of the eater and not the need for greater hygiene. Most people do not become sick. It is usually the <1% who are already compromised by medical treatments, such as antibiotics or babies on formula.

You have lots of small changes to make. The biggest changes should come with vitD, omega-3s (start with 2g EPA/DHA per day and increase) and eliminating veg oils. Probiotics and new bacteria will take time. Read about soluble fiber to feed your new bacteria.

Let me know of your progress.

Unknown said...

Dear Dr. Ayers,

I've just discovered your interesting blog and have some questions for you.
I've recently been diagnosed with endometriosis and about 4 weeks ago had a laparoscopic surgery to remove a nodule in the pouch of Douglas that was giving me a lot of problems. Not only excruciating pain, but especially gastrointestinal disorders and a chronic rectal inflammation. In 2011 I was misdiagnosed with ulcerative proctitis, but last October another colonoscopy revealed that I've no IBD since my severe inflammation was related to intestinal endometriosis. Now I'm feeling much better but still have this inflammation and my gut is really suffering.
After the surgery they gave me antibiotics so that my already poor gut flora has been destroyed.
Because of my hormonal imbalance and oestrogen problems I must avoid meat, sugar, dairy products and gluten. I'm actually following a celiac-like diet and eating a lot of rice, fish, potatoes, corn and rice pasta, oats and oats milk but still cannot tolerate veggies and fruits. Only eat zucchini, carrots, sometimes squash and tomato and bananas. Broccoli and cabbage make me bloating too much.
I'd like to eat much more vegetables (especially raw) but I'm suffering from bloating and my intestines are still unable to work properly (I have no diarrhea but the final result is "little and often"). My doctor told me that my gut simply needs time to adjust and gain its normal function. I'm using probiotics and would like to re-start taking omega-3 fish oil.
Last Summer I started the SCD diet and felt a little better but was eating alot of meat that for me is FORBIDDEN.
I'd like to follow a low-carb diet but I'm really underweight and MUST gain weight, so at present I'm putting up with this diet and waiting for something to adjust.
Sorry for the long introduction, here are my questions:
1. What daily dosage do you recommend for omega-3 fish oil?
2. Do you think I can immediately start eating fermented food as sauerkraut etc?
3. Do you think I should completely avoid grains?
4. What about meat consumption?
The endo diet allows whole grains, 5 servings per day of veggies and fruits, fish and eggs. If I eat too much vegetables I immediately feel bad and my GI doctor (as usual) recommended a no-fiber diet. What is your opinion about that?
Sorry for all those questions but I'm living in Italy and here really few people follow low-carb, anti-inflammatory diets and the medical community is completely unaware of that.
Really hope you can help me, thanks in advance


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This comment has been removed by the author.
Thomas Guy said...

Dr. Ayers

May I first commend you on your very informative blog. To offer such insight into this relatively unknown field and help many people is truly laudable. Thank you.

I would be interested to hear your thoughts on Alopecia Areata and the gut microbiota. It is common that people lose a small amount of hair in patches, only for this to regrow within a year.

Through antibiotic use, stress and general dysbiosis hair loss occurs, but then the gut fixes itself, possibly by unconsciously repopulating bacteria from the environment, hair grows back. Does this sound plausible?

I developed Alopecia Universalis 10 years ago. I now have a thinner covering of whitish hairs on my head and body which indicates temporary regrowth.

My question is, following your comprehensive guidelines into repopulating gut flora, are there any vitamins and minerals that are key for hair growth that I should be supplementing, or is the anti-inflammatory guidelines provided enough to reverse my alopecia. I believe biotin and the B-complexes are important.

Since taking only 1,000 UI D3 regularly for the last year I have not had a single cold. I'm thinking about increasing this amount.

Thank you again Dr. Ayers. Your thoughts are invaluable.


Hunterheatandair said...

The involvement of gut bacteria in immune system function is documented in the biomedical literature.
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Anonymous said...

The root issue is believing that because a product is marketed as "good for you" does not mean it's healthy for your body. These are usually FDA approved foods on the market to get you to buy more of it.

The problem with most advertised probiotics is it's laced with sugar, so the right type of fermented probiotics that contains no sugar is necessary for the gut to balance it's level of bacteria.

Here's the catch the issue is not the consumption of a the right bacteria but to cleanse the colon prior changing the long-term daily diet so that the probiotics will work.

Humans are carnivores and omnivores, not a one is better than the other for you. Therefore, solo carnivores or solo omnivores is not healthy for any human.

The other issue is believing that organic foods: hunting and farming foods is always bad or always good. The truth is in the quality not a quantity. The better the quality meats, fish, earth grown produce the better nutrients your body absorbs.

Problem with allergic food reactions, obesity and healthy athletes dying of heart-attacks is a imbalance in the gut and mitochondria (part of our DNA). When we consume too much of one type of food, such as food with high glycemic load, then our gut and brain start to de-evolve and our bodies stop rejuvenating cell growth (we change our DNA). We become sick, skinny or fat!

Things to think about when it comes to the part of the planet you live on and it's natural resources for food. Your gut needs a balance with nature.

If you are born and raised in Alaska do banana's grow there?

What are your regions natural food source?

When are those foods in your region in season?

Do you eat like your regions ancestors?

Do you know what grows wild and will grow in your part of the planet?

