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 .

Tuesday, July 15, 2014

Gut Flora, Disease and Obesity

The health of your gut flora (the interacting trillions of bacteria of a couple of hundred different species that make up the pound of bacteria that you carry primarily in your large intestines) is more important than your genetics to your overall health.  Thus, your health is a result of diet, gut flora adapted to your diet and exercise.  Everything else, your genetic risks, environmental toxins, etc. are of only minor impact.

I am trying to paint the big picture of how the food that you eat and your gut flora interact to determine your health, by which I mean whether you get sick, become obese and/or bloat with gas.

Health Depends on Gut Flora
If you are healthy, you have a couple of hundred different species of bacteria that help you to digest the protein, fats and carbs that you eat in meat and vegetables.  Your body easily digests protein and fats in meat, fish, eggs and dairy, because enzymes to digest them are present in your stomach and small intestines.  The only carbs that your body can digest are some simple sugars and starch.  The rest of the polysaccharides present in plants cannot be digested without the help of bacteria.  The polysaccharides that your gut flora can digest are fermentable, soluble fiber, e.g. resistant starch, pectin, inulin, arabinogalactan, xylans, beta-glucan, etc.  If you can’t digest soluble fiber, because you have damaged gut flora, dysbiosis, and are missing essential bacterial species normally found in a healthy gut, then the soluble fiber just passes through as insoluble fiber and readily dehydrates into hard, constipated stools.  Partial digestion due to just a few missing bacterial species produces the symptoms of food intolerances.  

Constipation Results from Dysbiosis
The bottom line is that the volume of healthy, soft, firm stools is made up of gut flora that digested dietary soluble fiber and converted it into more bacteria.  If you eat more soluble fiber, this food for your gut flora, will produce proportionately more bowel movements.

Gut Flora Guide Immune System Development
Most of cells of your immune system are in the lining of your gut and there are particular species of gut bacteria directly involved in the development of immune cells that have different functions as they spread throughout your body.  Some of these cells are aggressive and attack pathogens, while others make sure that the aggression doesn’t get out of control and cause autoimmune diseases or allergies.

Gut Flora Divided into Groups to Show Involvement in Disease
Recent studies have demonstrated the role of gut bacteria in producing nutrients, vitamins and neurotransmitters.  To highlight the essential role of gut flora in disease, I have divided the hundreds of species of gut bacteria into groups to illustrate their direct involvement in development of the immune system and regulation of the flow of dietary nutrients involved in obesity.  A recent study shows that an infection can produce a change in gut flora associated with marshaling additional fatty acid nutrients for the host instead of just producing more gut flora.  Chronic change of gut flora in this way leads to obesity.  Other types of dysbiosis contribute to infections, cancer, autoimmune disease, allergies, food intolerances, gas and bloating.

Group A Bacteria  Provide Aggressive Immunity
There are several dozen species of bacteria in healthy gut flora, including the filamentous bacteria, that trigger the development of the aggressive part of your immune system that attacks pathogens, and kills cells of your body that are infected with viruses or are cancerous.  Most antibiotics don’t permanently damage this group of bacteria, so after a course of antibiotics you can usually still stop infections.  Excessive suppression of aggressive immunity contributes to cancer.

Group B Bacteria Provide Suppressive Immunity
There are dozens of other species of bacteria, including Clostridia, that control the development of the suppressive half of your immune system that produces immune cells, such as regulatory T cells, Tregs, that stop the aggressive cells of your immune system from attacking your own cells and innocuous things such as food and pollen.  Many common antibiotics damage these species of bacteria and are thought to contribute to the development of autoimmune diseases and allergies.  Inflammatory bowel disease is characterized by a simplified gut flora with only half the healthy number of bacterial species.  Resistant starch preferentially feeds these bacteria to enhance suppressive immunity and in some individuals cure autoimmune disease.

