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, November 17, 2009

Bacterial Amyloid (Curli Fibers) Forms Biofilms

E. coli Curli Stacks in Congo Red Staining Fibers
We can’t cure diseases, because we don’t understand basic chemistry (what is hydrophobic) and biology (which came first the biofilm or the bacterial cell wall?)  Let’s look at a fundamental biological process, how bacteria form biofilms.

Biofilm Formation from Secreted Proteins and Polysaccharides

Investigators passed some E. coli through a special slide chamber so they could watch at high magnification as a single bacterium attached to the surface, divided to produce a colony of a few bacteria and then began to secrete proteins (curli fibers) and polysaccharides (colanic acid and cellulose) to make the biofilm matrix.  The matrix stained red with Congo Red.

Congo Red Stains Amyloids, Cellulose and Rare LPS

Staining with Congo Red shows that the spacing of hydrophobic patches on the surface of the biofilm matrix matches the flat hydrophobic, aromatic rings of the dye, Congo Red.  This particular dye is important, because Congo Red also specifically stains amyloid, e.g. beta amyloid of Alzheimer’s disease.  But Congo Red also binds to cellulose, a linear beta 1,4-glucan polysaccharide.  This seems paradoxical, because we are taught that the sugars of which a polysaccharide are made are hydrophilic.  That turns out to be a half-truth. 

Faces of Sugars Are Hydrophobic

The hydrogen bonding hydroxyl groups that make sugars water soluble and hydrophilic, radiate from a ring of carbons, and the faces of that ring cannot make hydrogen bonds.  The faces of sugars are hydrophobic and in most cases will bind to hydrophobic surfaces, such as aromatic amino acids, e.g. tryptophan, tyrosine and phenylalanine.  Thus, carbohydrate binding enzymes, such as shown in the figure bind cellulose (in grey and red) in a groove lined with aromatic amino acids (yellow and orange) so that each sugar orients over and sometimes sandwiched between aromatic amino acid residues.  This also explains why Congo Red binds to cellulose, since the aromatic rings of the dye bind to neighboring glucose residues along the relatively flat cellulose strand.  Most other polysaccharides and smaller sugars lack this spacing of sugars and they don’t stain red with Congo Red.

Basic Amino Acids Bind Hydrophobically

Another misperception is that basic amino acids, positively charged lysine and arginine, are hydrophilic.  The nitrogen atoms that make these amino acids positively charged, can form hydrogen bonds, but the hydrocarbon tails that have these nitrogenous tips, are hydrophobic.  Thus, basic amino acids and aromatic amino acids can stack to form tryptophan/arginine ladders in which they alternate.  A prominent example of these interdigitations are the way that nuclear localization signals, a quartet of basic amino acids, bind to importin via its projecting, spaced tryptophans and drag proteins through pores into the nucleus.  Similarly, the basic amino acids of heparin-binding domains extend across the hydrophobic faces of the sugars of heparin and hydrogen bond with their tips to the sulfates of the heparin.  In each of these binding examples the binding is primarily hydrophobic.

Amyloid Binds Congo Red by Stacked Heparin-Binding Domains

Amyloids are proteins that stack together like stacking chairs, so that each protein is oriented in the same way all along the stack.  In the case of the beta amyloid that makes up the toxic plaque in Alzheimer’s disease, each amyloid peptide is stacked like a hair pin on top of the next to make a fiber.  At the bend in beta amyloid, is a basic amino acid and the amyloid fiber has a band of basic amino acids along its length.  The spacing between the basic amino acids in an amyloid stack is just spanned by Congo Red, so amyloids are diagnostically stained red.  This same spacing of basic amino acids fits the sugars in heparin.  Thus, heparin can catalyze amyloid formation and is abundant in amyloid plaques in Alzheimer’s

Bacterial Biofilms Form from Amyloids and Polysaccharides

The E. coli cells that formed the biofilms that started this article secrete a protein, curli, that stacks as an amyloid into fibers.  These fibers stained by Congo Red and bind to the cellulose that is also produced by the E. coli.  It should not be surprising that biofilm formation is catalyzed by heparin and biofilm formation is a major problem in catheter infection, since heparin is used to coat catheters to keep them from forming blood clots.  Amyloids are also formed from stacked seminal acid phosphatase proteins that form fibers in the presence of heparin and facilitate HIV infection.

Do Biofilms Foment Amyloid Production?