Your health is more complicated than "just eat this". You need to think about your soil, your water source, the foods that grow in your region, your environment (city, country, suburb).

Anonymous said...

With regard to alopecia, you must eliminate all grains from your diet. If you follow Dr. Ayers guidelines your hair will grow back. I had serious alopecia areata for 10 years until I eliminated gluten from my diet. The nearest to how I eat is best described at I stress again you have to totally eliminate grains from your diet. Watch this video: The comment about the nun drives the point home. It took 3 years of being gluten free before my alopecia cleared up. With your universalis it may be even longer... Best wishes, Bill.

Thomas Guy said...

Thank you Bill, I am trying to eat an anti-inflammatory diet so will cut down on grains.

I suppose my question to D. Ayers was whether he thought Alopecia Areata, a very common autoimmune disease, is related and controlled by gut bacteria?

I believe for hair loss to occur an immune response initiates ULBP3 up-regulation and the resulting NKG2D activity target the hair follicle for attack by T cells. The question of whether this is triggered by dysbiosis of some kind is very interesting.


Anonymous said...

I absolutely believe you have to eliminate all grains to recover from alopecia, not just reduce.
I am not prepared to have a binge on bread for a week and 2 or 3 months later have bald patches.
It's worked for me and I've just accepted that bread and grains are in the past for me now.
I just hope that it works out for you.
In 3 years time when hopefully you have a full head of hair, you'll have to come back here and post.
Sincere best wishes with your success.

Dr. Art Ayers said...

Hi Bill,
Glad that you are still watching my blog. It gives me a lot of pleasure to know that I helped you.

I think that alopecia may be one of several auto immune diseases that derive from gluten intolerance. Others are Hashimoto's thyroiditis, Grave's, and Sjogren's. The gluten intolerance exaggerate antigen presentation, because the heparan sulfate circulation system is messed up by the polyglutamin eps in gluten. This explains why all of the autoantigens contain a basic amino acid triplet. One of those triplets is also present in the auto antigen of alopecia, trichohyalin.

All of these autoimmune diseases can be cured by eliminating grains to avoid gluten, and by repairing the gut flora, I.e. Clostridium spp. that are needed for normal function of the suppressive part of the immune system.

So, Thomas, Bill is correct in eliminating grains, but he also repaired his gut flora and without eating bacteria to permit repair, the autoimmune diseases will persist.

Kay Dee said...

" The gluten intolerance exaggerate antigen presentation, because the heparan sulfate circulation system is messed up by the polyglutamin eps in gluten."

This happens independently from HLA DQ2/8 !!??

Thank so much d.Ayers

Dr. Art Ayers said...

Kay Dee,
When I say "antigen presentation," I include antigen internalization, clipping into peptides, binding HLAs and display of antigen peptides in HLA troughs on the presenting cell surface. The HLAs of different types only prejudice the selection of displayed peptides. Note that the HLAs that are a problem for celiac have heparin binding domains in the alpha helices adjacent to the displayed peptide. This suggests that heparin binding is also important for the complementary T-cell receptors involved in mediating celiac.

Kay Dee said...

I catch the sense but it’s difficult to me…
Can we summarize this way?
1. Gluten polyglutamine epitopes (all, I’ve read they are more than 30, is it true? )
2. Glutamines – (tTG) > glutamic acids
3. Inflammation > heparan sulfate circulation
system overload
4. Antigen presentation/internalization up regulation
5. (Auto) antibodies production – Not Only anti-tTG (HLA-DQ2/8) !!! – even anti-TPO (Also Not HLA-DQ2/8) !!!

Thomas Guy said...

Dr. Ayres and Bill, thank you for your thoughts on Alopecia and gluten, I hadn't realised there was a direct link.

If I could ask one final question with regard to gluten grains. There is some confusion about which grains don't contain gluten. I believe it is ok to eat;

Rice (white and brown)
Oats? - I have porridge every morning

Would a gluten intolerance test at the doctors be accurate? As you've outlined in previous posts Dr. Ayres, would following your guidelines to replace gut flora help Clostridium spp directly, or are there other methods to fix this?

Thank you again.


jelqing said...

What do you think about medically induced flora disturbance?
Developing countries are using antibiotics like hell.

Anonymous said...

Third world countries "aspire" to our wonderful western medical system. I have not had antibiotics for 7 years. The last time was when I had a deep wound from a dog bite. In retrospect I should have refrained, unless the wound became infected. My healthy gut bacteria is so important. To compromise that, it would have to be a serious infection/illness where I had no alternative. Antibiotics are handed out too freely, especially at this time of year when low vitamin D levels and compromised immune systems are endemic. It's a pipe dream, but if health care concentrated on creating strong immune systems by optimizing vitamin D levels and having healthy gut bacteria it would be far more beneficial. As Doctor Ayers says: HEALTH IS VERY CHEAP AND READILY AVAILABLE, BUT IT IS NOT COMMERCIALLY AS VIABLE AS ILLNESS.

TonyD said...

I've been trying to figure out how to get more fermented probiotics into my diet. Then I read about how root beer used to be medicinal (that's why we associated a soda bar with old pharmacies - sodas were used to administer herbs and spices!). So I've started making my own homemade root beer from scratch with a fermentation process (as opposed to the forced carbonation used by modern manufacturers). I use this recipe:

And there is the added benefit of improving the water quality, too. I read a New York Times article about all the thousands of chemicals that have been observed in water but are not tested-for. So going back to drinking boiled and fermented beverages may be a good thing.