Group C Bacteria Convert Soluble Fiber to Short Chain Fatty Acids (SCFA)
The fermentable soluble fiber in your diet is typically from vegetables and it is converted by the largest and most diverse group of bacterial species into short chain fatty acids.  Each different plant polysaccharide, and there are hundreds, requires many enzymes for complete digestion to the simple molecules used by the bacteria to make its own proteins, fats and polysaccharides.  Absence of bacteria that are specialized for the digestion of particular polysaccharides or other dietary components can disrupt gut flora and cause digestive disturbances that are experienced as food intolerances (also confused with food allergies that are rare.)  Some of the bacterial species convert polysaccharides into butyric acid and other short chain fatty acids that are the major source of energy for cells that form the lining of the intestines.  These SCFAs are also a major food source for other gut bacteria.

Group D Bacteria Convert SCFAs to Fecal Bacteria to Produce Bulk of Bowel Movements
In healthy people, the SCFAs produced by gut flora feed the intestines and the remainder produced in the large bowel is converted into more gut bacteria, which forms soft stools.  Antibiotics typically damage these bacteria and result in constipation.  These bacteria are typically more sensitive to antibiotics than those that digest the soluble fiber and produce SCFAs, so the excess SCFAs pass into the blood stream and contribute to obesity instead of stools.  Lean mice with gut flora exchanged from obese mice, become obese.  Cattle are fed antibiotics to enhance the conversion of corn polysaccharides into SCFAs and body fat prior to slaughter.

Group E Bacteria convert Soluble Fiber to Methane and Hydrogen, Bloat
Increased volume of the intestines, bloating, results from conversion of soluble fiber into methane, hydrogen and carbon dioxide gases.  Some of this gas is absorbed into the blood and can pass from the large intestines, through the blood, and back to the stomach and small intestines.  Helicobacter pylori, the cause of stomach ulcers and gastric cancer, can utilize hydrogen from the blood as an energy source.

In Summary:
A+B+C+D = healthy, normal weight
A+C+D = normal weight, autoimmunity and allergies
B+C+D = normal weight, susceptibility to cancer, chronic Lyme disease, food poisoning
A+B = normal weight, constipated
A+B+C = obese, constipated
A+B+D = normal weight, food intolerances
A+B+C+E = obese, constipated, bloated

Cure for Dysbiosis and Associated Diseases is Repair of Gut Flora
The excitement about the use of resistant starch (RS) and probiotics with Clostridia and other soil bacteria to reverse the symptoms of autoimmune diseases is based on the ability to repair gut flora damaged by poor nutrition and antibiotics.  Low carbohydrate diets that do not provide soluble fiber to feed gut flora lead to dysbiosis and chronic diseases.  Resistant starch, as the name suggests, passes on to the colon by avoiding digestion with amylases in the small intestines and acts as a soluble fiber to feed gut flora in the colon.  Clostridia convert the RS to sugars and SCFAs usable by other gut flora.  Note that some species of Clostridia produce toxins and it is these pathogens that take over in hospitals after the healthy species are killed off with antibiotics.  Fecal transplants are the best treatment for these hospital acquired infections. 

 I have discussed the role of hygiene, muddy veggies, fermented foods, etc. in several other posts on repair of gut flora.  

Complete repair of gut dysbiosis is possible, but it requires more than just changes in diet and dairy probiotics, as typically recommended erroneously by the medical industry.

Health is dependent on:
  1. an Anti-Inflammatory Diet,
  2. gut flora adapted to your diet
  3. exercise and
  4. adequate sleep
The rest (genetics, vegan vs. paleo, environmental toxins, organic veggies, GMOs, etc.) are minor contributors, less than 10% in aggregate, to overall health.



Tim Steele said...

Great post. I'd like to see the terms 'soluble' and 'insoluble' retired from common usage in favor or more appropriate terms like 'butyrogenic' or 'bifidogenic'.

I think solubility only really applies to food manufacturers. The two main fibers found in nature, inulin and RS, act almost the same in the gut but one is soluble and the other is not.

More important is the effect of the NSP or OS to create an environment rich in SCFA producing microbes and a pH favorable to ABCD and inhospitable to E.

The food industry only cares about the "High in Fiber" label that is easily achieved with added sawdust.

Jeremy said...

Could you explain what types of fiber feed group E? I am supplementing with many types of fiber and worry that I might promote group E, particularly as I do have foul smelling gas on some days I supplement.

