Anti-Inflammatory Diet

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

Thursday, January 23, 2014

Gut Flora Risk and Repair

….All 190 posts here….
The two most important contributors to health are diet and gut flora.  All of the other contributors, such as exercise, genetics, environmental toxins, hygiene, etc. are of minor importance.  A healthy diet, such as The Anti-Inflammatory Diet that I recommend on this blog, is simple and relatively easy to follow after weaning from the Standard American Diet.  One version of the healthy diet is just eating meat, fish, eggs, dairy and plenty of vegetables, but avoiding vegetable oils and grains.  Most people will be healthy with that general diet, but if and only if, they also have a healthy gut flora that is adapted to the food they eat.

Most people make themselves sick by not matching their gut bacteria to what they eat, so let me repeat the main point of this article:

You will get sick if the bacteria in your colon can’t digest your food.
And sick means allergies, autoimmunity, cancer, etc.
Read and Heed or Dead

What Killed American Gut Flora?
There are hundreds of different species of bacteria growing on partially digested food (soluble fiber) in your colon.  Americans are sick, not because they are too poor to buy food, but because they have the worst, i.e. least diverse, gut flora in the world.

Do:  We pick up, recruit, eat new bacteria and repair our gut flora by:
  • touching surfaces, people, pets, etc. and putting our fingers near our mouths,
  • eating live fermented food, or semi-clean vegetables,
  • not cooking/killing/sanitizing all of the bacteria around us,
  • eating probiotics and transferring some of their genes to our gut flora.

Don’t:  We wipe out or reduce the diversity of our gut flora by:
  • using inappropriate hygiene that kills the bacteria we need for health,
  • taking antibiotics that kill gut flora and compromise our immune system,
  • trying to eat a wide variety of foods, which is counterproductive and only permits a few varieties of bacteria to survive.

Hygiene Kills Beneficial Bacteria
Nothing comes from nothing…  For bacteria to come out, bacteria must go in.  You have to eat bacteria to extrude them by the pound.  Each day a single bacterium growing and dividing in your gut once per hour will produce a million daughter bacteria (24 doublings, estimate that doubling two, ten times is about a thousand, and 1000X1000= million.)  So if you mixed a milligram (about the size of the period at the end of this sentence) of gut bacteria with ample food, you would have a kilogram (pounds) of bacteria by the end of the day.  Similarly, it takes about a day for a single bacterium applied to a petri dish of nutrient agar to produce a colony weighing about 10 milligrams.  The point here, is that a single bacterium that makes it through the acid bath of the stomach can be a major player in your colon in a couple of days.  This is a very good thing.  We want to kiss babies, because babies systematically vacuum up bacteria from the darkest  of corners and with shameless generosity present them in an irresistible pucker.  We need those bacteria, and so do the babies.  Hygiene, e.g. antibacterial hand soap, bleaching surfaces or closing toilet lids isolates people from potential sources of beneficial gut bacteria. 

Traditional Food is Fermented (with Live Bacteria)
In most cultures, extra food is mixed with something like salt or spices to kill local problem microbes and then bacteria are permitted to grow.  The result is fermentation of the sugars available in the food with production of organic acids, e.g. vinegar, that stop the growth of other bacteria that might grow on protein and cause objectionable flavors.  Homemade fermented veggies contain a wide variety of happenstantial bacteria that can adapt to productive gut growth.

Cooking Kills
We cook to dissolve and soften foods.  Meat can be eaten whole and our stomach enzymes will easily digest the protein and fat to provide all of our nutritional needs.  The only plant material that can be digested by our enzymes is starch.  The rest of the plant requires cooking to make the protein available and the remaining carbohydrates, soluble fiber, require digestion by hundreds of different enzymes produced only by microorganisms.  Cooking will release soluble fiber to feed gut flora, but it also kills bacteria, so some raw foods must be eaten to make sure that the gut is always supplied with fresh bacterial recruits.  Cooked or pasteurized foods do not contain live bacteria and are not useful as sources to repair gut flora.