Unknown said...

Thank you for the excellent post, Dr Ayers.

I started adjusting my diet in November 2012 to combat persistant acne (on and off for about 7 years), which I also did a round of Tetracylcine for in 2011 (bad idea :p).

My diet is essentially the Primal Diet found on Mark's Daily Apple (but without fruits and nuts, all carbohydrates I eat are bascially vegetables). I also drink Kefir and eat home made Sauerkraut to repopulate my gut flora.

In addition to this, I take about 50 billion CFUs of probiotic supplements twice daily, along with drinking fermented milk with added probiotic bacterial strains (including LGG) - while taking three tablespoons of inulin along with these supplements. I also take 1 tbsp of Norwegian Tran (cod liver oil) to get enough omega 3-fatty acids.

While I'm seeing great progress, your post about the probiotic bacterial strains only being temporary fixes sort of scared me, and I was wondering if there was something else I might start doing to ensure I do not suffer from an acne relapse once I stop the (rather excessive) probiotic supplementation? (I've already decided that I should start taking 10,000 IU of Vitamin D3 daily as per your diet suggestion)

Thank you ver much :-)

Sincerely, Nicolay

BigWhiskey said...

Say, Doc, looks like the "Gut Flora Repair" idea got a write-up.

Anonymous said...

This is starting to make sense for me then... when I'm in the States (from there) I had issues losing weight. But each time I moved to South America for an extended period of time, 4-6 mos, I lost weight, I mean it fell off, no change except diet - as it was just different food. But now, I've lived in SA for 2 years and after being here for 8 mos, the weight stopped falling and started coming back. Would gut flora be partially related to this?

Anonymous said...

Start juicing! Cut out sugars, caffeine, and processed junk. Watch fat, sick and nearly dead. Your life will turn around completely. With low thyroid, you are likely to be low in iodine! If you have a facebook site, look up juicing vegetables, it's by Drew Canole. You can join his methods and join jui ing animals for a monthly subscription if you want. Peoe in this group are very supportive, they are getting over their health issues and starting to li e life again to the fullest. Your body craves nutrition, both micro nutrients and macro nutrients. The micro nutrients will come from home juicing organic produce. Don't give up! Juicing will give you a new lease on life. I have been sick for over 20 years, started juicing in February. My life has changed completely.

Anonymous said...

You could use some omega fats and amino acids in your diet!

Anonymous said...

Start juicing! Test your stomach acid! Balance your ph in your body, and your gut flora.

Anonymous said...

Start juicing. It stopped my 20 year long fibromyalgia!

Anonymous said...

Dr. Ayers, Here is a recent unhealthy "health tip" from Dr. Oz.

Dr Oz recently recommended consuming two tablespoons of pumpkin seed oil a day (as best I recall).

Pumpkin seed oil is roughly 50% linoleic acid (LA). Two tablespoons of pumpkin seed oil therefore contains about 135 calories as LA, or almost 7% of a 2000 calorie diet. Excessive intake of LA is a major cause of fatty liver, among other things.

You commented above that people should get rid of all vegetable oils. Pumpkin seed oils is about as bad as any of the vegetable oils.

Anonymous said...

Hello Doc.

Why not add good bacteria by swallowing 'healthy' bacteria (poop) placed into enteric coated capsules?

Art, do you see any problem with that, in theory?

Thanks, Ramsay

Anonymous said...

I have been put on antibotics at least three times a year for as long as I can remember due to health problems.
Last time I was advised to load up on probiotics by my pharmacist and doctor. Since I had recently had to take florastar for a week and then large doses of priobotics to maintain my flora level after.
Once again I find myself with the same symptoms (actually more acute) and was wondering why this keeps occurring.
I will heed your advice and try to load up on good bacteria. Ofcourse I can't due the not washing my hands after doing number two..that is just too gross for me.
I appreciate your blog for shedding light on something that my gastro doctor and other specialist seemed to be oblivious too. I will follow up with them and mention your take on this seemingly chronic condition.

Anonymous said...

Just read another suggestion about starting juicing. I have been doing this for the last few months and that is when my problems began, perhaps it is best to eat the veggies and fruit in their natural state rather than to smush them into liquid form. Just like our bodies create gases, perhaps whole veggies have qualities that are released when smushed, cooked or excessively chopped up that our bodies need to maintain a balance. I think I will try eating whole foods, whole and see if that helps...can't hurt.

Cathy said...


I've had a long history of gluten intolerance, along with nutritional deficiencies, eczema and keratosis pilaris and possible other food intolerances from leaky gut, possible parasite infection, toxic overload.
So if i were to exclude gluten and correct my gut flora (with a fecal transplant) would i be cured? Without the need for l-glutamine and other gut healing supplements? But following a healthy diet ofcourse with fermented foods, bone broth, coconut oil etc.
An answer would be much appreciated!

Dr. Art Ayers said...