Tim Steele said...

Jeremy - My view is that Group E is a product of modern eating...a diet high in sugar, refined carbs, and vegetable oils (the "Inflammatory Diet"). I doubt there is a fiber out that that is 'bad', but lack of a wide variety of fibers and diet very low in all-type fermentable fibers will ensure a gut that produces smelly farts and bloating at the drop of a hat.

Dr. Art Ayers said...

Hi Tim,
I agree. I cringed a little when I wrote "fermentable, soluble fiber" because I didn't know what would be recognizable. I also wanted to make the point that all polysaccharides can be hydrolyzed in time with the right enzymes. That is how wood rotting fungi, termites and ruminants make a living. But if the needed bacteria are missing, then perfectly good polysaccharides, even the fundamental resistant starch, are not fully digested.

The flow of metabolites from fiber polysaccharides to various sugar to SCFAs or methane or hydrogen, etc. is important, because the intermediates or end products can accumulate and cause symptoms of food intolerances, if a mediating bacterium is missing.

I don't know how to get across the major point that diet means nothing without appropriately paired, adapted gut flora. Diet and exercise will make you unhealthy without the right bacteria, and once they are gone, you need to eat them again to regain health. Your immune system would be destroyed by IV nutrition alone or by protein, fats and starch without polysaccharides to feed your gut flora.

Thanks for your comments.

Tim Steele said...

I suppose 'fermentable' and 'non-fermentable' would be good descriptors for fiber, too, but as you said, without the right gut bugs in place it could all go unfermented.

Here's a funny story...a few people have commented this summer that sweet corn used to come out the next day looking like it did when it was eaten. After a year of increased RS, I can eat 2-3 ears of sweet corn and see absolutely no sign of corn kernels in the toilet, others have noted the same effect.

So, not only have we put hospitals and toilet paper makers out of business, we'll have to stop using the term 'corn-hole' as well.

On another note, regarding our convo about Lyme disease the other day, I wonder if the increase in occurrence of Lyme disease is more a statement about the condition of people's guts than an increase in tick populations?

Anonymous said...

Hi, you wrote that resistant starch preferentially feeds group B bacteria. Is there an equivalent for group A? Thank you I appreciate the time and effort you put into this blog.

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

Dr. Art Ayers, First of all, thanks for all the info you provided here! I am adopting a anti-inflammatory diet now but my gut flora is not very healthy, daily products doesn't really work but after i read your blog, I am fully awared of its potential hazard, so I am determined to do something about it, starting by learning how to make fermented food!

During my research on soluble food, I stumble upon "soluable fiber" products recommended by blogger Chris Kresser called Heather's Tummy Care Tummy Fiber™ Organic Acacia Senegal Pouch.

I would be grateful if you can comment on this product.

Will it help restoring my gut flora together with fermented food?

Thanks a lot!

Dr. Art Ayers said...

Can you introduce your new blog and make a few comments about repairing gut flora with RS, supplements like acacia arabinogalactan, and whole foods.

Dr. Art Ayers said...

Hi Raj,
Thanks for watching.

I have been thinking about the involvement of bacteria in cancer and will probably write a post soon on the relationship between bacterial migration from gut to breast to milk, and breast cancer.

I have also noticed the importance of adjacent pairs of basic amino acids which are an alternative nuclear translocation signal, but I think that they are also an alternate to the triplet internalization signal involved in antigen presentation for autoimmunity and allergies. I think that lactoferrin uses the adjacent pairs for internalization of bound iron, similarly to bacterial siderophores. Also note the adjacent pairs in insulin prior to post translational modicfications.

Another topic on my mind is nucleophil extra cellular traps composed of DNA and antimicrobial peptides. I suspect that they may be important in rosacea, since one of the antimicrobial peptides is cathelicidin.

Nigel Kinbrum said...

Hello again. Long time, no comment!

I'm tweaking my diet in order to re-start weight & fat-mass loss.

