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, November 5, 2009

Biofilms as Human Gut Mycorrhizals

Are Biofilms Healthy Extensions of Intestinal Villi?

If soil is the stomach of the earth, then plant roots and mycorrizal fungi must be the intestines.

Mycorrhizal fungal hyphae extend from root hairs of plants into surrounding soil and enhance the uptake of phosphate and other nutritents.  Many plants cannot colonize new soil without taking their fungal partners with them.  It would seem obvious that the highly adapted human gut flora would include bacteria and fungi that actively communicate with intestinal epithelial cells.  Perhaps that communication includes both nutrients, e.g. hydrogen, ammonia, etc., vitamins and bacterial wall components, e.g. LPS.

Plants Sit and Mine Soil, Humans Mine Nutrients Passed through Their Gut

I want to try to give a plant’s view of human digestion.  Plants elaborate roots that branch repeatedly and the final extensions sprout hairs from individual epithelial cells.  Mycorrhizal fungal hyphae further extend the reach of the plant into the soil for nutrients. 

I think that a plant would look at us and see us stuffing soil/food into our mouths and watch it come out the other end.  It would then try to figure out where are roots are, i.e. how we absorb the water and minerals from our moving internal stream of soil.  The villi of the small intestines would look like root hairs, but where are the mycorrhizal fungi?  Another problem is that the soil keeps moving past the root hairs and would break off fungal hyphae extending into the soil.  Still another problem is the constant shedding of epithelial cells from the tips of the villi.  The plant would be perplexed, but closer inspection would reveal that biofilms could solve the problems.

Biofilms Coat the Intestinal Villi

Biofilms coating and perhaps spanning the villi of the small intestines may enhance the transport of nutrients into the villi.  This may be controversial and the biofilms may be more commonly limited to the smoother surface of the colon.  The point here is that biofilms may enhance the intestinal uptake of nutrients from food.  Biofilms may, therefore, be essential for health and extend the reach of the intestinal epithelial cells.

Bacterial Community Composition May Be Determined by Diet

A biofilm is composed of some type of linear polymer, such as DNA, heparan sulfate or bacterial acidic polysaccharides, with bacteria that bind to the polymer and to the intestinal epithelium.  Diet determines the bacterial composition of the biofilm.  Thus, the newborn starts without biofilms, gut development is finished by growth hormones in milk and a single species of Bifidobacteria excludes biofilm production, until solid food or formula initiates adult biofilms.  The bacteria in the biofilm depend on diet, so the biofilms can be either beneficial or pathogenic.

Communication within Biofilms and with the Intestines

The bacteria respond to the presence of other bacteria by quorum sensing, which involves release of small molecules that alter the gene expression of other bacteria in the community.  As a consequence, genes, e.g. antibiotic resistance, are exchanged and metabolism is altered.  This is how Klebsiella nitrogenase and hydrogen production is controlled.  The biofilm bacteria also produce compounds, e.g. vitamin D (?), that alter the behavior of the intestinal epithelial cells.  The intestines can respond with inflammation to recognized pathogen components or by triggering development of cells of the immune system.  The intestines are the home of most of the body’s immune cells.

Stimulation of Tregs

Helicobacter pylori adhering to the stomach lining increases the stomach’s quota of regulatory T cells that are involved in immunological tolerance.  Presumably, the supply of Tregs in the intestines is also regulated by biofilms.  Disruption of this system by chronic inflammation can deplete Tregs and lead to unrestrained immune attack that is observed as inflammatory bowel disease.  Thus, Crohn’s disease and ulcerative colitis may be triggered by damaged biofilms.


Anonymous said...

Hi Dr. Ayers
I like this blog very much and lurk here all the time. Tho most of what is said is way beyond my scope, I get enough of the "gist" to keep bringing me back. I'm writing now just to let you know how fascinated I was by this post. As someone who has done a lot of gardening, I was actually thrilled by the parallel you draw between mycorrhizal fungae in the soil and the human gut. How startling and yet completely apt! I had the same reaction reading this as I had when I first learned about mycorrhizal threads connecting plant root hairs and soil nutrients. It changed the way I looked at and felt about gardening--it was such a concrete manifestation of the interconnectedness of life. Instead of "this" and "that"--i.e. instead of plunking this plant into that substance,I realized there is no real separation, the connection is always mediated by ever finer and more subtle forms of life. Wow. Thanks. Like reading a good poem.


