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, February 20, 2014

Paleo Gut Flora Repair

I was shocked to learn that there were some paleo (meat and veggie) eaters who were getting cured with resistant starch.  I didn’t know that some were sick and, as I said in a previous post, I would not have guessed that starch was good for anything, but spikes in blood sugar.  I was rudely awakened by the shouts of Richard Nikoley on Free the Animal, though I suspect the sanity behind the argument came from Tim and Dr. BG (She is always right.)  He presented a kind of Second Coming of Paleo with resistant starch to feed the gut flora as soluble fiber.  How could I question food for flora?  (How could I question Nikoley without my karate gi?)

Paleo is not Paleo
It took me a while to realize that paleo is not the same for everyone.  I thought my Anti-Inflammatory Diet (meat/fish/eggs/dairy and veggies, without vegetable oils or sugars or grains) was paleo.  The way that I used this AID, it was high in saturated fat, low in polyunsaturated fat, high in protein, low in high glycemic carbs and ample in soluble fiber.  Some would say it is low carb.  Judging from comments on Free the Animal, I think I would be cast out by some of the more carnivorous (LC and VLC) in the paleo community for including soluble fiber.  Some people don’t want to feed their flora.  It is a kind of “Let them eat meat,” mentality.

Gut Flora are Friends
I think of my gut flora as fellow travelers on my life journey and what’s good for them is good for me.  I don’t intentionally abuse them, but I also forget that they might not enjoy bourbon or the phytoalexins in herbs and spices.  I don’t begrudge them the soluble fiber that they need, and I think that they are a little happier with each apple (pectin) I feed them.  I simply forget that most people haven’t taught micro, DNA sequencing and the biochemistry of plant cell wall polysaccharides.  My wife starts to roll her eyes at any sentence containing “flora”, “antioxidant”, “inflam-“, “omega-“, “carb”, “paleo”, or even “microbiome.”  And the list gets longer.  I think that I'm out of touch, until I read Nikoley.

Paleo Diet without Soluble Fiber is Hard on Gut Flora
People get sick on paleo, because they don't feed their flora.  Gut flora are needed to supply vitamins, short chain fatty acids and immune system stimulants.  If you don’t feed your flora you get vitamin deficiencies, gut inflammation and autoimmune diseases (Treg deficiency).  It is very important to remember that feeding your flora means matching the soluble fiber with the existing flora.  Most people make the mistake of assuming that if they change their diet, then their flora will also change.  Their flora will adapt with each of their hundred different species of gut bacteria increasing or decreasing in numbers, but no new genes will be present to digest new soluble fiber.  Eating a meat diet will eventually eliminate gut bacteria needed to digest some plant materials and produce intolerances.  The missing bacteria will not be regained upon return to eating plants again.

Changing Diet Does Not Repair Gut Flora
Many people lose species of gut flora as they change from diet to diet, eat processed foods lacking soluble fiber or use antibiotics.  The loss may be permanent, but need not be.  Food intolerance and most “allergies” merely reflect missing species of bacteria, and introducing new bacteria fix the problem.  Lactose intolerance, for example, can be cured by eating live yogurt.  Similarly, many immunological problems, such as autoimmune diseases, result from species of gut bacteria that are needed for the development of the immune system, which takes place in the lining of the gut in response to gut bacteria.  New bacteria need to be introduced to fix the deficiency and diet alone is not enough.  Just to be clear;  meat-exclusive paleo can lead to autoimmune diseases, because of deficiencies in gut flora diversity/species and adding back soluble fiber can only cure the diseases, if the bacteria needed to digest the fiber polysaccharides are still present or are reintroduced.  Also note that there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora.

Dairy Probiotics Do Not Repair Gut Flora Destroyed by Antibiotics
Don’t expect dairy probiotics to cure diseases caused by deficient gut flora.  Bacteria that grow on dairy cannot survive in the gut.  I know that physicians, including Dr. Oz, recommend that patients treated with antibiotics eat yogurt to repair their gut flora.  It ain’t  gonna happen.  That treatment is just for the doctor’s benefit (and provide some temporary functionality), to make her feel like she is addressing the problem responsibly.  I suggest that the antibiotic-damaged gut flora will screw up the immune system and bring the patient back to the doctor’s office even sicker.  Antibiotics are very good for business.

Health in a Crock
So, here comes the part that was missing from Nikolay’s Paleo plus RS.  He left out the missing gut flora.  RS is a panacea for those with some gut bacteria that can digest RS, but for those with profoundly crippled gut flora, e.g. some of those with autoimmune symptoms, RS is just inert fiber, not flora food.  

New bacteria must be eaten, and I think that the cure, short of the real deal fecal transplant, is still available in the original, paleo form of naturally fermented, live foods.  The answer (and please forgive the fervor, because I think health can be this simple) is Fermented Vegetables, by Kirsten and Christopher Shockey.  Their book, right, is coming out in September, and I think that the most important part of this cure is that it looks and tastes fantastic.  This is not canned, dead sauerkraut.  These are culinary delights from simple recipes in which the natural bacteria do all the work.  Since they are long time friends of mine, I have coerced Kirsten into giving me some advance access to some of her recipes.  She has also tentatively agreed to share on my blog some of her personal fermentations on happy bellies.  So check back for future posts.

Pay close attention, because some of these recipes may cure what ails you.  They have the potential to repair your gut and are the healthful fix for a sickening faux “paleo” diet.  Note that homemade, live fermented veggies contain 1) fermenting bacteria responsible for acidifying the brined veggies for storage, 2) additional bacteria of the species missing from your gut flora and are just along for the ride, and 3) veggies that have their soluble fiber intact and ready to feed your gut flora.  Cooking, pasteurizing or otherwise harming the live, working bacteria in fermented vegetables destroys their benefit in contributing to your gut flora.  It only takes a few of the bacteria that do survive passage through your acid stomach to fix your gut flora.

Major Points of a Healthy Paleo Diet
  • Meat/fish/eggs and veggies, without dairy, grains, vegetable oils and processed foods.
  • Nikoley and others pointed out that a healthy paleo diet has soluble fiber, e.g. RS, to feed gut flora.
  • Resistant starch is a unique category of soluble fiber with health benefits.  (Other types of soluble fiber may also be needed.)
  • Diet alone is not enough for health, add gut flora.
  • Diet and gut flora need to match.
  • The natural paleo source of gut flora bacteria is homemade fermented vegetables.