Now that I'm definitely insulin-sensitive (by OGTT), I'm experimenting with slow starchy carbs, from orange-flesh sweet potatoes, Basmati rice, various types of bean, and mixed vegetables. I'm finding that eating such a diet during the day is resulting in weight loss, despite the high %E from slow starchy carbs. I prefer to use the terms "slow" and "fast" when referring to starchy carbs, to represent the length of time taken to hydrolyse into glucose.

I wonder what my gut flora are making of the above foods? They're probably in shock!

Cheers, Nige

Jan said...

Hi Dr. Ayers, this post is full of great info for many of us on the path to healing our guts. I'm A+C+D with maybe a little B in there, too. I have followed the RS info since December and added it into my diet. I eat raw sauerkraut at least once a day. I have tried several SBO probiotics without noticing much change in my digestion of FODMAPS, like broccoli, onions, as well as many fruits. What bacteria am I missing to be able to eat these important nutrias foods? Digestive enzymes don't help either, so I have eliminated a fairly large group of foods from my diet to avoid IBS distress. I wonder if these are foods that my ancestors didn't eat so it's fine to just eat the foods that I can properly digest? I have family members that cannot digest the very same foods. I'd appreciate any thoughts you have on this. Thanks.

Tim Steele said...

Hey, Art - You found me out! I wasn't going to publicize it all. It's kind of a long-range thing.

I'm starting a Master's Degree in Biotechnology next month and the classes are mostly done electronically using Google Drive/Docs and all the Google+ stuff you see. As I was signing up, I saw a place to put a blog, so I thought this would be a good time to start one. Here's the degree I'll be working on:

"The biotechnology regulatory affairs specialization assists students with understanding the regulatory and policy issues that face the field of biotechnology. The curriculum covers the impact of regulatory and policy issues on domestic and international affairs, clinical trials and various aspects of a product's life cycle, good laboratory and manufacturing practices, quality control and assurance, bioethics, and the business of global biotechnology.

The Master of Science program in biotechnology serves a number of careers at the entry-, mid-, or high-level positions, depending on the prior level of experience of the candidate.

Graduates of the biotechnology regulatory affairs specialization, depending on their background, can find positions such as:

Senior managers in regulatory affairs

Specialists in regulatory affairs

Quality assurance specialists

Clinical specialists

Other health care and biotechnology professionals"

My real passion has always been in agriculture, so I'm going to try to get some credentials and figure out a way to actually make a living doing this stuff. It seems like the field of biotechnology is in a Wild, Wild West phase and there are plenty of openings for a guy to break ground ancestrally with a focus on the gut. Maybe it will all come together over the next couple years.

If anyone wants to see it, it's called Inspired by Dr. BG's AnimalPharm.

Dr. Art Ayers said...

This is what Wikipedia says about:
FODMAP is an acronym, deriving from "Fermentable, Oligo-, Di-, Mono-saccharides And Polyols".

This is confusing for me. I was trained as a carbohydrate chemist and the classification of veggies on this basis seems silly. All plants contain these types of carbs and polyols is a strange name for polysaccharides, commonly called starch and soluble, fermentable fiber, which is essential food for gut flora. Food intolerances just indicate missing species of gut flora and avoiding the food is only a temporary avoidance of symptoms.

I have oversimplified the gut flora with my facile groupings. People have IBS, because they have killed off half of the species of bacteria in their guts with antibiotics, extreme diets, processed foods lacking soluble fiber and excess hygiene. It is not genetic and only runs in families because bad eating habits and gut flora are inherited.

The problem with IBS, is that so many species of bacteria are missing that the gut and immune system are also damaged and the gut flora can't be reconstituted easily one species of bacteria at a time. That is why babies start with a specialized gut flora of dairy probiotics supplied and maintained by breast milk, which develops in an ordered succession to adult gut flora related to the mother's.

I think that the answer for IBS is for whole families to improve the gut flora that they share. Look up the posts that I have provided in my article and note that fecal transplants provide at least temporary improvement for IBS. It should be curable, but the cure requires repair of the gut flora and not just elimination of the remaining gut flora with antibiotics.

I hope this helps. Let me know about your progress.

Dr. Art Ayers said...

What a treat to hear from you. I was just playing with the structure of synuclein after reading about the toxic effects of internalizing amyloid fibers and then subsequently reading about using Curcumin to visualize fibers in the retina as an early diagnostic for Alzheimer's.