Yes, it is as simple as eating a diet consistent with the diet used by your fecal transplant donor. All of the rest of your symptoms will be reversed and your gut will quickly heal. All it takes for most aspects of health is a reasonable diet of unprocessed foods, such as I have outlined in my Anti-Inflammatory Diet (meat, fish, eggs, vegetables), combined with an adapted gut flora. That simple combination will gradually eliminate most autoimmune diseases and diet-based chronic inflammation. Most genetic contributions to diseases and environmental toxins are of minor importance (in the absence of chronic inflammation) and are neutralized by a healthy diet/gut flora.

Anonymous said...

Hi Dr. Art. Ayer, I read your blogs very much. My son who is turning 9 soon has been diagnosed with juvenile dermatomyositis since 2010. It's nearly 3 years now. He is not responding to any immuno suppression medications. 3 months ago, his inflammation marker(ck) went up to 16000. After that I started gluten free and white sugar and Processed food free and partially dairy free diet on him. His ck level started to fall.I have a major cconcern. Because he is a born vegetarian , will any of these diets will make him to be a mulnutriant person. Could you please help me to make my son better soon. Thanks. Mathi from Australia.

elena said...

Hello DR. Art Ayers,
Great comprehensive article and solid advise. Thank you for summarizing and sharing this!
In my case, as well as some clients I work with fermented products are not an option, as well as dairy. So I am relying on other ways you mention on restoring and balancing my healthy gut bacteria. As far as probiotics - don't you have to take the right kind for your particular gut? Do you think just a general probiotic is sufficient?
Thank you, Elena

John said...

Hello Dr. Ayers,

Thanks a lot for the informative blog, I appreciate your efforts.

I'm suffering from alopecia areata and hashimotos for few years now.

I would appreciate if you could answer my query related to gut dysbiosis. If because of antibiotics use the gut was cleared of both good and bad bacteria and over a period of time the bad bacteria grew in much larger number taking most of the gut space. Does adding good bacteria through vegan diet, probiotics etc will help ?

Should we use antibiotics again purposely to clear all from gut and then immediately start taking good bacteria to create better equilibrium ?

Would really appreciate your response..


Anonymous said...

Going gluten free and following an anti inflammatory diet seems to have cured my alopecia areata, and osteo arthritis issues too. If you are vegan I don't see where you'll get your protein from. I eliminated legumes too. I hope the good doctor will input here. Best wishes.

John said...

@Bill, Thanks a lot for info.
Please could you tell me if you took any specific multi vitamins & minerals, probiotics and some specifics about your diet. Thanks

Anonymous said...

Paleo has helped my Crohn's diseased son gain 17 lbs in 2 months and reduced his Calprotectin from 1250 to FORTY-EIGHT in the same period. Normal for him is between 2500 and 3000!!!

Victor Venema said...

Could a reduction in stomach acid be an adaptive reaction to a lack of microbial biodiversity?

Dr. Art Ayers said...

I can't think of a mechanism for dysbiosis to reduce stomach acid. Low stomach acid most typically results from H. pylori infection.

Victor Venema said...

Me neither. :-)

That a bacterium is involved does not rule out an adaptive mechanism.

H. pylori is present in half of the population but normally not symptomatic (or even beneficial).

Thus there could be a reason why the body lets H. pylori off the leash or at least modulates its activity. The reaction could then be too strong nowadays.

There is a similar theory about Omega 3 and 6 fatty acids.

Anonymous said...

Dr. Ayers,

Can you please comment briefly on "diet diversity" in a whole-foods (vs. SAD) diet? Do you feel it's better to eat a wide variety of vegetables or a smaller variety?

You mentioned that you think that our diverse diet leads to bacterial "generalists," but I read many articles encouraging us to eat as many different vegetables as possible to encourage bacterial diversity. Thank you.

Dr. Art Ayers said...

I think that expecting a diverse gut flora from eating a large variety of vegetables is nonsense and is inconsistent with all observations. The rationale comes from assuming that humans need a complex array of vitamins, mineral and nutrients that can only be found in a wide variety of plants. Observation of diverse cultures show just the opposite; humans only need basic nutrients, with all vitamins supplied by gut flora and all micronutrients supplied by most plants. The problem is usually getting enough calories and/or damaged gut flora. Antibiotics, processed foods and hygiene can dramatically increase requirements.

Thanks for your comments.

Anonymous said...

Thanks for your answer. It makes sense on a lot of levels.

Anonymous said...

dirt has been a Chinese folk remedy for traveller's indigestion.

(just carry a small bag of your hometown soil when you travel. & sprinkle a little on food)

makes sense,

Helen Phillips said...

I took a trial protease inhibitor for 6 months as part of treatment for hepatitis c. As the treatment progressed the food intolerances got worse until all I could digest was meat, eggs and a few root veg. Because of the hep c I was already glucose intolerant and now sugars/carbs seem to cause autoreactive hypoglycaemia fairly quickly. I dont know how to repopulate my gut bacteria because nearly everything suggested causes severe diarrhoea - fermented food seems to be out because of the sugar content but I havent tried it yet. Do you have any suggestions - I am happy not to eat sugar but a tomato or some broccoli occasionally would be nice.....
Many thanks

Unknown said...