Dr. Art Ayers said...

Life is a fractal poem.

Nigel Kinbrum BSc(Hons)Eng said...


The more I read, the less I realise I know!

Cheers, Nige.

Anonymous said...

Hello Dr. Ayers, I read this article about segmented filamentous bacteria (SFB) in the gut and immune response --TH17
and Inflammation.

Are you familiar with this SFB and their role in the gut?


Dr. Art Ayers said...

I am not familiar with these segmented filamentous bacteria, but their manipulation of the immune system is consistent with the concept of probiotics and beneficial biofilms. It also starts to put helminth-enhanced tolerance into a broader picture and makes sense of the developmental relationship between immune tissues and the gut. It has always amused me that B cells get their name from the avian Bursa of Fabricius, near the cloaca. I tried to get students to induce B cell tolerance by adapting thymus injection for T cell tolerance to the corresponding B cell organ. An excellent experiment, but not for the chicken-loving squeamish.

Connor said...

In your (fascinating) previous posts, e.g.

you've highlighted the likely role that pathogenic biofilms play in chronic disease and inflammation. Now, the picture appears to be more complex, if what you say is true, and symbiotic bacteria also form beneficial biofilms in the gut.

I was wondering if you might comment on how exactly the composition of one's diet affects the composition of one's gut flora. For example, do pathogenic bacteria use different carbohydrates for energy, use different mechanisms of adhesion to the intestinal wall? Basically, I'm curious what interventions you'd suggest which can preferentially increase the proliferation of beneficial microbes and/or selectively decrease the growth of pathogenic biofilms.

Thank you for your blog, which is always riveting.

Anonymous said...

I'd like to second Connor's question, because my NP has been trying to determine why my ferritin level has been so slow to rise despite supplements. She knows I am on a paleo type, (no dairy) rather low carb diet. A genova stool test showed that I had no "good bacteria" but no bad bacteria either. She wants me to take probiotics, but I think I should be able to be healthy on this diet without supplements. So Connor's question is of interest to me. My thyroid meds are finally sorted, and my cycles are much lighter, so I think the iron problem could resolve itself soon, but perhaps I need some sort of bacteria for that also.

Dr. Art Ayers said...

Connor and anon,

Oh, it is so embarrassing. I don't know how to control gut flora/biofilms with diet. Clearly communication between gut and flora are important and this is all perturbed by food. Prebiotics/probiotics can alter gut flora, e.g. the monoculture (Bifidobacteria) of exclusively breastfed babies. Reciprocal fecal transplants can make obese lose weight and lean gain. Transplants of whole guts survive if maintained by retaining the gut contents.

The immune system is developed and maintained by secondary school in the gut. The gut holds reserve bacteria in the appendix to reseed the gut after diarrhea sheds biofilms and all.

Unfortunately we don't know the requisite bacteria stored in a healthy appendix. Otherwise, at any time we could reset the gut by pushing the diarrhea button and return to health.

I think that pre and probiotics are a hedge to shift the meaningful biofilms toward health. I don't understand the whole gut community and it may include unsavory characters such as H. pylori and parasitic worms. Some of these characters, such as Hp and Klebsiella may cause ulcers or cancer when the body gets out of whack. So we may have to make some unnatural adjustments. Little is known.

Thanks for the comments.

Jay said...