Probiotics are not Gut Flora
Commercial probiotics are made from bacteria used in dairy products (dairy probiotics) or bacteria used to make enzymes in other products, such as laundry detergents.  
These bacteria can be repackaged and sold as probiotics, because they have already been tested for toxicity.  These bacteria don’t normally grow in the gut and if you swallow them, they just pass through.  These “probiotics” can temporarily provide some of the functions of gut flora, because they are bacteria, but they don’t grow in the gut.

Gut Flora are Bacteria Created in the Gut
Gut bacteria produce chemical signals that coordinate the metabolism of food by hundreds of different species of bacteria.  We call these chemical signals vitamins, because humans extract the vitamins from the bacterial biofilms that always line the gut, so humans don’t need to produce their own vitamins.  Gut flora can produce all of the vitamins that we need, so it is not surprising that multivitamins do not provide any health benefit and concentrated vitamins my be harmful by disrupting normal metabolism of gut flora.  Biofilms also promote the exchange of genes between different species of bacteria, so the concept of species does not actually apply to gut flora, where new species are rapidly being created.  A common example of this process is the curing of lactose intolerance by simply eating small amounts of live yogurt for a couple of weeks.  The cure results from the transfer of a gene that produces an enzyme to digest lactose from the yogurt probiotic bacteria to the regular gut bacteria.  The new species, a natural GMO, continues to grow in the gut, digest lactose, and cure lactose intolerance.  The yogurt probiotics just get flushed away and that is why dairy probiotics must be eaten continuously to provide some of the benefits of healthy gut flora.

Antibiotics Kill Gut Flora, Compromise the Immune System and Cause Disease
Antibiotics are a huge benefit in curing and avoiding infectious disease.  Unfortunately, antibiotics can cause lasting damage by killing beneficial species of bacteria of the gut flora.  Loss of essential bacteria is commonly seen as food intolerances (true food allergies are rare) or constipation.  Since gut flora are needed for development of both the aggressive and suppressive parts of the immune system, which occurs in the lining of the gut, then antibiotics slowly lead to loss of function of the immune system that leads to autoimmunity or allergies.  Probiotics typically administered following antibiotic treatments do not repair the gut flora and leave the immune system damaged and prone to autoimmune diseases and allergies.

Variety in Foods Leads to Loss of Diversity in Gut Flora
It may be more entertaining to eat a new cuisine at each meal, but it confuses your gut flora.  Your gut is a river that endlessly moves food from mouth portal to pottie.  Bacteria divide and eddies cast some of the bacteria back to mix with food upstream before inevitably moving with the masses down and out.  Bacteria that don’t multiply as quickly as others eventually become extinct.  Bacteria that grow well on broccoli may wither with onions.  If you continue to eat some broccoli and some onions, then your gut flora will adapt, but if the type of polysaccharides, the soluble fiber, changes continuously, then you will end up with the stunted gut flora of Americans.  Diversity of gut flora is reduced by too much variety in food.

Matching Food to Gut Flora Takes Time
All of the gut problems that people complain about, gas, bloating, diarrhea, constipation, food intolerances/allergies (except gluten and a couple of others), etc. are due to a mismatch between food and the digestive enzymes of gut flora.  Modern food processing retains protein, fat and starch and removes the polysaccharides/soluble fiber that reaches the colon, feeds gut bacteria and produces short chain fatty acids (acetic acid, butyric acid, propionic acid) that feed the colon and reduce inflammation.  It takes time for gut bacteria to adapt to new soluble fiber in new foods by recruiting or creating new bacteria, and this is only possible, if inappropriate hygiene is avoided or if homemade fermented foods are eaten.


Charlie Currie said...

Lots of interesting things going on over at Free The Animal, Animal Pharm and the American Gut Project, with resistant starch, primarily from raw potato starch, and the gut microbiome. You should check it out...fits nicely with this post.

Iris said...

I am still new to your blog and I'm reading it whenever I can. I have been taking vitamin D3 since Monday and I think that it may have boosted my skins healing! My diet is already like your anti inflammatory diet. I was seeing improvements with fermented foods that I started eating after reading about them on Donna Schwenk's cultured food life on Facebook. Now I feel even better and D3 is the only supplement I have taken. Is there anyway to heal a gluten intolerance with food? I used to be fine with flour type foods. I grew up eating Icelandic pancakes, flatbreads, and donuts my mom made. I have had migraines all my life until I quit the gluten….but I never had eczema. Just wondering. If not I'm ok I have figured out how to live without it. Thank You so much for helping me find out about vitamin D3 I feel I may finally get over this eczema I've had since last Easter :)

Brian Hassel said...