I am a new poster in need of serious help with my non functioning stomach and bowels. I have scleroderma which I took 12 years of antibiotics for:( 12 months ago, I had my gallbladder removed because it was only functioning at 6%. Since that time I have barely been able to eat because of extreme pain (inflammation) in my stomach (possibly due to bile reflux (GERD) and low stomach acid) and slow moving inflamed bowels. I have always ate a strict diet and I have been on the GAPS diet. My problem is my low weight. I weigh about 95 lbs. My usual weight was around 110. I cannot seem to gain weight. I have become very lactose intolerant and I also have a difficult time with oils and fats. Cannot do hydrochloric acid because of my GERD problem. Refuse to take PPI’s so I have been treating the inflammation with slippery elm. Hard to take liquid probiotics because it seems to burn the stomach.

My diet at the moment consists of poached eggs, oats, coconut and a wee bit of coconut oil, brown rice, cooked vegetables (I avoid nightshades except a potato here and there) yams, sprouts, avocados, apples, beets (cooked), tiny scrapping of almond butter. Legumes are out and the only thing raw I can really tolerate is an apple and avocados. Coconut yogurt is about all I can stomach. Eventhough I eat this strict diet and take probiotics, I am still suffering with terrible GERD and stomach inflammation. I have rotated my probiotics continually because a Dr I have has told me that it is necessary. I have been tested for h-pylori, C difficle, Celiac etc.... Medical experts cannot find anything wrong. I am getting hydrogen peroxide IV’s and I get a B12 shot in the IV at that time. However the Vit B levels on the last blood test were a bit high.

My pancreas did have two cysts on it prior to the gallbladder surgery, they are now gone. Seems my gut is a mess and I have had little success in even getting a bit better no matter how strict I am. Fecal implant? Would that still be an option even though I do not have C Difficle? Dr. Ayers, you stated in one of your posts that the person should practically eat 'dirt.' Not sure what you meant by that. I am outside quite a bit because I have a horse. I am so desperate for some advice and cannot seem to break the vicious cycle my body has been in. What would your suggestions be or if someone else has been through something like this what could you recommend?

Thank you, Suzanne

Bris said...

Eating fermented foods will NOT change the gut bacteria. You can only change to a healthier gut microbiota by PERMANENTLY altering your diet to a low fat/high fibre plant-based diet.

Dale Almond said...

I have a question about the "hygiene hypothesis". I believe Dr. Ayers is absolutely correct that we need bacteria in our guts that we were historically exposed to. However, I don't see anybody distinguishing between these "healthy"soil bacteria and the pathogens that abound. How does one protect oneself from norovirus, salmonella, c. difficil, etc. yet at the same time maintain exposure to the kinds we need? Norovirus nearly killed me.....

vonsachsen said...

Dear Dr Art Ayers, I recently came across a product that is called Prescript assist see link for ingredients( ) and since you were writing about how good microbes from soil would be if we could control them, I was thinking of trying out these. I appreciate your opinion very much, so I wonder what you would think about trying these? Thanks in advance!

El Librero said...

Anonymous said...

Dear Dr. Ayers,

I eat healthy, recently aligned almost completely with your anti-inflammatory diet.

I was on anti-biotics 2 months ago, I believe my problem is not from that rather from the changes in my lifestyle and diet.

Only difference is I drink a LOT of fresh turmeric juice daily.

I eat a lot of vegetables, raw and cooked, raw fruit, a lot of smoothies, tempeh, little meat, very little dairy, super foods (chia, maca, greens/chlorella). limited fats, coconut oil, butter, the ultimate diet many would say.

Since I increased my fiber and the turmeric juice, exercise, skin brushing, water intake, and all the other healthy stuff I am doing I have started having dry hard stools that cause a lot of pain. (since 3 weeks) however, 90% of mornings I can usually empty/or partially empty my bowels.

I am completely frustrated!!! I do not know if my digestive system needs to fast (risk being worse constipation)) lol.....

or what I need/can do. Please suggest, recommend, would a 1 to 3 day fast (either water or juice) perhaps be recommended..?

what do you suggest please doctor?

thanks kindly, brenda

Jackie Patti said...

I just want to clarify - GAPs does address repopulating bacteria. Fermented vegetables are required on all phases, even stage 1 of introduction requires at LEAST sauerkraut juice added to the bowl of soup. As it goes on, fermented veggies are like broth, required at each meal. If and when dairy is added, it starts with ghee and moves on to yogurt, kefir, sour cream, etc. The book even includes recipes for fermented fish which she includes from an early stage (luckily not RQUIRED else I'd have never tried GAPS). All of this is on top of the recommended probiotics. It'd be difficult to do GAPS as written and NOT repopulate the buggers.

yogurt said...

I would like to say I've suffered from Lyme since 1990 and was previously very active. I went to Mayo Clinic in 1991 and they missed it respectfully, but then began the regime of claphorin and rocephen intravenously.

Mayo stated my top priority was to gain weight at 90 lbs and 5'7 female. Now I'm same height and 185lbs with no change other than antibiotics. I still try and run even though I'm exhausted.

I would like to share this with you, because many Lyme Disease patients not only feel that antibiotics cause this, but inflammation of the pituitary, thyroid and adrenals cause the fluctuation. Is that a possibility as well? Not one doctor has done any kind of investigative work other than saying thyroids are low, but no one will check pituitary. Full body infection?

Anonymous said...

For many years, I have been saying that MANY of our current disease (many of which *oddly* enough have gut inflammation involved) have a primary point of weakness when the gut flora breaks down.