103 comments:

Anonymous said...

Would unpasteurized store-bought Kimchi be a good start?

Jose Marino Bernardez said...


What about fermented meat?

Raj said...

Hello Dr.Art,

I per-ordered Shockey & Kirsten book through amazon.
Mean time I started making my own RS food too.

In Kerala, India people eat Plantains fried in coconut oil, my mom used to make yam elephant foot. Also I think unripe Jack fruit should be good source too.

My question today is Bob's red Potato Starch nutritional sheet says

Total Carbohydrate 10.00 g 3 %
Dietary Fiber 0.00 g 0 %
Sugars 0.00 g

1. Why it says Fiber = 0 ?
2. Isn't carbs == sugar and insulin spike ?

Thanks
Raj

Raj said...

Sorry to have asked you a silly question, just read Total Carbs = Sugar + Dietary Fiber + Starch and that answers the question.

Raj

Ann said...

I get that we need the "soil based organisms" that culture in home ferments, but I guess I'm not understanding why yogurt and kefir won't help to fix the gut. The raw milk yogurt I make has L. bulgaricus, Sthermophilus, and L. acidopholus. Doesn't the acidopholus colonize?

Man, those fermented dairy treats sure make my tummy feel nice, though!

Dr. Art Ayers said...

Hi Raj,
The whole point of the labels is to promote sales even when the customer is asking the right questions and wouldn't buy the product if he knew its ingredients. Helpful categories would be absorbable sugar/starch, fermentable fiber, non-fermentable fiber, saturated, short-chain omega-6, LC O-6, SC O-3, LC O-3, fat etc. The ingredients should be listed based on body impact and not marketing.

Dr. Art Ayers said...

Kimchi and fermented meats can both be useful sources of gut flora, but commercial products contain carefully designed mixtures of lactic acid bacteria and not the additional bacteria present opportunistically in homemade ferments. The commercial varieties will only grow well under manufacturing conditions and not in the gut.

The gut provided a series of highly selective growth conditions of temp, oxygen, salinity, pH, nutrients, etc. Bacteria in the biofilms lining the gut are stimulated to release and exchange their DNA to form mixtures of all of the hundreds of species of bacteria in the gut. The growth conditions select for the combinations of genes that grow best. Those key genes are used to characterize species of gut bacteria and the remaining genes may differ dramatically. Thus, E.coli in Boise and E.coli in Paris share the typical Ecoli genes that determine is growth location, but the rest differ. That is why gut microbiome analysis based on species rRNA may not be as significant as the genes and total metabolic diversity present.

The bottom line, from my perspective is that health is based on a steady stream of candidate species/genes to produce a stable, diverse gut microbiome. Processed foods produce the opposite.

Raj said...
This comment has been removed by the author.
Dr. B G said...

Hi Art,

I appreciate all of your thoughts and GI KARATE~!!! Richard, Tim and I love U! I am super fortunate to work with Richard and Tim. Richard is a master integrator and fearlessly recognizes/spreads only truth. Tim is a master engineer and thus knows how to fix broken things including broken guts.

You said "Changing Diet Does Not Repair Gut Flora." I think that is sooooooo VALID AND TRUE. Unfortunately there are so many factors for this. If we think of our gut as a zoo, then for many of us those zoo cages are E-M-P-T-Y.

It takes only one round of antibiotics to wipe out our intestinal infantry in the gut. By age 20, the stats are that the average person has received 18 rounds of antibiotics (and no probiotics).

Low fiber diets -- you hit it. Paleo, ketosis, low fiber SAD are all in the same sad boat, starving our gut flora.

Glyphosate --
http://nhrighttoknowgmo.org/BreakingNews/Glyphosate_II_Samsel-Seneff.pdf

Bt GMO corn and the animals they feed -- Bt is an ENTEROTOXIN and the DNA from corn and the animals they feed have laterally transferred now to humans. We are secreting Bt it appears into our blood streams and unborn babies.
http://www.fondazionedirittigenetici.org/fondazione/files/allegatonews27aprile11numero2.pdf

DIRT -- you eloquently discuss our exposures to healthy dirt and their benefits. Most of us including Richard and I don't have a farm or garden.

Excessive exposure to parasites -- many are not aware but we have multiple exposures to parasites (besides putting our tooth brush into a toilet bowl OMG LOL). Parasites eat our mutualistic microbes! They take up residence and become very hard to eradicate. They erode our small intestines if they get a chance. We get wacky food intolerances to dairy and minimal gluten that we never had before.

In this current post-industrial age, we actually don't have enough commensals to wage strong immunity against them imho, thus parasites take more of a toll then perhaps ever in human history. I don't buy the 'old friends' Rook's theory that we need helminths and pinworms because our ancestors had them. Nope. That's BS. LOL I don't need Ice Ages either.

I think and concur with you that the old friends we need are the soil symbionts -- they keep roots from molding and pathogenic bacteria, viruses and fungi from manifesting overgrowths -- and they keep all animals and humans healthy as well. We co-evolved eating them, seeding our gut from birth and feeding them (fiber+RS). They in turn make their house their home -- controlling pathogens, feeding us their vitamins and by-products, transforming fiber into FAT and turning on our immunity (70% of which is the gut, Peyer's patches, lamina propia, myenteric lymph circulation, Ig's, etc).

So parasites are an unrecognized problem. Modern medicine relies on 200-year old primitive technology to 'find' them (eg microscope viewing). Integrative medicine relies on DNA which is reliable and accurate, without relying on chance and random vision.

The great majority of ill people have them. They are 100% overlooked in autism cases as well (hat tip Keith Bell).
http://stage.metametrixinstitute.org/content/presentations/IFM%202008%20GIfX%20RSL.pdf

Here's my story about parasites
http://drbganimalpharm.blogspot.com/2013/09/my-n1-pre-and-post-microbiome-digestion.html

Here's Renee's story in the comments about parasites
http://drbganimalpharm.blogspot.jp/2014/01/two-case-studies-diarrhea-ibs-and.html

Dr. B G said...

Glyphosate is what they spray all over municipal parks, green belts, public schools and spewing out of Round-upTM ready crops like soybeans, sugarbeets, Alfalfa, Canola, Corn, and Cotton.