Basic amino acids, sugars, aromatic amino acids and plant phytochemicals all bind each other via their hydrophobic surfaces.  It would not be surprising that bacteria that produce proteins and acidic polysaccharides that interact hydrophobically would also interact with host molecules with a similar spacing of hydrophobic surfaces, which are common in heparin-binding interactions and nucleic acid interactions.  The bacteria in biofilms produce both proteins and polysaccharides that may catalyze amyloid production.  The acidic biofilm polysaccharide, colanic acid, may replace heparan sulfate and curli should bind to heparin.

Berberine Binds Heparin and Blocks Amyloids and Biofilms

Just as bacterial products may compete for host heparin and heparin-binding domains, phytochemicals that interact with heparin, such as the phytochemical berberine, should disrupt heparin mediated molecular interactions, and by extension also biofilms.  There is experimental evidence for berberine both disrupts amyloid formation and biofilm assembly.


Nigel Kinbrum said...


On the subject of amyloid plaques, have you ever investigated the effect of progesterone & its metabolite allopregnanolone on them? Mum used to use a transdermal natural progesterone cream (to reverse hair loss) but she stopped using it some time before she became mentally impaired. I found a half-full pot of the stuff in mum's house and have instructed the nursing staff to rub a blob of cream on mum's skin each day to see if it makes any difference to her mental function.

Getting mum to eat more smoked salmon has perked her up a bit. I've also just managed to re-introduce turmeric into her diet by getting the nursing staff to occasionally stir a teaspoonful of turmeric powder into her orange juice (I & she can't taste it).

See Regeneration in a degenerating brain: potential of allopregnanolone as a neuroregenerative agent. and Regenerative potential of allopregnanolone.

Cheers, Nige.

Stephan Guyenet said...

Hi Art,

Do you think one of the reasons there's so much heparin in the intestine could be to promote the formation of symbiotic biofilms?

Dr. Art Ayers said...

Good to hear from you and get an update on your mum.

The steroid hormones bind to transcription factors and alter gene expression. They also control inflammation by competing with NFkB. Estrogen is also highly protective for brain trauma. So, there is a lot of potential for altering brain regeneration. Neuroregeneration may differ a lot from region to region within the brain, so even if there is no brain-wide effect, there may be a change in behavior.

Steroid hormones may affect plaque development by altering either the scaffolding heparan sulfates or the production of the beta amyloid. Both would be altered by reducing inflammation with progesterone. I would also expect these hormones to transit the BBB.

Based on the vagal stimulation/inflammation interactions, I am starting to rethink my views on subjects such as reflexology. Maybe we are like horses and out health is dependent on pressure applied to our feet.

Thanks for your thoughtful input, as always.

Dr. Art Ayers said...

You bring up a new twist related to my previous speculation on the benefits of biofilms.

Heparin is a mixture of heparinoid fragments of many different sizes and sulfation patterns. Mast cells must frequently degranulate and release histamine, protease and heparin onto the surface of the epithelial cells of the lung and gut.

Many bacterial and viral pathogens bind to the heparan sulfate proteoglycans that form and dominate the rapidly recycling coating at the cell surface. Short, haptenic heparin interferes with pathogen binding. Heparin lowers HIV infection.

Heparin should interfere with biofilm formation, if it competes for binding of bacterial adherence proteins for the matrix components of the biofilm. But in vitro studies show that heparin can stimulate biofilm formation, especially if it is immobilized on surfaces, such as catheters. It would be interesting if heparin facilitates healthy biofilms, but inhibits pathogenic biofilms. The same question holds for phytochemicals.

Thanks for watching.

Helen said...

Dr. Ayers,

I find your blog really interesting, and you have a lot of great insights, but I am a non-scientist (though geeky), and, as a mother of toddlers, I am usually too tired to concentrate on technical stuff that doesn't immediately make sense to me these days.

So, could you tell me (or tell me where to find on your blog), in summary, what is the significance of biofilms to inflammation, and what should I do about them, via diet and lifestyle?


Dr. Art Ayers said...

This article indicates that biofilms may be important in any disease that involves amyloids and there is a very long list (see Wikipedia.) Biofilms also coat parts of the gut and communicate with the gut to stimulate the development of the immune system. (Approx. 70% of the cells of the immune system are stored in the lining of the gut and it is there that they receive their final signals to change into T cells that can suppress allergies, for example.)