Many people seem to confuse cause and effect here. They speak out against gluten (grains), without knowing that a *healthy* gut can regrow its lining in 3 days. The villi and micro-villi of the small intestine are constantly being damaged (and then regrowing) as a part of normal digestion. This isn't a problem unless something is WRONG enough that your gut can no longer heal as fast as it breaks down.

- think about this....can you imagine Roman Centurions taking over that much land with all of them suffering from IBS, Chrones, FMS/CFS? What about over 10,00 years of history in which earths empires were ALL based on grain agriculture? How could the Assyrians, Phoneticians, Persians, Babylonians, Romans (and on until you hit the BRAND NEW era of IBS)...manged to have EMPIRES with every single soldier in intestinal agony?

Rome was built on "Free bread and circuses" and yes I know that their bread was predigested (like a sour dough), however the Roman gladiators had diets high in legumes and GRAINS (barley), and I doubt they would have made good combat blood-sport if they all suffered from extreme gluten intolerance.

- next - think about the worries about antibacterial soaps.

Much of our current ones use Triclosan - (and other things very much like it) and Triclosan is a biocide that kills healthy gut bacteria. Skin is not a barrier. Every time people wash their hands or dishes with that stuff...they kill off VITAL gut flora. Every time you use a 'wipe' your hands and a phone at the office...

Now think back to the news...just a few years ago...

About a decade (or more) ago there was serious concern over antibacterial soaps on the basis they might not be biocidal, and using the stuff might just create resistant strains of bad bacteria (which we do not need more of). A part of this discussion involved mentioning that some (many at the time) of these soaps used PESTICIDES to kill bacteria (so it can/does kill gut flora).

Also recently (I just read a paper about this last month) the role of environmental exposure to pesticides (in all of our air, water, and non-organic food) has come up in publications...with proof that pesticides damage the villi (which we need in order to take in nutrition).

Until VERY RECENTLY in human history, all food was organic. Today it is drenched repeatedly in sprays (many of which started life in DARPA research grants for chemical weapons). A standard conventional crop is sprayed several times with different chemicals at different stages of growth. The sprays wind up ON and INSIDE of the plants... and then we eat it....and it damages our villi, and kills gut bacteria.

People's lawns, parks (city grounds), lawns in front of businesses... all of them are sprayed...and again - our skin is NOT a barrier to this stuff, and we breath it in as well.

GLUTEN and grains are not the great evil of ill health. The inability to digest gluten and dairy is an EFFECT not a CAUSE.

Anonymous said...

More on Triclosan

Much of the news is quite alarming. As with some other supposed "biocides", Triclosan is actually a pesticide (and legally registered as such). It is also NOT just limited to items LABELED as anti-bacterial, or even to soaps. Triclosan is also in plastics, including kids toys & high chairs (children are very vulnerable to pesticide damage). It is in the plastic cutting boards in people's kitchens and their dish soap.

Triclosan attacks bacteria indiscriminately - including our gut flora. IT is inside of us even if we don't use it. It breaks down into dioxins. It is in such WIDE use that we cannot get away from it.

It is found in the breast milk of women who NEVER knowingly use items containing it, and in our waterways, sediments, etc.

These soaps are in massive use now, and WITHOUT a good advertisers used fear campaigns to get higher sales. Meanwhile in the science based world, testing of various possible cleaning methods (done in hospital environments) has shown that old fashioned soap and water does a better job at killing the DANGEROUS bacteria that that junk does - even in killing off Golden Staph.

As a result of all those fear based advertising campaigns, people now assume that the bacteria that surrounds us is terribly dangerous when this is not the case. Very little of the bacteria around us causes diseases, and much of it is helpful to us. Most of us don;t know that our bodies have far fewer human cells in them that they do other non-human cells (like those bacteria we have been told to fear).

For every human cell we have in our bodies, we have roughly 9 non-human cells living within us.

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Unknown said...

Dear Dr. Ayers:

This is a very long comments section, and I am sorry for adding 1 more question. I have been following your suggestion for 1 month and have already lost 6 lbs.

Question - Can you provide more clarification on what qualifies as a fermented food? Are there any broad guides on the types of gut flora found on different kinds of fermented foods? Vegetables, root vegetables, fish/anchovies, soybean paste, olive/pickles, beer; pickled/fermented with salt, with red hot peppers, fish oils or lard, garlic/ginger, etc. Are most pickled and otherwise prepared foods that are supposed to last several days without refrigeration considered fermented, or do the item needs to be buried/aged for 6+ months to be fermented? I searched for all "fermented" key words in your blog, but I am still confused. Perhaps if I explain that I went back to the traditional Korean food diet, which seems to have hundreds of different fermented or pickled foods, my question might make more sense.

Thank you so much! Even if you don't have time to reply to this question, I have benefited a lot from your blog. Thank you for sharing your knowledge. Jennifer

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Anonymous said...

I read some of your other posts and they were informative... but then linked to this article which references "Dr."Oz.. I mean... seriously? It's like if huffpo decided to use fox news as their source for something.

Nate said...

So how do I heal my gut flora?. I have been going around in circles for years now but it is too difficult to put all this info together yourself when your brain is already not functioning optimally because of poor gut flora and functioning. Can you recommend anyone that I can speak with and consult with about gut and gut flora repair?. Can someone get in contact with me?

Anonymous said...