So you're playing with soluble fiber, but don't want to get into the whole RS thing. Slow starch indeed. The issue is feeding gut flora and blood sugar is secondary. Most of the "slow starch" is actually converted into SCFAs and that is the crux of fat metabolism. Fix the flora and fix the fat.

Your flora are saying, "Feed us some RSPS and we will let you know who's missing."

Nice to hear your voice.

Susan said...

Thanks so much for your work on this fascinating topic. You've probably addressed this previously, but since food intolerance is because of missing gut flora, and eliminating specific foods only works for a while (which was my exact experience as a person with rheumatoid arthritis -- my first year on paleo was almost a miracle. Now, not so much), what do you think about plans like the autoimmune protocol that various paleo writers recommend? It's basically eliminating yet more foods. I seem to do better when I do that, but to what end? Should I stop eliminating foods (for example, egg whites now seem to be a problem) and just work on my gut flora via ferments, etc??

Paleo Phil said...

Dr. Art Ayers said...
"The issue is feeding gut flora and blood sugar is secondary. Most of the "slow starch" is actually converted into SCFAs and that is the crux of fat metabolism. Fix the flora and fix the fat."

Bingo Doc! Nice article.

Debbie said...

What a wonderful post. Thank you so much. And thanks to Tim too for all his work in this area. I have improved my constipation a lot to a movement virtually every day, although it's usually after the morning coffee. I've been doing the Dr. BG protocol - PS-green powder-SBOs-psylium- and I add Vit. C just for the heck of it. I also eat fermented vegetables, but haven't made my own yet - that is coming up. I also have bone broth every day. I just bought some colostrum powder and gelatin.

I also eat sweet potato and orange squash every day. But sometimes I do have stomach cramps and/or the constipation returns, and I'm unsure as to why that is. My diet doesn't really change, so I can't pinpoint. So, I'm going to keep doing what I'm doing. It feels great to just go normally every day! If I have to take this stuff forever, so be it.

I do wonder why many people have zero elimination problems, and they eat horrible diets. Or they eat an Atkins type diet, which contains little soluble fiber, and they have no problems. Why?

Thanks again!

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

You mention constipation and the lack of gut bacteria a lot on your blog but I've not seen you talk about loose stool. I'm curious if you know what the sort of general bacterial profile someone with chronic loose stool and autoimmunity would be.

Debbie said...

Tim, I can't log onto your blog. Is it accessible yet? Just wondering; I'd love to see you have a site!

All the best going forward with your program.

Tim Steele said...

Debbie - cut and paste this into your browser:

Basically, I went all over the internet and cut and pasted articles, interviews and blogs that talk about RS. Plus a tab that describes the 'Potato Diet'.

Not sure how often I'll update it, it's part of a long-range plan and I just wanted to make sure I could get the name VegetablePharm. I was really surprised it wasn't taken, I even bought the .com domain at GoDaddy.

I'm not really sure how I stumbled into helping people with their guts, my real interest has always been in soil and growing things/wildcrafting, but maybe that's the path to gut health for many people.

Unknown said...


This somewhat addresses a question I have asked myself a few times in the last 6 years of severe dysbiosis.

I have always been extremely lean (and lanky) my whole life. 6 years ago I was put on almost 90 days strait of broad spectrum anti-biotics to treat what was then prostatitis. Post anti-biotic treatment I developed IBS-Constipation, environmental allergies, food sensitivities, chemical sensitivities, chronic fatigue, yeast syndrome, etc.

Still after all of this I remain very lean (regardless of "good" or "bad" diet). I thought such an extreme blow to my gut flora would certainly lead to weight gain or possible obesity???

Looks like I am A + B.
Was it my gut lacking "C" a reason for this?


Marcus said...

Hey folks

I have commented here and have been trying the RS + SBO for a while now. I have the three main probiotics suggested and have been taking most days. I also take potato starch + PH most days.

I guess my questions are:

- How long should this take to impact an AI disease?

- are there any other negative factors?

I have been doing this but drinking more than usual. I also eat Paleo and have for nearly five years.