Dr Ayers
Although I am not a biologist I have a little knowledge of the subject and find your blog very interesting.
I am worried though that you have overlooked something important in this post.
You say:
"Plants elaborate roots that branch repeatedly and the final extensions sprout hairs from individual epithelial cells."
Now as I understand it, in the intestine it is the MICROvilli that are the hairs sprouting from individual cells.
This is important because in many cases of Inflammatory Bowel Disease including Celiac, Tropical Sprue (AIDS under the Bangui definition) and Crohn's there is villous atrophy and few, if any, microvilli.
It appears that the microvilli are needed to absorb certain nutrients, particularly fatty acids and fat soluble vitamins and there are deficiency diseases associated with these inflammatory diseases.
In addition the microvilli are not just passive bystanders, they are also (as I understand it) the sole source of disaccharidases in the body and without them monosaccharides are the only carbohydrates that can be absorbed
without help from microorganisms - the amylases in the saliva and pancreatic juice only break the polysaccharides down into disaccharides.
Therefore many people with IBD have completely changed biofilms that supply the missing disaccharidases.
Unfortunately the disaccharide eating organisms appear to prevent epithelial cells from reaching the tips of the villi where they would sprout microvilli and the epithelial cells are passed out of the body at a higher than normal rate.
A new epithelial cell is formed in a crypt and starts to move up the side of a villus but before it gets to the top and produces microvilli it is shed into the intestine.
Your illustration does not seem to show that microvilli are only found at the top of the villi as I believe to be the case.
Around 1920 a New York pediatrician (Sydney V. Haas) discovered that children with IBD could be cured by removing all carbohydrate from the diet except RIPE (spotted) bananas and grape-juice gelatine and low lactose dairy products to provide extra protein to increase the production of epithelial cells.
Ripe spotty bananas contain virtually no starch even though green ones are almost completely starch (in dry matter) including about 10% resistant starch (RS) which cannot be digested by any human enzyme. Yellow bananas as normally eaten by American and British people and analyzed by the USDA contain starch including RS.
As their workers lived on a diet high in bananas the Chiquita company was well aware of the health damaging effects of non-spotty bananas and they put out this commercial to US cinemas in the 1940s to encourage people to eat them "flecked with brown":
Haas then developed the Specific Carbohydrate Diet (SCD) and this is still being further developed.
I think that for people with IBDs and villous atrophy sucrose is worse than honey, RIPE bananas, grape juice or a 50:50 mixture of pure glucose and pure fructose (invert sugar), commercial glucose and HFCS usually contains various oligo- and polysaccharides and is not suitable.

Dr. Art Ayers said...

Thank you for the added details of intestinal epithelial cell, villi and microvilli development. You bring up many very important points that reveal communication between gut and flora involved in gut development. The influence of nutrients also shapes the gut. There is an implication that removing the disaccharides, including the indigestible amylopectin that specifically feeds Klebsiella, that symptoms of IBD are reduced.

It is also interesting to note that the planeth cells in the crypts at the bases of the villi are the major producers of defensins, antimicrobial relatives of the cathelicidin (LL-37). Defensin production is controlled by vitamin D receptor, and defensins are deficient in IBD.

Your observations seem to indicate that the Anti-Inflammatory Diet, that I suggest, would also be excellent for treating IBD, especially since it shift the energy source away from carbs to fat.

The only problem that I have with your suggestions is the use of fructose, which I think is problematical as a contributor to inflammation. I think that it would be easy in the case of IBD to shift the gut flora to permit use of lactose.

Thank you for your input.

Dr. Art Ayers said...

A special note of appreciation for the Chiquita banana advertisement: It is brilliant.

Aaron said...

Hey Art, long time!

Check this out:

Now I wonder, how can we establish the good biofilms after we help remove the bad ones?

Jim Purdy said...

I'm a longtime reader, but I just noticed this statement at the top of your blog:

"All health care starts with diet."

So very true.

hellaD said...

Thanks so much for this great site with so much info on biofilms! I have been on the GAPS or SCD diet in order to restore beneficial biofilms to my gut. I have been on this diet for 2 years and have been improving exponentially until 6 months ago when 8 wireless smartmeters were installed right under my room. My condition then started to backpeddle.

As a result I have been keeping an eye out for posts that discuss the influence of wireless frequencies on gut flora. I have since found that by boosting my probiotic (supplement) intake I have been able to get back on my path to health.

I particularly like this article as I have also studied biodynamic agriculture and have come to think of my intestines as my roots to connect me to the world. I also have come to wonder if biofilms also help us to communicate with each other on a more intuitive level.

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