Nate or anyone else who is needing some gut help, Of course everyone's bodies are different and respond differently to interventions, but I have heard of countless people experiencing relief from symptoms caused by their bad gut flora by using some natural supplements offered by a company I work with. I currently use them myself and am seeing some good results. They offer a probiotic and a cleansing supplement that are both all-natural, safe, plant-based and are designed to kill bad flora AND replace it with the good kind, which a lot of probiotics don't do. It's amazing how gut health impacts SO many areas of our overall wellness, sometimes in ways we would have never even thought! If you are interested to know more, I can send you all kinds of information! Hope you find the relief you are looking for and if I can be of help to you, let me know. You can email me at

Anonymous said...

had a course of antibiotics that led to constant loose bowels,gut floral damage,using probiotics now for the last four months now with no long does it take to repaire gut flora..did stool tests for blood and mucus that all came back normal.kindly advice

Anonymous said...

Dear Dr Ayers and all the other caring, sharing and helpful writers on this blog. Thank you so very much. After years of digestive problems, food intolerances and extreme food allergies, I am now on the mend. I have spent days reading all the advice and comments under many of the posted topics.
Personal message to Dr Ayers - Please clone yourself ;-) so we can continue on improved health from your brilliant information. Kindly, Mrs. Anonymous

Donna said...

Probiotics are a great source to aid in digestion. However, they will not cure gut flora that has been severely damaged. Patients with Clostridium difficile take courses of antibiotics to be rid of them. In increasing number of cases, they do not work, so patients turn to probiotics which might give some relief. The stool transplants have the greatest recovery rate. The process requires strict guidelines that donors must meet, just like donating blood. Similar flora from the host and donor have to match. Patients gladly turn to this method after months of deadly diarrhea. Stool transplants can potentially be solution for any long-term antibiotic use that causes inflammation in the gut.

Dr. Art Ayers said...

Just a quick note on stool transplants. People with healthy gut bacteria have relatives who share the same healthy bacteria, so those relatives are a good donors of stool transplants if someone in the family has to take antibiotics. Similarly, people with gut dysbiosis, e.g. autoimmunity, constipation, obesity, food intolerances, should avoid stool transplants from relatives, since they probably share problems with their gut microbiota. Health is contagious, via gut flora, but so is sickness.

The strict guidelines for stool transplants are designed to limit the use of these transplants, in order to preserve the use of more expensive medical procedures and pharmaceuticals. Ostensibly, the guidelines reduce the spread of pathogens.

There is no need to match flora between donor and recipient. I think that it would be better to have differences. The point is to have gut microbiota that are adapted to whatever diet is eaten. Healthy people tend to have gut microbiota that adapt more readily. Sick people are likely to lack some essential bacteria and are less likely to adapt without additional bacteria from their environment. Hygiene limits sources of needed new bacteria and keeps people sick.

Anonymous said...

Dr. Ayers --

I have just discovered your blog, and thank you for sharing your knowledge.

In general, there is a great deal of information to digest and I am trying to understand and learn as much as I can about repairing gut health after taking antibiotics for 6 months, in fact, around the time you wrote this post, and the subsequent problems I have experienced.

Regarding your view on fermented foods versus probiotics... as you share, I understand that most probiotics cannot recolonize, however, does this hold true for probiotics in spore form? Would a spore form of probiotic assist in recolonization in addition to fermented foods?

Many thanks for your incredible contribution to these issues.

Dr. Art Ayers said...

Commercial probiotics are marketed because they are readily available for some other commercial application, not because they are particularly adapted for growth in the human gut. Most do not remain in the gut and pass on through. They won't become part of the gut flora. The spore formers are no different. They may have some temporary benefit, as will fermenting probiotics.

The hundreds of species of bacteria in a healthy gut come from exposure to dirty surfaces, people, pets, fresh raw vegetables, etc. Thus, hygiene and antibacterial soaps are the biggest threat to health in overly clean modern life. We don't have cultural mechanisms to provide for adequate exposure to fresh sources of environmental bacteria, and still avoid pathogens. Antibiotics are a modern health risk not encountered by our perpetually dirty ancestors.

Anonymous said...

Thanks, Dr. Ayers. I sincerely appreciate the additional insight and response.

In addition to your blog, do you know of any reliable sources I can trust/use to be best inform myself about repopulating gut flora? Especially regarding stool transplants?

Henderina said...

Dr. Ayers, I am learning a lot from your blog. Thank you! But I am surprised about your statement about the GAPS diet: "The problem with GAPS is that it fails to provide a way to introduce new types of bacteria and avoid the contributing problem of excess hygiene."

The core goal of the GAPS diet is to restore the gut flora. Fermented foods like fermented vegetables are a cornerstone. Dr. Natasha advices you to eat raw organic vegetables every day if your gut can handle them. She also encourages you to take a pet, be outdoors as much as possible, not to clean to much (water is in most cases sufficient) and to swim in clean natural waters. She is only maybe a bit on the cautious side when it comes to starches and fibres.

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Unknown said...

Here is my biggest dilemma Dr.Art. In order to repair gut microbiota I need to eat more fiber which I knew from nutrition courses I have taken but I have a SIBO and it seems like a dead end. Double bind so to speak. Would you be kind enough to point me in the right direction. I feel that I can't get back my healthy gut if I stay on a SIBO diet, which is essentially a low fiber diet.