My AI is just psoriasis but my wife has MS. We do well on a anti inflammatory leaning paleo diet but I do feel this is an avoidance of problems rather than a cure.

My goal here is to get my psoriasis healed up and then to work on my wife but some idea of timescale to fix a broken gut with this approach and sensible diet in line with the AI diet here and general paleo good habits would be great.

Weeks? Months? Years?

Thanks guys, loving all you do.

P.S. Tim - I run a web hosting company. If you want to get your .com up and running let me know, it's on the house!

Tim Steele said...

Hey, Marcus - As to AI conditions, I have seen some people turn small things like psoriasis around pretty quick, like in just days, with a few dietary changes and probiotics. L. plantarum seems to be one of the probiotics that helps with that condition really well. Dr. BG just blogged on a similar topic yesterday:

When you start talking about things like MS, it gets a bit hairier. One of my favorite ladies, Nora Gedgaudas, seems to have the MS thing figured out. She was on the Bulletproof Exec podcast the other day, the tag-line says she talks about RS...I'm going to go listen as soon as I hit send, been meaning to all week!

Web hosting, eh? Well, here's what I did. I bought the domain at GoDaddy for like $14/year, first year was only $2. Then I parked the domain name and forwarded it to the blogger URL. Says it can take 48 hours to work. Do I need to do more? The forwarding seemed to be free. I'm a total tech-tard on this stuff. Does it sound like I did it right?

Tim Steele said...

OK, I've heard enough...

Nora is totally clueless on gut microbes. Jump straight to about 41 minute mark on the Asprey podcast and you'll see. Dave handled it all pretty well, just trying to be a good host, but I don't think he agrees with her.

marcus said...

Hey Tim

Really interesting. I have basically been Paleo for three to five years with intermittent use of fermented foods (as and when I get time - 3 young kids etc). I have been on PS + PH with the three probiotics for a few months now but it took us some time to build up to using the AOR P3 as it gave me (and my wife) serious digestive issues and we had to scale up super slowly.

I have just purchased a pure L. Plantarum probioitic ( so will give that a blast and report back.

I know that certain foods make my psoriasis itch straight away (dairy / wheat) but I don't tend to eat those foods being paleo but I am weak enough to grab a hunk of cheese or a nibble of my kids chocolate every now and again that reminds me.

I also know that strict adherence with no alcohol can almost get rid the psoriasis but it's no cure and if I start to have some wine etc it comes back so that's not maintainable.

I am going to give the potato diet a blast for 3 to 5 days this week after reading the post on your new site (very cool by the way) and see what that brings + the new probioitc should be here in a couple of weeks and I can see what that brings.

Re the web hosting that all looks fine to be honest. There is a lot of sense in using a hosted platform like blogger where you have no technical background as you have no exposure to technical problems, hacking and all that nonsense. If I can ever help though in the future please feel free to look me up at and any time you need is on the house.

Will check out the Nora podcast (and been meaning to read her book for a while now). I am pretty sure this can be fixed but at five years in I understand it sometimes needs patience.


Sven said...

Dear Art.

Your blog has meant lots to me, healing from disbiosis, IBS, Allergies and autoimmune flares.

I'm currently on your anti inflammatory diet, which has helped me get better but I'm still struggling with some carbs though. Trying to add in some prebiotics with my probiotics but FOS, Inulin and lots of other polysaccharids are making my prostate hurt and I get skin rashes.

Last week, after you blogpost I started doing RS and Probiotics-3 to se if that can balance my gut flora. I also started drinking green tea and taking curcumin supplement for Treg support.

I have one question though!

This talk, online, about TH-1 / TH-2 imbalance... Is that something to take seriously in your opinion? I know Chriss Kresser have made a blog post about it and he seem to be a sharp guy.

There seem to be a lot of foods and supplements that enhance th-1 or th-2 making it important to know if your allergies and autoimmunity comes from a th-1 or th-2 dominance.

Kindest regards. Sven

Nick said...

Hi Dr. Ayers,

I love your blog, and have a question for yourself if you don't mind. It would be awesome if you ever did a study on gut flora and how it relates to OCD and/or strep throat.