The Seneff article is

Interdiscip Toxicol. 2013; Vol. 6(4): 159–184.
Glyphosate, pathways to modern diseases II: Celiac sprue and gluten intolerance

b said...

I do think there is way too much focus on probiotics , dairy and even vegetable cultures with lactic acid producing bacteria. After years of eating yogurt, drinking kefir etc and feeling like I had fibromyalgia I finally figured out it was lactic acidosis. I was not consuming overly huge amounts either. Felt better avoiding but a round of rifaxamin and I felt much better. Stool sample later showed low lactobacillus and I felt better than I had in years. I avoid dairy now as I can start getting that achy feeling again when I feed the lactose loving bacteria. I totally agree with the good doctor nurture the bugs you were born with.

Dr. Art Ayers said...

Dr. B G,
As I have been told, you are always right, but you make me feel like a wild eyed optimist.

I agree with many of the possible problems, but most are dwarfed by just processed foods, vegetable oils, sugars, wheat and amylase-sensitive starch. That means that the rest are not major problems, any more than are bad genes. I fear not GMOs or glyphosate, yet I know them well.

Thus, all we need do is fix our gut flora (always possible with homemade ferments) and eat good food. The rest fixes itself. The healthy body skips over environmental toxins and eats parasites. Pathogens are just undomesticated friends.

With a cheap $10M project to develop a factory scale system to produce freeze dried fecal transplant capsules, I think that the American health costs could be reduced by a billion dollars. Such initiatives coupled with real diets could quickly revolutionize healthcare and eliminate the medical personnel shortage while permitting universal medical care.

Did I balance your Debbie Downer? I seriously think that the human body's compensating capacity is underestimated based on extrapolation from the unusual fragility imposed by attacking gut flora by starvation and antibiotics. Evolution can't compensate for food processing, antibiotics, Caesarian sections or formula, but environmental toxins (plants are much worse) and GMOs are no big deal. Not that we have to put up with other people's sloppy money making schemes, but biology is more potent.

Thank you for being there.

Dr. B G said...

Art,

Your optimism buoys my realism ;)

Thanks Art for opening up very important conversations that beg attention. I'm so grateful for your observations and the technology of the internet to connect so many brilliant guts (our second brains) and minds!

In college I used to work in a nutrition lab to try to produce GMO strains of low raffinose beans in order to make legumes more consumer-friendly. The PhD that was in the lab told me a few years ago that he believes even now that that research was a 'bad idea' knowing the effects of GMO. He grows his own food, eats only organic and raises goats and cows with his local CSA for raw dairy in Mt Shasta.

It was startling for me, a burb girl, to learn that if Ijust soak/ferment and eat the beans regularly which are coated with assorted bacteria, eventually my gut microbiome will increase to include the DNA of the microbial enzymes that digest more raffinose and thus fart less! Nature wins.

But my arguments won't change the greed that threatens our guts. And it's extremely funny to me that we are turning to COPROPHAGY to solve our gut problems

Who is laughing? Greed! lol

g

Del said...

What a timely couple of posts! I'm doing a course tomorrow with one of the world's most renowned "fermenters". I am desperately unwell with "IBS" whatever the $#&* that is and hope this will get me on the right path. I am not an optimist but am completely buoyed by your optimism about this. If this doesn't work then it will be FMT for me! It's funny - I've always been so paranoid about bacteria and "off" food and tomorrow I will be learning to deliberately grow bacteria to ingest!

flame93 said...

Also check out this nice recipes www.paleo99diet.com

Anonymous said...

Art, I cannot eat fermented vegetables due to the fact that they cause unbearable itching where a woman should never itch...even a very small amount of something like raw sauerkraut.

Naxossa said...

@Dr B and Dr Art the criminal thing about Monsanto's assertions is the half truths more than anything else. We may not directly be affected by Bt Corn but our bacteria are. The use the same shikimate pathway for metabolism as the Bacillus thuringiensis. In other words it does affect your gut in a way that is quite detrimental, but won't kill you immediately and therefore hard to prove its devastating effect James Pott

Colleen said...

Dr. Ayers: You state: "Also note that there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora." I have read this idea in several of your posts. Could you explain this in more detail?

You have also stated that the diversity in the diet causes the gut flora to simplify and eating the same diet is better for diversity. Would you say the same foods need to be eaten on a daily basis? Is weekly sufficient? Please explain your thoughts on this.

Thanks for your very informative blog!

steve said...

Prof Ayers:
" My Anti-Inflammatory Diet (meat/fish/eggs/dairy and veggies, without vegetable oils or sugars or grains"
Question: Beans in or out of your recommendation? Elsewhere you seem to say in. Appreciate clarification.
Bubbies brand of kraut and pickles from Canada says contain live cultures.
Thank you

Anonymous said...

I also wonder if beans/legumes are in or out and also where raw tree nuts fit into the paleo picture given that both are sources of resistant starch.

raphi said...

@Dr.Art
I’m enjoying your blog very much as well as your podcast with Jimmy Moore!

I think everyone serious, thinking person agrees having a healthy gut flora is a fundamental component of ones health. Pro & prebiotics are different means to achieve the same ends: a healthy, diverse gut flora enabling proper absorption of nutrients, a balanced milieu for our immune system, daily quick-n-easy bowl movements without bloating or chronic ‘excessive’ flatulence (basically…). Agreed 100%!

I’d like you to clarify 2 points you made I may have misinterpreted or not understood:

1. “I would not have guessed that starch was good for anything, but spikes in blood sugar”
Isn’t talking about RS as a “starch” misleading in terms of its actual function (as a fiber)?
- From my understanding RS walks & talks like a fiber and most importantly isn’t digested into absorbable monosaccharides.