Thank you so much for all the work you put into healing people.


Alison said...

Hi Dr Ayers
In a number of your posts you write about the benefits of fresh vegetables from the garden. Preferably with some traces of dirt. What about fresh fruit from the garden? We have a fantastic apple tree (organically grown). Are there bacteria on the skin of the apples? Are windfall apples better because they may pick up some dirt/dirt borne bacteria?. Does the overdose of fructose we presumably get while eating these apples for a couple of months outweigh the benefits? I'm assuming since traditional cider relies on naturally occurring bacteria there must be some on the skin.

Nikki said...

Hello I just passed your blog and was qondering if you can help me. November 2015 I was on three rounds of antibiotics after I came off I have this strong body odor that follows me everywhere upset stomach and when I eat my stomach always hurts for couple months I had loose stools. I went to a naturopath doctor she told me to take probiotics and something for digestion which I did and chlorophyll for body odor.The stomach pain subsided somewhat and then I developed constipation but the body odor never left. Can you please help me I'm 24 years old and this is ruinning my life My odor takes up a whole office and sometimes have to miss work for the pain and odor

Unknown said...

Hi, I'm going on 30 years old. After a few years of being exposed to black mold (unknowingly) I have become very sick. I was a natural perfumer, so I worked with natural essential oils, absolutes, resins, etc pretty much on a daily basis. Inhaling them, and putting them on my skin to test out my fragrances. Not only that, but I was painting the inside of my new home. After I year I started getting earaches that turned into an ear infection, so I was prescribed antibiotics. A few months later I had a sinus infection.. back on the antibiotics. And finally.. a respiratory infection, antibiotics again. I then started to get vertigo, post nasal drip, and noticed I had problems eating certain foods: grains, corn, anything from a box, bag or can. I've never had any issues with any foods. I then became pregnant, but miscarried at 8 weeks. Doctors could not tell me why. I was very sick during my pregnancy still, with vertigo, earaches coming and going and food sensitivities. I had to get a D&C, and they had me take antibiotics after the surgery. Months later I had to get my wisdom teeth removed, they were causing pain due to being impacted. I did not receive antibiotics, but I took medicine for the pain. Almost 3 years later (and thinking my body was just giving up) I became desperate and looked up my symptoms online since all doctors kept giving me was nasal spray and said I had "seasonal allergies" which I'd never had in my life. I also became very depression, angered easily and my anxiety was through the roof. I could not sleep easy either. So I became desperate and looked up my symptoms online, mold kept coming up. I then got strep throat, which again took antibiotics for. A month later I found the mold in my home.. no smell, no visible signs because it was inside the wall. We cleaned the mold, not aware it would harm us and my tonsils got inflamed. I noticed a white patch on my tonsil. Went to an ENT, told them about mold etc. They looked at me like I was crazy and said I had tonsil stones, they were common. Now it's 3 years later. I've since tried following the Paleo diet, coconut brings back symptoms and nuts. Bloating, gas, headaches, dizziness, upset stomach. I've tried the candida diet- not working for me. I've tried autoimmune protocol- too much coconut. So now it's been almost 3 years since I've been away from the mold. For a year I stayed away from all sugar possible. I didn't eat any grains, industrial seed oils, refined sugars, I basically ate grass fed meats, homemade broths, homemade everything. No dairy. No nuts. I seemed to be doing much better, but my anxiety was getting even worse. My periods were abnormally heavy (gyno found no fibroids, cysts, said my hormones were fine, neg for anemia) I'm not scared for my life daily. I'm scared to try and have another child. I'm depressed. I've tried probiotics, to only get intense cramping that bring me to the floor. They also make me dizzy. I've tried kefir, yogurt, raw cheese, and of course natural probiotics like sauerkraut, kimchi.. all make me dizzy. I now still have tonsil stones, and my breath is so embarrassing. I don't want to leave the house. I chew gum full of soy which bothers me when I go out, for fear I'll run into someone I know. Doctors want to take my tonsils out. And I now just got an abscess on my gum, which I received a topical antibiotic in the form of a rinse to clean out the bacteria in my mouth. I fear of getting an infection and now here I have one. This is my last straw, I don't know what to do. Who will take me seriously and that's how I stumbled upon this blog. If you could please respond and fill me in on something I don't know in the past several years I've been desperately reading, and looking.. please I don't know what else I can do.

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kwoods said...

Dear Dr. Ayers - I've recently been diagnosed with CDiff, most likely caused by over antibiotic medications from an H.Pylori bout followed directly by a UTI. The CDiff has been treated with Flagyl, a horrible med that felt as bad as the CDiff.
Long story short, I want to be cured! I want my old life back.
I've introduced probiotics Kefir and Florastor into my daily routine to help replenish my gut flora. My diet is sparse right now due to the CDiff, brown rice, salmon, egg, toast, occassional baby food and green leaf juice. That's about it.
I've also taken buspar for over a year to help with anxiety. When they put me on the antibiotics I didn't know they'd interfere with the buspar and I had a complete panic attack. I took myself off the buspar, having a "gut" feeling. Dr was not happy but I had to do something.
I know my system is a wreck.
I'm considering adding CBD oil to my regime to help with the anxiety as CDiff tends to increase or cause anxiety in patients.
Any thoughts on CBD oil and the gut?

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