In line with what Chuck said, what do you think about supplementing with some soluble fiber in the form of resistant starch (potato derived?)

I know from past posts that you're a big fan of inulin, but I don't know how potato starch stacks up.

Ashley said...

I wondered what Dr Ayers thinks about the reported use of fecal microbiota transplantation, apparently available now in tablet form since October of last year. I'm seeing this reported from several online sources and ironically being hailed as the greatest medical advance since antibiotics.

I have an autoimmune condition that causes painful chronic inflammation in my body. It hasn't improved in any way with the prescribed medicines over the last 18 months, so I stopped them all a couple months ago and I've since been absorbing a lot of information from this blog.

I eat home made sauerkraut and lots of raw vegetables plus I take vitamin D3, while avoiding all sugar and processed foods but I'm still waiting to see real signs of progress.

Peter said...

Hi Dr A

What are your thoughts on commercially available SBO probiotics v a chap falling over in his garden and inadvertently munching on a half a pound of soil?

A great resource you've put together here! Thanks.

Jim G. said...

Hello Dr. Ayers,

First, I'd like to thank you for your willingness to use your education and experience to help out so many people (for free nonetheless). I hope you know it's appreciated.

My question has to do with your current (and previous) comments on dairy probiotics. I've been making and consuming raw milk kefir at home for the last 2 1/2 years. You suggest that it doesn't do much in terms of populating our gut bacteria. Have there been any conclusive studies on this matter? Is kefir a waste of time when it comes to our gut microbiome?

Thanks again.

Unknown said...
This comment has been removed by the author.
Unknown said...

Hiya Dr. Ayers,

great post!

Have you ever thought about an Twitter account? Theres a huge group of scientist, exchanging insights. We would love to have you there :-)

Best regards,
Nina K.

Kor said...

Dr. Ayers, yours has been my very favorite blog for several years.

What to do about SIBO... I have found greatest bowel regularity avoiding all forms of bacteria. When I drink homemade kefir regularly, I become completely constipated. Resistant Starch (potato starch) bloats my belly like a balloon and constipates. Yet when I cut out all supplemental bacteria and eat a non-inflammatory diet of meat and veggies, I become quite regular. Unfortunately I'm not able to digest all plant matter very well, and I know my gut flora is deranged; I also have tested very high for yeast in stool, blood, and urine tests.

Have also tested positive for SIBO, and I just feel that when I make an effort to directly feed my bacteria or introduce new populations, they get stuck in my small intestine and eat up all my food before my body gets any.

Really just want a fecal transplant!!

Third Chimp said...

I think the growing body of knowledge about the human biome is very exciting. Although the idea that gut flora diversity is enhanced by stable type of food sources is counter-intuitive for me. I would expect that any ecosystem's diversity is reduced by a simpler set of inputs. Is it that the "ecosystem" view is simply an analogy that doesn`t hold for this aspect of gut behavior ?

Anonymous said...

I'm not following the logic on a diverse diet causing loss of diversity. It seems that the reasoning is that the bacteria specific to certain foods die out because we have those foods so rarely (leaving us with more of the "generalists").

But in the ultimate "simple" diet, we'd be eating what is seasonally available locally. Available foods would vary greatly season to season in non-temperate climates.

Isn't the more likely cause of poor gut diversity in the average American more likely linked to eating mostly processed food with its lack of soluble fiber?

Thanks - Karen

dabney rose said...

Dear Gut Guru
Apologies for putting you on the spot like that but in my wretched state of unhealth, you are a real beacon of intelligence. Currently, in said state, i am unable to tolerate the superheros of fermented veggies and kombucha (they blow me up w/gas, bloating and minor cramping) i feed myself small portions to inoculate and keep a going?
Also, how might one safely purge the bad bacteria guys (from possible leaky gut)??? I have Mahonia (berberine) growing all around me. Could this be another 'health practitioner'?
Again, many many thanks for blogging. Dabney

Carlos said...