From “Resistant Starch— A Review” [M.G. Sajilata, Rekha S. Singal & Puspha R. Kulkarni]:
“ Type B: The type B structure consists of amylopectin of chain lengths of 30 to 44 glucose molecules with water inter-spread. This is the usual pattern of starches in raw potato and banana.
Type C. The type C structure is made up of amylopectin of chain lengths of 26 to 29 glucose molecules, a combination of type A and type B, which is typical of peas and beans. “



2. “meat-exclusive paleo can lead to autoimmune diseases, because of deficiencies in gut flora diversity/species and adding back soluble fiber can only cure the diseases, if the bacteria needed to digest the fiber polysaccharides are still present or are reintroduced […] there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora”

- Doesn’t “LEAD to autoimmune disease” suggest a causal role in producing outright autoimmunity & “there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut floraI” imply that such a diet isn’t unhealthy per se, but that it may not be sufficient to fix an already broken gut flora?
There appear to be 2 different claims being made…could you point to some literature showing how fiberless diet play causal roles in autoimmunity? No just a chain of reasoning, which I understand & agree in it being quite plausible [in addition to the anecdotal evidence]. However I’d appreciate some verifiable evidence as I’ve failed to find any demonstrating this so far.
Thanks!

raphi said...

@Dr. B G
Hi, I follow your work with interest and find a lot of value in it.
There is something that surprised me (negatively, unfortunately) in your comments however:

“Low fiber diets -- you hit it. Paleo, ketosis, low fiber SAD are all in the same sad boat, starving our gut flora.”

- [Leaving SAD aside for a moment] People trying out these diets may fail to incorporate fiber, but I do not understand why you’d categorise them as such. Eaton, Cordain, Lindberg & others never described a Paleo diet as being fiberless to any stretch of the imagination. [Granted, Stefansson’s might be the exception be the exception]. If this is based on “blog comments” of what some are doing then it’s quite the unfortunate mischaracterization…
- Ketogenic diet literature nor in its principles ever excludes fiber. Why would they? It doesn’t go against reaching nutritional ketosis - does it? The first iterations of keto for epileptic patients *might* not have incorporated fiber, but surely not because it defeated the point of the diet.
- Paleo & Keto are all in the same boat as the SAD diet?? Well, I never! [flustered Southern lady exclamation]

Thanks for your considered response :)

Anonymous said...

Could you talk a little about individuals who cannot tolerate fermented foods because they are high in glutamates, histamines, and ammonia? Also, Dr. Campbell-McBride, creator of the GAPS diet, believes the damaged gut of the MOTHER effects the baby and is one of many factors that can lead to autism. She also states that oral contraceptives damage the gut?

G said...

Raphi,

The 'strict' Paleo version does not include potatoes (or ancient sedge tubers) or whole gluten-free grains, though our early and late ancestors did thrive on them, respectively. Yes. Please read the literature!

I think the problem lies in our potential to 'burn' the viable carbs (eg net carbs). When we are born from hypothyroid, dyspeptic moms, that is hard. This newest generation has received mercury from day zero (childhood vaccination schedules) which is criminal for guts and brains; it's a gut toxin and neurotoxin. Their moms are filled with pesticides, pthalates and plastics which are potent endocrine disruptors and may cause hypothyroidism or subclinical hypo. It's difficult. Insulin sensitivity becomes even harder.

Yet fiber aids the gut-brain axis by being fermented into butyrate (if someone has the full suite of healthy gut flora -- this doubtful in my mind). Butyrate is anti-inflammatory as well as antimicrobial and an HDAC inhibitor to correct DNA editing problems. This is not happening in low-fiber diets. Also fiber by several mechanisms (GI bulking, GPR41, etc) to stabilize and normalize blood glucose and improve insulin sensitivity. Fiber helps particularly to decrease pathogen adherence to small intestinal cells (pectins like g plantain).

thx Raphi!

G said...

Raphi,

The 'strict' Paleo version does not include potatoes (or ancient sedge tubers) or whole gluten-free grains, though our early and late ancestors did thrive on them, respectively. Yes. Please read the literature!

I think the problem lies in our potential to 'burn' the viable carbs (eg net carbs). When we are born from hypothyroid, dyspeptic moms, that is hard. This newest generation has received mercury from day zero (childhood vaccination schedules) which is criminal for guts and brains; it's a gut toxin and neurotoxin. Their moms are filled with pesticides, pthalates and plastics which are potent endocrine disruptors and may cause hypothyroidism or subclinical hypo. It's difficult. Insulin sensitivity becomes even harder.

Yet fiber aids the gut-brain axis by being fermented into butyrate (if someone has the full suite of healthy gut flora -- this doubtful in my mind). Butyrate is anti-inflammatory as well as antimicrobial and an HDAC inhibitor to correct DNA editing problems. This is not happening in low-fiber diets. Also fiber by several mechanisms (GI bulking, GPR41, etc) to stabilize and normalize blood glucose and improve insulin sensitivity. Fiber helps particularly to decrease pathogen adherence to small intestinal cells (pectins like g plantain).

thx Raphi!

Per Nissilä said...

Would soil based probiotics like Prescript Assist be enough? How about home made "water kefir"?

Zarona said...

Gut Flora don't enjoy bourbon?

raphi said...

@G

Hi,

Forming a personal idea of what is Paleo & what is not is fine when applying that to ones personal lifestyle choices. However, when discussing it as a concept it’s important to have as good a working definition as can be agreed upon. Hopefully my literature references show tubers were included (with a lot of variation).
So whether you are a lower or higher-carb ‘proponent’ of Paleo, it should be recognized that tubers (& other starchy foods) were eaten - notice, I made no claim as to how much, if this was ‘good’’/bad’ or if this was universal to all hunter-gatherers (likely wasn’t).
Grains consumption was so insignificant (by most accounts) that they can essentially be disregarded as being part of the diet: totally agreed - grains are NOT Paleo. Can certain grains (like rice) be included in our modern iteration? That’s a whole other discussion…

Yes, low-fiber diets are low in fiber - this is a tautology. But you need to be more specific in order to have a advance the conversation: how low fiber are we talking? 0g, 20g, 60g? or more? What kinds of fiber?

I’m happy to follow any references showing that Paleo, LCHF & Ketogenic diets are on *principle* “low in fiber” - again, compared to what? SAD diet? Vegan/vegetarian diet? Low & high are useful only to the extent that we know the reference frame in which we’re using these terms.


- Stefansson Vilhjalmur “The Fat of The Land” 1961
“According to the geologists, the gathering stage, or apeman period, lasted several million years. During this time man ate roots and tubers, shoots and succulent leaves, fruits and yams and nuts, worms and snails and rodents, eggs and fledgling birds.”
“Rather would they be heavy eaters of what, seriously as well as humorously, we call "monkey food"—the things to eat which are discoverable in tropical forests by ape or primitive man, such as fruits, shoots, tubers and succulent plant.”