Gut biofilms adapt to the food we eat, so if you get sick or develop a disease, there is a good chance that your diet was a major contributor. Probiotics are a way of altering gut bacteria and changing gut biofilms toward useful and not pathogenic consequences.

If you are healthy, it is because you have established healthy biofilms. The Anti-inflammatory Diet and Lifestyle that I outline (see the top of the blog for a link) should help to produce healthy gut biofilms.

If you are sick, it may be necessary to strip off your gut biofilms to quickly shift toward healthier replacements. This is successful for autism treatment for example. I have an article on approaches to destabilize and dissolve biofilms.

For toddlers, breastfeeding is the most important consideration to develop healthy biofilms. Even a single bottle of formula makes a huge difference before solid food. Most sources recommend breastfeeding 1-2 yrs. with exclusive breastfeeding for the first six months. (My wife is a lactation consultant and I did research on passage of immunity from mother to baby, so I have to put this in.) We never used formula or baby food (mashing our own worked fine) for our three daughters. I think that I once calculated that I spent close to a year of my life in night rocking of my daughters -- that was the deal, my wife nursed at night and I did the rest of the night duty.

That is the quick overview, but if you have particular questions, just ask.

Helen said...


I'm with you on the breastfeeding, and know from experience how much work it is.

We did end up using formula some of the time because I had twins and didn't have enough milk initially, though over the first eight weeks it became less and less, finally tapering off into nothing. Although I feel bad about using formula at all, I feel proud that I was able to increase my supply and get my babies off it. It usually goes the opposite way.

I was told in the hospital and by my pediatrician that we really needed to supplement for the sake of the babies (so they could be hydrated and gain enough weight), but I do wonder if I'd gotten better lactation consulting from someone experienced with twins, if I could have avoided it. (I did get lactation consulting, but I think I needed, well, more. It is *crazy* having newborn twins, especially when they won't latch.)

Anyway, they did get food allergies, probably due to the formula. One has outgrown them, one still has a wicked allergy to eggs. But otherwise they're really healthy and are getting a diet much like the one you recommend.

Thanks for your work!

nick said...

Hi Art,

Could you please post the link to your article on destabilising and dissolving biofilms. I am especially interested in treating candida biofilms.



Dr. Art Ayers said...

You can do a search of the blog for "biofilm".
You can also look here:

Unknown said...

Hej Konst :)

Have a look at the recent paper in PLOS One about Aβ:

The Alzheimer's Disease-Associated Amyloid β-Protein Is an Antimicrobial

Dr. Art Ayers said...

That paper on amyloid beta as an anti-microbial peptide related to cathelicidins is brilliant.

That paper would suggest that rosacea is an amyloid disease like Alzheimer's of the facial skin.

Alzheimer's and rosacea both involve aberrant clipping of anti-microbial peptides that then form amyloids with anionic polymers, DNA or heparin. The amyloids in both cases stain with Congo red. I think a similar process can be invoked in beta cell death in type I diabetes.

In all of these cases, heparan sulfate proteoglycans (HSPGs) are secreted and rapidly taken up again. The amyloids bind to HS and probably disrupt normal reuptake. Inflammation disrupts normal HSPG synthesis and circulation and probably participates in the origin and maintenance of the diseases.

Thanks for the making me read this paper.

naseer said...

Dr. Ayers,

I believe that stretching the fiber disturb the glucan hydrophobic spacing. If so, there wont be a perfect stacking of aromatics of congo red with glucan hydrophobic face ? Comments on this would be appreciated.
Do you think that this alteration significantly affect the dye affinity ?

What should be the Congo red affinity to stretched cellulose fiber ?


Dr. Art Ayers said...

Mohamed Naseer Ali,
I don't understand the signifcance of stretching cellulose. Under what circumstance would it be stretched? Is this in the context of human interaction with cellulose? Most of the cellulose in the diet is left untouched and doesn't interact with human cells.

Interactions between sugar/polysaccharides and proteins/receptors are mediated by tryptophans in active sites. This is true of enzymes, receptors and antibodies. The relative positions of these tryptophans, determined by protein structure, is responsible for proteins orienting these multiple hydrophobic surface to find to the series of hydrophobic faces of the polysaccharides. If the polysaccharides are mechanically stretched, then their cooperative affinity for the protein or Congo Red, would be altered.

I hope that I have answered at least part of your questions. If not, please try again.

General Post said...

This is really a remarkable topic close to my heart thanks. Keep up the good working!Biofilm