Dr. Ayers,

Following a couple of the comments above, it would be nice to hear what you think about Kefir. I haven't come across anything on the subject on your posts.

I've also started taking very small amounts of Kefir per day. It definetely has an effect on my stomach, I'm still regular to the toilet but less (once per day).

Any feedback will be much appreciated.


Elizabeth said...

Hi Doctor,
I am so confused and frustrated with the diet issue. I know meat is inflammation causing in the body and I do not see how fragile people with advanced Crohn's Disease can even touch it. Having 3 members in our family suffering with CD I know first hand and see first hand how meat, or any animal flesh puts them into a severe flare. That is why they have to maintain a vegan diet. Not to mention we avoid it at all costs due to its contribution to cancer and just being cruel.
Probiotics have always been a part of their diet but we do need to add fresh fermented foods as well I think. I am getting a strong signal that that may be very important.
I need to study your low inflammation diet more closely and see if I am missing something.
Thank you for all that you do!!!
Peace & Raw Health,

Dr. Art Ayers said...

I think that with hard work, it is possible to devise a healthy, anti-inflammatory vegan diet and acquire a complementary gut flora to produce all of the necessary vitamins. Unfortunately, most people outside of cultures that are traditionally vegan, don't also acquire the needed bacterial species or eat unhealthy grains, starch and vegetable oils, and end up with inflammatory bowel diseases and vitamin deficiencies.

Meat is the easiest food for humans to digest, because it just consists of protein and fat, both of which humans produce pancreatic enzymes to digest. The saturated fats are also healthier than the omega-6-rich vegetable oils. Meat also has connective tissue made of polysaccharides (glycosaminoglycans, .e.g. chondroitin) that are anti-inflammatory and also provide soluble fiber to feed gut flora.

Gut discomfort after eating any food results from an incompatibility with resident gut flora. This is the basis of food intolerance/allergy. Celiac is a major exception, since gluten and bran are both hard on the gut. Plants are also loaded with thousands of very toxic phytochemicals (see my Science and Engineering Encyclopedia article on phytoalexins) that are called antioxidants for commercial purposes, but must be aggressively detoxified by the liver. Most plants cannot be digested without hundreds of enzymes produced by gut flora and that is why there are so many plant food intolerances.

The biomedical literature is very clear that meat and/or vegetables can be the basis for a healthy, anti-inflammatory diet. Complementary bacteria and sufficient fat and protein to stimulate normal bile and pancreatic function are required.

Inflammatory bowel diseases are related to severe disruption of gut flora and the dependent immune system. It may be difficult to add back bacterial species, because of the complexity of the bacterial interactions. Medicine has not studied how to repair gut flora and it should not be surprising that IBDs have only relatively crude and expensive therapies and not cures.

Thanks for your comments.

Sandra said...

When you say "don't eat a wide variety of foods", what exactly do you mean? Would 3 kinds of meat and 20 kinds of fruits and vegetables be considered "wide"? I guess what I'm really asking is how narrowly our diet should be defined to promote optimal colonization?

P1 said...

Speaking to the issue of probiotics, how do you feel about brands like Prescript-Assist, which claim to contain a "broad spectrum of Soil Based Microorganisms" up to 35+ different types.

I guess even if the bacteria is the right type, the question becomes how can enough of them survive the stomach acid to make a difference in overall gut flora.

Dr. Art Ayers said...

I think that even if there are 35 different species of bacteria that don't usually reside in the gut, they are just like the dairy probiotics. They may be of temporary use, but they are not going to repair gut flora.

The stomach acid is no big deal. Only a few need survive.

la femme natale said...

Dr. Ayers,

I've been enjoying reading your blog.

I see you recommend regaining health from GI maladies by restoring the beneficial gut flora. I also read one of your old posts about biofilms, and I wanted to know if you have any updated information about disrupting biofilms?