- Ian Spreadbury “Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity”
“Kitavan Islanders, one of the metabolically healthiest populations yet studied, eat a high-glycemic index, high-carbohydrate diet with staples of starchy tubers and fruits.”

- Carrera-Bastos; Fontes; O'Keefe; Lindeberg; Cordain “The western diet and lifestyle and diseases of civilization”
“Table 4 Foods consumed during the Paleolithic Era (refs: 14,64,65,154,155,157) [includes] Tubers”
“During the Paleolithic period, most of the carbohydrate (CHO) sources were wild fruit, berries, vegetables (typically presenting low glycemic index [GI] (26), and sometimes tubers, with cereal and honey intake being scarce (14,26,65).”

- George H. Perry, Nathaniel J. Dominy, [...], and Anne C. Ston “Diet and the evolution of human amylase gene copy number variation.”
“Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch.”

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BigWhiskey said...

any comments on Kimchi/ferments are risks factors for gastric cancer?
http://www.wjgnet.com/1007-9327/11/3175.pdf

Katie said...

@Dr Art - fascinating post!

You say, 'Many people lose species of gut flora as they change from diet to diet, eat processed foods lacking soluble fiber or use antibiotics.' You talk about people on a 'mainly meat' Paleo diet but what about people who have been meat-free and switch to a Paleo diet?

I was meat-free for 9 months having read 'The China Study' but switched to a Paelo Diet (Chris Kresser's 'restart' diet of meat, fish, veggies, some root starches, nuts, good fats) 10 days ago. I haven't noticed any digestive problems and wonder if this means I don't lack the bacteria for breaking down meat and fish?

But if it's possible I do, would eating fermented veggies fix that? Or is that only for people switching from no veggies?

Paul said...

Wow. This explains a lot. Looking forward to the next installment!

Dexter Yard said...

Dr Art, Never have forgotten your posts on polysaccharides, ie burdock root, chicory, jerusalem artichokes, artichokes, pectin, & jicama as being excellent for gut health. 2/3 times a week I get this into my gut...mixing with Greek Yogurt.
Thank you.

G said...

Raphi~

Good thinking. We evolved much faster after our brains got big. The last 10,000 years cannot be ignored -- some of us have the genetic machinery for bettery carb utilization and others just don't.

My kids and I are negative for FUT2 - the conscript that designates how much fucose our mucosal lining divies out for the microbiota to graze on. Fucose is part of the glycoylated protein assemblies and ABO tissue/RBC typing. Less fucose may've meant our ancestors ate more food and fuel for the microbiota, rather than endogenously secreting.

ApoE2/E3 -- this is me and my kids too. Again our ancestors I believed were not the ketotic hunter-gatherers exclusively the last 10,000 years; we have the ability to create fat from carbs better than apoE4 who don't handle carbs as well.

AMY1 -- I don't know if we are high-copy or low but since we are Asian and from rice farmers, I strongly suspect high. My worst health ever was when I cut out rice.

Where are your ancestors from? Where do you think your gut came from?

g

G said...

Raphi~

Good thinking. We evolved much faster after our brains got big. The last 10,000 years cannot be ignored -- some of us have the genetic machinery for bettery carb utilization and others just don't.

My kids and I are negative for FUT2 - the conscript that designates how much fucose our mucosal lining divies out for the microbiota to graze on. Fucose is part of the glycoylated protein assemblies and ABO tissue/RBC typing. Less fucose may've meant our ancestors ate more food and fuel for the microbiota, rather than endogenously secreting.

ApoE2/E3 -- this is me and my kids too. Again our ancestors I believed were not the ketotic hunter-gatherers exclusively the last 10,000 years; we have the ability to create fat from carbs better than apoE4 who don't handle carbs as well.

AMY1 -- I don't know if we are high-copy or low but since we are Asian and from rice farmers, I strongly suspect high. My worst health ever was when I cut out rice.

Where are your ancestors from? Where do you think your gut came from?

g

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

@G

My ancestors are from Northern Europe and the Mediterranean. I’ll know more precisely once 23andMe is available once again. I’d like to know my ApoE genotype too.
My ‘gut’ is most likely is the result of my ancestry, where I grew up (South of France) and childhood anti-biotic/cortico-steroid use due to misdiagnosed bronchitis (turned out I’m asthmatic).

Not sure that that our relative number of AMY1 copies are enough to go on to tell us how we handle carbohydrates overall - although they are hints as to how we handle their initial digestion which isn’t unimportant.

What did you replace the rice with? What else changed?

G said...

Raphi,

Have you read any of Ruth Ley's work? She has fasinating thoughts. Our guts are ancestrally carnivorous, then elongated to reduce transit to gain time for fermentation.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649005/

Some things haven't evolved but perhaps for everyone, it's different. I was just reading how junk processed fatty foods are loaded with fat emulsifiers and these break the gut (increase permeability across CaCO cells). It's this battle. We need selective permeability for nutrients to cross both ways; yet, we don't want excessive permeability because then undigested food cross and bacterial and fungal overgrowths occur in the small intestines.

Antibiotics are not good -- the commensals are fragile and we need the gatekeepers to guard permeability..... I developed asthma in my teens after a lot of antibiotics and steroids for a third degree burn. I think I avoided septicemia but there was probably a consequence (none of my siblings have asthma -- only me).

Certain probiotic strains are shining now -- for burns I was shocked to see they work to thrwart Pseudomonas and other nasties (instead of using heavy metals, topical silver).