Do you believe their is a coincidence is OCD and an unhealthy gut flora?

Reason I ask is I have a young family member that was diagnosed with OCD but also does not eat correctly, and it was also brought on by strep throat. In Which case he took anti-biotics.

Just wanted to get your thoughts.


Dr. Art Ayers said...

I think, since OCD has been studied and can be treated effectively with omega-3s, it is reasonable to treat it with diet and adapted gut flora.

Since OCD is an inflammatory disorder, it would be expected that it would be aggrevated by inflammation and both the reason for the antibiotics and damage to the gut flora would contribute to inflammation. The inflammation in turn would be expected to produce a vitamin D deficiency that may resist supplements.

Read my posts on repair of gut flora and let me know of your progress.

Natasha v. Potato said...

Dear Dr. Ayers,

Hi! I am working on myself but feeling pretty down. I did a week of the Eades PP, taking most of the recommended supplements. I lost a few pounds - the same few I lose. I ran out of protein powder and so ate normal meals for two days. Kept carbs moderate but gained back the few pounds I lost.

I am beginning to think I only had a couple of chances in life to lose weight. That a diet - any diet, including calorie reductions - alter the microbiota. Do "x" diet and bingo, weight loss. But eventually, after one or two or maybe three major weight loses, it doesn't work anymore.

I read so much. I understand my microbiota was always compromised (bottle, soy formula fed). Despite trying all the recommended SBO probiotics, I have had the worst allergies ever. I also have tingling on my lips and tongue, and I can't figure out what new allergy I am developing.

I wish I knew someone healthy enough to give me a FT. Perhaps it seems shallow to want to be normal weight, normal reaction to foods, allergens, etc. but I really just want to normalize.

Apologies for the complaining. I really enjoy your blog. Brilliant thinking.

Kind regards, N.

Dr. Art Ayers said...

This is my attempt to cheer you up.

First of all, it is a myth that your current or past gut flora is your destiny. All of the studies show that gut flora will persist, but only if diet is not suddenly changed and antibiotics are avoided. Unfortunately, all common pharmaceuticals have sufficient antibiotic activity to make significant changes in gut flora that may persist.

So, your current gut flora are merely a snapshot showing recent and past history, but open to daily amendment. Biofilms even rearrange and recombine genes from different species of gut bacteria to create new species on a daily basis. Your gut flora is dynamic.

I think that the extra fat that we carry is regulated by our gut flora and a change in energy consumed and expended alters our gut flora to maintain our fat storage. Increased consumption of calories and stored fat alters the gut flora to produce more bacteria/poop and less contribution to fat. Starvation does the opposite. The Drs. Eades Whey shakes aren't just protein shakes, but rather literally milk protein shakes that attack adult gut flora and disrupt weight equilibrium, so that eating less can cause weight loss without gut flora compensation.

The point is that flitting from diet to diet just damages gut flora, causes inflammation and produces the symptoms of inflammation: obesity and depression.

The SBO probiotics will have no impact if you don't also eat that soluble fiber that your gut bacteria need to eat, e.g. resistant starch.

Allergies are a symptom of loss of your suppressive immune system that develops in response to gut bacteria, e.g. Clostridium that grows on resistant starch. Read my posts on the subject.

Just follow the Anti-inflammatory Diet that I recommend, repair your gut flora and explore resistant starch. That should put you in a much better mood and give your some vivid dreams.

Let me know what happens.

Anonymous said...

Does pollen allergy result from repopulation of aggressive part of T-Cell / Filamentous Bacteria rather than from loss of T-Reg / Clostridium Butyricum Bacteria?
Immunocompetence regain passes even through more reactivity/inflammation (at least at the beginning)?

El Librero said...

Anonymous said...

Dr. Ayers, thank you for your wonderful blog. So much great information here. I am trying to help my child with an autoinflammatory condition (recurring fevers + pains etc.). Is the mechanism for autoinflammatory the same as for autoimmune. I am not a scientist, but it's my understanding that autoinflammatory only involves innate immune system.

Thank you!

Anonymous said...

Dr. Ayers,
I am a new blog reader, am in a health-related field, and am enjoying your perspective.