Dr. Art Ayers said...

le femme natale,
You are observant that I have gradually changed my views on biofilms. I think that in most cases that sick people can improve the health of their gut flora simply by making small changes in their gut flora community of hundreds of bacteria and reinforcing those changes with diet. Biofilms will not normally persist in a static way on the dynamic surfaces of the gut. They are in a dynamic equilibrium that changes to adapt to diet, but the changes are limited by the species of bacteria that already exist in the gut. To get from sickness to health may also require repair of the gut flora and new species of bacteria. In Crohn's IBD, for example, about half of the needed 200 species of bacteria have been eliminated.

In cases where the gut flora is severely damaged and the existing biofilms are dysfunctional, then disrupting biofilms may be necessary and fecal transplants may be the easiest approach. To be successful the transplanted gut flora need to be supported with a complementary diet to feed the new flora. Prior eating habits will be a problem if they persist. I still think that PEG may be the best approach at destabilizing biofilms.

Thanks for the comments.

Dr. Art Ayers said...

I wouldn't worry about purging bad bacteria. I think that most of your symptoms are due to missing bacteria and not the effects of malfactors. I think that most of the symptoms of food intolerance are the results of missing bacteria/enzymes needed to metabolize the food you are eating. With no gut flora, the food would just pass through. With half the need gut flora, then you get gases produced instead of just healthy short chain fatty acids.

I think that you should just eat small amounts of fermented vegetables and gradually get used to them by building up more useful gut flora.

Food intolerances are not responses of your immune system in the form of antibody interactions, but they may involve inflammation related to gut permeability issues. The problem is still that you need new species of bacteria and avoidance will not cure that. You can't fix it with diet alone.

Phytochemicals such as berberine are very potent and have lots of side effects. They should be used for treatment by knowledgeable medical care givers. I have used berberine in the lab because it binds to heparin (and DNA) and makes it fluorescent. It also disrupts amyloids involving heparin (most do), but heparin is also involved in most hormone and lipid (LDL) binding to receptors, as well as clotting and the complement system. That means that berberine will alter more than a hundred biochemical interactions throughout the body and the liver will modify the berberine to produce a series of deriviatives that have additional interactions. Phytochemicals are reactive with body biochemistry, but in unpredictable and usually negative ways.

I would never try to treat myself by eating a plant that contains a phytochemical with a known biochemical activity. Phytochemicals are naturally toxic and that is their function in plants.

Thanks for your comments/questions.

Glenn Taylor said...

Hooray Sir! My name is Glenn Taylor, I am a Food Microbiologist and I run the Taymount FMT Clinic in the UK. To the best of our knowledge the Taymount is currently the only specialised clinic in the Northern Hemisphere offering a dedicated and complete Faecal Microbiota Transplantation which is the process of returning the human gut flora to as near as normal as we can. We cheat outrageously by coaching our small group of regularly tested donors to produce a good microbiome and then borrow their gut flora to implant it into a dysbiotic gut, returning it to normal. We are currently researching the effects of FMT with the correct regulation of the immune system.

You are talking our language and I fully support what you say on your site. Thank you for your efforts in raising awareness of the importance of the health and diversity of the human gut microbiome.

Unknown said...

What are you're views on Helminths. Aren't worms part of the human biome?

Anonymous said...

I wonder if you could expand on this comment as I don't think it is true:
"With no gut flora, the food would just pass through"

If you do a bit of resesrch you will find that the flora of the small intestine is rather sparse at 1000cfu/ml and some have tested to have none.

Yet, digestion occurs in the duodenum using our own enzymes and the products are then absorbed in the jejunum where there is 1000cfu/ml or less bacteria.

How is it that bacteria participate in this process ? Those with overgrowth of small intestinal bacteria experience nausea, bloating, fatigue etc.

سما احمد said...

شركة مكافحة النمل الابيض بجازان
شركة رش مبيدات بجازان
شركة مكافحة حشرات بجازان
شركة تنظيف خزانات بجازان
شركة مكافحة حشرات بابها
شركة مكافحة حشرات بخميس مشيط
شركة رش مبيدات بجازان
شركة مكافحة حشرات بجازان
شركة تنظيف خزانات بجازان
شركة تنظيف خزانات بخميس مشيط
شركة رش مبيدات بخميس مشيط
شركة رش مبيدات بأبها
شركة تنظيف خزانات بأبها
شركة مكافحة حشرات بجازان

Anonymous said...

And now, two years later, any change ?