Int Wound J. 2009 Feb;6(1):73-81. doi: 10.1111/j.1742-481X.2008.00577.x.
Bacteriotherapy with Lactobacillus plantarum in burns.
Peral MC1, Martinez MA, Valdez JC.
Author information
Abstract
Bacterial colonisation and infection remain the major causes of delayed healing and graft rejection following burns. Topical treatment is necessary to reduce the incidence of burn wound infection. Silver sulphadiazine (SD-Ag) is an often used microbicidal agent. However, this treatment produces adverse reactions and side-effects. On the basis of experimental data and clinical application of lactobacilli as probiotics, we performed this exploratory study to establish the effectiveness of bacteriotherapy with topical application of the innocuous bacteria Lactobacillus plantarum cultured in De Man, Rogosa and Sharpe medium to provide an alternative method for burn treatment using SD-Ag as a reference. These innocuous bacteria would compete with other bacteria that are wound pathogens and would modify the wound environment and promote tissue repair. Eighty burned patients from the Plastic Surgery and Burns Unit were grouped into infected (delayed) second- and third-degree and non infected (early) third-degree burns and treated with L. plantarum or SD-Ag. The proportion of patients with delayed second-degree burns was 0.71 for L. plantarum and 0.73 for SD-Ag (relative rate: -2.72%) with respect to the decrease in bacterial load (<10(5) bacteria/g of tissue), promotion of granulating tissue wound bed and healing. In early third-degree burns, the values were 0.75 for L. plantarum and 0.84 for SD-Ag (relative rate: -1.07%) in preventing wound infection and promotion of granulation tissue, 0.90 in graft taking for both treatments (relative rate: 0%) and 0.75 for L. plantarum and 0.77 for SD-Ag (relative rate: -2.60%) in healing. In delayed third-degree burns, values were 0.83 for L. plantarum and 0.71 for SD-Ag (relative rate: +16.90%) with respect to the decrease in the bacterial load (<10(5) bacteria/g of tissue) and providing a granulating tissue wound bed, 0.90 in graft taking for both treatments (relative rate: 0%) and 0.75 for L. plantarum and 0.64 for SD-Ag (relative rate: + 17.19%) in healing. Although the number of patients (between 12 and 15 per group) did not enable the application of a power statistical test, these results suggest that the L. plantarum treatment should be studied in greater depth and could be used as a valid alternative for the topical treatment of burns.

Anonymous said...

I looked at the Fermentista web site with thought to buying the book, but I am not comfortable with what I saw there. They suggest that you check the ferments for mold every day or two and, if you find some, simply SCRAPE IT OFF. That is nasty at best, and downright dangerous at worst. Mold forms penetrating tendrils long before it forms a film, you cannot simply scoop it away and eat. Plus, finding mold in the first place means you aren't really fermenting because fermenting requires an absolutely anaerobic environment. If you have mold, then you also have aerobic - and potentially dangerous - bacteria.

Ashley said...

Hi Dr. Ayers,

Firstly, many thanks for your informative blog. I am pre diabetic with high inflammation & suspected Hashimoto's & I've been following your diet & even started fermenting cabbage, thank you.

I just wanted to bump Coleen's question as I would also like to know these questions:

"Dr. Ayers: You state: "Also note that there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora." I have read this idea in several of your posts. Could you explain this in more detail?

You have also stated that the diversity in the diet causes the gut flora to simplify and eating the same diet is better for diversity. Would you say the same foods need to be eaten on a daily basis? Is weekly sufficient? Please explain your thoughts on this."

Clelia said...

Dear Dr Ayers,
I'm also interested in your opinion about soil-based probiotics ( like Prescript Assist). Could they be useful to rebuild a healthy gut flora?
Thanks a lot!

Dr. Art Ayers said...

Prescript Assist,
As far as I can see from the list of bacteria and fungi listed as ingredients, this "probiotic", is a bunch of spore forming organisms mixed with Leonardite, a relative of coal that prevents compaction. The choice of organisms seems to be based on availability, because they are used commercially to produce ingredients for other industries. One of the fungi used, for example, is the source of the enzyme, cellobiose dehydrogenase, that I discovered in Stockholm. Most won't grow in the gut, so they are transients, similar to dairy probiotics. They will not repair gut flora, but they may provide temporary benefits in cases of severe dysbiosis. Homemade fermented veggies are better.

Dr. Art Ayers said...

Ashley,
Meat soluble fiber
Your gut flora can survive on meat depleted by digestion of protein and fat. That leaves polysaccharides, glycosaminoglycans (GAGs). You have heard of these before. What are the "plaques", as in amyloid plaque and arterial plaque, made of? Protein strung on GAG (heparin). Chondroitin sulfate is a GAG made of glucosamine, a glycosamine. Connective tissue is held together by GAGs and GAGs are the main ingredient in cartilage and the contact surfaces of joints. The most common drug used in hospitals, heparin, is made GAGs in cells and is secreted with histamine in allergic reactions and also in huge amount in the gut, where it is used to block pathogens from binding to the lining of the intestines. Pathogens bind to GAGs that project like the hair of fur on the outsides of cells (glycocalyx.)

The bottom line is that animals don't have cell walls (soluble fiber polysaccharides) like plants, but they still use lots of polysaccharides (GAGs, soluble fiber polysaccharides) to hold themselves together. Gut flora can be assembled that can grow on GAGs instead of plant soluble fiber. Fermented meat would be better to repair the gut flora of strict carnivores rather than fermented veggies.

There is a big difference in the soluble fiber of plants, animals, and algae for that matter, and gut flora adapted to digest each are quite different. That is why it is unhealthy to switch from strict carnivore to strict herbivore, although a consist mixture of omnivore can also host a healthy gut flora. The gut flora can pretty much adapt to any consist diet unless it lacks soluble fiber, e.g. the modern American diet.

Significant changes in diet require eating new and different bacteria to construct a new gut flora. New and different bacteria can be found in the random bacteria present in homemade ferments.

Anonymous said...

Dear Dr. Ayers,
Thank you so much for these articles on gut flora, they are so enlighening.

What do you think of the supplement AOR Probiotic 3?

Claim:
"Lactic acid and butyric acid-producing probiotics inhibit the growth of pathogenic bacteria while promoting the growth of the beneficial Bifidobacterium strain."

Contains:

Streptococcus faecalis
Clostridium butyricum
Bacillus mesentericus

Other Ingredients: lactose, potato starch, polyvinyl alcohol, polyvinylpyrrolidone. Capsule: hypromellose, water.

Dr. Art Ayers said...

Anonymous,
Supplements are for temporary use.
For example, I recommend that people suffering from inflammatory diseases first try to suppress the symptoms just by eating more DHA/EPA and no vegetable oil. They just eat more and more until the symptoms are gone. That shows them that if they control their inflammation, they can improve their health.