In spite - or, perhaps, as a result - of following conventional treatments and diets, I am now finding myself in poor health for someone my age, despite eating moderately and exercising regularly.

I have been diagnosed with Hashimoto's thyroiditis, PCOS, obesity, allergies (particularly to nightshades, ragweeds, grasses, animal dander, molds), asthma, rosacea and other dermologic sensitivities, and I regularly experience painful gas, bloating, and constipation.

Despite this, my blood pressure, ACH, and cholesterol levels remain excellent (actually, my doctor said I have the higest HDL level he has ever seen in 15 years of practice), all of which I attribute to omega-3 consumption/supplementation, and exercise.

Might you have any advice as to where I might start making changes to address some of my personal inflammatory issues? My old school doctor is little help - he is convinced that drinking low-fat diet shakes to lose weight should be the focus of my health care interventions, at this point.

Also, might there be a post somewhere outlining some sample menus that follow your eating recommendations, including foods to properly maintain intestinal flora?


Dr. Art Ayers said...

It is pretty clear from your description that you have lost most of your gut flora from celiac and that led to your autoimmune Hashimoto's and allergies. You can also expect vitamin deficiencies and particularly vitamin D deficiency. Of course, obesity is a symptom of chronic inflammation due to the celiac.

Not to worry. This can all be fixed by simply following the general guidelines of the Anti-inflammatory diet that I outline on this blog. It is basically a low carb paleo diet. PLUS As you have noted, you have trashed your gut flora and eliminated your Tregs, hence your immunotolerance is gone and you have autoimmune diseases and allergies.

Fixing your diet will only change your symptoms if you repair your gut flora. Constipation means you have about 10% of your flora diversity left.

The difficulty that you and many others have is that it is hard to introduce the hundred different species of bacteria that you are missing without causing lots of new problems. It is like clear cutting a forest, planting corn for ten years and then trying to get back to a forest which is lacking a thousand plant and animal species in addition to a million different soil microbial species. You can't fix that by just planting a monoculture of harvestable tree.

Probiotics can return a lot of function by mimicking a baby's first simplified milk-based gut flora. Maybe your gut flora is not as bad as you indicate, and you could start with small amounts of resistant starch and soil-based probiotics. You might see how well you tolerate fermented veggies, which are like probiotics plus soluble fiber to feed your composting gut flora.

It is essential that you measure your serum vitamin D, supplement aggressively to fix your deficiency and then retest. Repeat until you reach 60 ng/ml. Most people remain deficient, so persist.

I have dozens of posts that address gut flora repair, excess hygiene, autoimmunity, PCOS, infertility, allergies, etc. I don't do recipes, because there are hundreds of sites that have low carb, high fat, moderate protein diets that eliminate grains, vegetable oils and trans fats, and retain meat/fish/eggs/dairy/vegetables.

grains are your main problem
carbs make fat
processed foods starve gut flora
antibiotics kill gut flora and make you sick
fat is your major source of calories
saturated fats are safe
cooking is essential -- I do it. So can you.

You should see some quick results, but the autoimmune symptoms may take months.

Let me know how you progress

Lesley said...

Dr. Ayers,

Would you mind listing some specific strains that are a part of group B? I'd like to know a bit more about them and how to get more of them in my system.

If there are certain types of RS they prefer, I'd like to hear about that, as well.

Tim, you're welcome to chime in!



sailing said...

I read here:

About resistance starch.

I am confused regarding eating potatoes - just boiled or baked without skin and some butter..

Are potatoes good forms of resistant starch, or more inflammation producing? I'm not talking about processed potato products.
Are any types of pasta ok, I'm guessing not. Pasta has been a staple for me.

I have HLA-b27, in remission with Uveitis I've had 4 times in 13yrs. Haven't had it in over 5 years now. Just trying to be cognizant of inflammation in my body with the gene I have.


Anonymous said...

2nd article on resistant starch:

Ok to eat potatoes or inflammation producing? See my previous post 'sailing'

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and funding planned to continue this site into the future. Big pharma has their paid lobbies.
We have you. A much heartfelt
appreciation. Thanks!

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