The same is true of probiotics. If they actually repair your gut flora, then a couple of capsules is all that is needed. If they recommend more then that, then they are a scam for repair. The business model for probiotics requires routine use, which means that they cannot fix anything. That is the same model followed by many drugs. Some provide no benefit, but produce negative symptoms when discontinued.

Kirsten Shocky said...

Hello Anonymous,
(on mold concerns)

One of the absolute beauties of fermenting is that there has never been a case of reported food poisoning with fermented vegetables. If it is bad you know it is bad—all of your senses tell you do not eat this food. (unlike botulism) If you haven’t removed all the mold it will taste moldy and again you will not eat. In the book (where there is room for a complete discussion) there is an extensive troubleshooting section where we talk about what exactly bad looks like.

The mantra to live by with fermenting is to keep everything under the brine—anaerobic! Submerge in Brine and all will be fine!

But there is the top of the brine which comes into contact with the air and that is where the nasties can develop—scum vs. yeast vs. mold. Which is exactly the reason to scoop it out when it has just begun on the top of the brine that protects the ferment. That said even if you don’t scoop it out immediately the fermentation process kills parasites and digests mycotoxins. The nasties are competitors for the lacto fermenters and the fermenters always win (and clean up the remains of the nasties.) If they didn't, the mush remaining would be inedible. Removal of mold (or scum if you will) is common in all fermenting cook books. The hyphae don't extend beyond the hyphae mycelium, because they are the mycelium. You can see that on agar or liquid medium by microscopy.

G said...

Art,

I'd love to hear your thoughts on Clostridium both as a probiotic and as a commensal key leader in the human gut?
http://www.gutpathogens.com/content/5/1/23

Some SBOs probiotics are definitely gut colonizers -- have you seen this study looking at ancient coprolites via 16S rRNA PCR sequencing?

They resemble COMPOST!
http://www.gutpathogens.com/content/5/1/23

Anonymous said...

Kirsten,

I respectfully disagree that simply removing mold from the top of the ferment is adequate. Here is an article and a series of references that explains WHY this is poor practice.

http://www.intentionallydomestic.com/three-lies-about-lacto-fermentation-that-are-affecting-your-health/

raphi said...

@G

The study by Ruth Ley you linked to was a very interesting one, thanks, I’ll follow up on her more recent stuff as well.e

The idea of “Bacteriotherapy with Lactobacillus plantarum in burns” where the wound is ‘crowded out’ of its bad bacteria, essentially outcompeting them for resources by a ‘nicer’ strain is really forward thinking and makes a lot of sense to be honest.
How widely applied is this anti-effective method?

Alex said...

Hi Dr. Art,
Thank you for this fascinating blog. Do you have any thoughts on how to shrink swollen adenoids and tonsils in a otherwise healthy 5 year old boy suffering from sleep apnea? It seems to me that the adenoids and tonsils are swollen due to inflammation, but standard medical practice is to remove them rather than identify and treat whatever is causing the inflammation of the adenoids and tonsils.

Dr. Art Ayers said...

Alex,
Tonsillitis is associated with vitamin D deficiency, and vitamin D deficiency is typically caused by chronic inflammation, and chronic inflammation is typically caused by an inflammatory diet, antibiotics and lack a dog that likes to dig. That means to me that your boy would benefit from the whole family gardening, making and eating homemade fermented veggies, lightening up on hygiene, following my Anti-Inflammatory diet, and supplementing with fish oil and vitamin D.

There is a profoundly practical reason for kids to make mud pies. Your kid is too clean, you don't eat enough soluble fiber and you can't produce enough vitamin D by solar exposure of skin, because of dietary inflammation.

That's just a first impression based on 100,000 cases like this.

Thanks for the questions. Let me know how your son does. Tonsillitis was common in my family until I stopped paying attention to doctors and started a hobby of explaining disease. Medicine is only complex because so few doctors understand science.

Anonymous said...

http://www.nature.com/news/policy-how-to-regulate-faecal-transplants-1.14720

http://blogs.scientificamerican.com/observations/2014/02/19/hey-fda-poop-is-not-a-drug/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+observations%2Ffeed+%28Blog%3A+Observations%29

Ms.Pearl said...

"Tonsillitis is associated with vitamin D deficiency, and vitamin D deficiency is typically caused by chronic inflammation, and chronic inflammation is typically caused by an inflammatory diet, antibiotics and lack a dog that likes to dig."

Dr. Ayers,

That's fascinating; I had no idea. I grew up in the South and typically had plenty of sun exposure, as well as exposure to dogs and cats (and one horse) that I loved to kiss. Problem, though, was all the soft drinks in our diet, along with liberal use corn oil by my mother. She also used bacon fat, but I'm pretty sure the corn oil topped the bacon fat.

I had tons of antibiotics until the docs finally figured out that what looked like colds (which they were treating with antibiotics) were actually allergies (another rabbit hole).

Long story short, I had my tonsils out when I was 19 because every time I had an allergy attack, I developed tonsillitis. Imagine what Vitamin D, along with your anti-inflammatory diet, would have done.

Anyway, I appreciate your blog; I've been a follower for a long time. I didn't realize you had retired until you mentioned it in either a post or a comment on one of your posts. By any chance, are you still in Idaho?

Judy

Jenn said...

I'm a few days away from starting an anti-biotic protocol in an attempt to treat auto immune issues. Your article has me questioning my path? Do you think there is EVER a time that long-term AB's are needed? Then work on repairing the gut during and after.
I assume Dr. Meyers is quite busy and would appreciate opinions from all.

Victor Venema said...

I just came across a BBC article on the microbiome and your brain. Interesting. The mainstream start to pick up the idea.

What struck me was that this researcher had the opposite advice for a diverse microbiome, he advices to eat a diverse diet:

"Thankfully, Cryan has a far more appetising method on offer. “Diet is perhaps the biggest factor in shaping the composition of the microbiome,” he says. A study by University College Cork researchers published in Nature in 2012 followed 200 elderly people over the course of two years, as they transitioned into different environments such as nursing homes. The researchers found that their subjects’ health – frailty, cognition, and immune system – all correlated with their microbiome. From bacterial population alone, researchers could tell if a patient was a long-stay patient in a nursing home, or short-stay, or living in the general community. These changes were a direct reflection of their diet in these different environments. “A diverse diet gives you a diverse microbiome that gives you a better health outcome,” says Cryan."

Now I work on variability myself and realize that both statements can be right simultaneously, because variability is a matter of what you look at and in this case especially on the temporal averaging scale. Still I would be very much interested in a blog post on the question what a simple or diverse diet exactly is and how strong the scientific evidence is for this advice.

Marybeth said...

@Jen-
Not sure what auto-immune issue you have but I can chime in on the antibiotic protocol as I went down that path for RA. I can tell you that Dr. Ayers will tell you NO! And I will second it.

If you haven't done so already, clean up your diet and start making bone broth from grass fed bones and fermented vegetables. I use three different web sites for fermented recipes (my kitchen counter looks like a experimental lab). Also bought the Art of Fermentation for a reference guide.

I went to an alternative doctor as well as a rheumatologist during my antibiotic protocol. I used a product called Opti-Cleanse to help repair my gut along with using
supplements (Vitamin D, fish oil, vitamin C, KappArest, GI Retrieve, a probiotic and made my own coconut milk kefir). Lots of exercise. I stayed away from all the nightshades and legumes because of what I read. I have since started adding them back to my diet. I don't find that I have any food intolerances. The two things I do not use on a regular basis are gluten and processed sugar (and naturally all processed food). I do allow myself to cheat with pizza and Indian bread every so often.

I have now been off ABX for 7 weeks, started using Potato Starch at the same time and 6 weeks of fermented food.I feel fine, not sure how to judge my gut flora.

If you have any questions I would be glad to answer them for you. You can send me your email address instead of filling up the comment section on Cooling Information.

Marybeth

Alex said...

Thanks for your reply. I'll keep you posted. By the way, I already have him on a diet similar to your anti-inflammation diet and he's taking cod liver oil several times a week. I think the key difference between what he eats and your recommendations is that he eats a lot of starch/sugar in the form of sweet potatoes (almost every day), fruits, and oatmeal for breakfast (2-3 times a week). He's not a big eater of green veggies.
Maybe we need to get a dog...I like the idea of getting him involved with gardening and making fermented foods. Maybe if he helps make the fermented foods, he'll be more likely to eat them.
Do you regard diary as inflammatory? He's not interested in drinking milk but he loves cheese and I give him yogurt for breakfast several times a week. What do you think of raw milk? Thanks again.

Dr. Art Ayers said...

Alex,
I don't have problems with sweet potatoes, oat meal, cheese, yogurt. His diet is probably OK and that didn't make him sick. I would suspect that he got an antibiotic treatment and his gut flora never recovered. But you seem casual about the big issues that are keeping him unhealthy/inflamed:

Vitamin D deficiency
Omega-3/6 imbalance
GUT FLORA dysbiosis

Cod liver oil and thinking about fermented veggies is not going to cure him.

Alex said...

Oh I am not at all casual about those big issues. The cod liver oil contains vitamin D and he does not wear sunscreen most of the time - perhaps that's not enough - I'll get him tested at his next appointment in a few weeks. He's only taken antibiotics once in his life and that was long after his adenoids and tonsils became swollen. He was breastfed for the most part, but there were times when that was difficult, especially early on, and we supplemented his diet with formula - perhaps that disturbed his gut bacteria and it never recovered
I take the omega 3/6 balance very seriously. We cook only with butter or coconut oil, eat very little restaurant food and try to eat salmon or mackerel 2x a week. Plus the cod liver oil. He eats nuts, but mostly macademias, never walnuts.
What's new to me from your blog, is that the probiotics in dairy products are not enough to restore the proper gut bacteria colonies - that we need to get him eating more fermented foods and perhaps more dirt. Getting him to eat fermented foods besides yogurt and kefir is going to be a challenge - enough of a challenge that I'd seriously consider getting a dog if it will help him get better. Hence the need for thought before action. I do appreciate your input - perhaps I appeared casual in my comment - but I most certainly am not.

Dr. Art Ayers said...

Victor,
Variability, variety, diversity -- It is difficult to distinguish noise from signal. The study is difficult and in medicine, there is no profit, therefore, little study.

Elimination of soluble fiber, gut flora food, is called food processing, and combined with antibiotics, leads to the modern malaise: inflammation, autoimmunity, allergy, cardiovascular disease, depression, pain, etc. The modern diet is simplified to macro- and micronutrients. Absence of gut flora adds the additional requirement of vitamins.

First level diversity adds back purified soluble fiber, e.g. resistant starch, to produce the rudimentary gut flora with the bacterial remnants. The same result can be obtained in a random way with veggie juicing to match extant "gut flora" with a scattershot of dozens of different cell wall polysaccharides. Diversity in soluble fiber is useful to find a rare match. Dairy probiotics are useful at this level, because even transient bacteria are better than nothing.

Second level diversity is a healthy match between a complex gut flora of a couple of hundred species of bacteria that can fully digest the soluble fiber in in a stable diet. The gut flora stimulates the aggressive half of the immune system that attacks pathogens and virus-infected or cancer cells, and the suppressive half that prevents autoimmunity and allergies.

Third level diversity in diet is a shift in diet that is too rapid and exclusive for adaptation by the gut flora. Combined with hygiene and inadequate introduction of new bacteria, e.g. fermented veggies, that limit the gut flora diversity to the species already present, and the result is extinction of keystone species of gut flora and a collapse of the immune system. Shifting between restrictive diets lowers the diversity of gut flora.

The major hazards to healthy gut flora diversity are:
Antibiotics
Hygiene: antimicrobials, tooth paste
Diet fads
Food processing

Cures:
Kissing new friends, babies, pets, etc.
Homemade fermented veggies

Dr. Art Ayers said...

Alex,
I am reassured. I didn't want to not dot i's and cross t's on something this important.

Please note that if there are signs of chronic inflammation, such as swollen tonsils, then vit.D deficiency is suspected, because the inflammation stops skin production of vit. D regardless of sun exposure. There is not enough vit.D in cod liver oil to lower inflammation enough to permit solar production. Solar production in the skin is hundreds of times greater than supplemental vit.D in capsules or oil. Most propel under doctors care for vit. D deficiency remain vit.D deficient, because the supplements are low, silly amounts and the doctors don't retest.

Don't feel guilty about using formula, it is pushed subtlety, but forcefully by medical staff. Formula aggressively kills baby gut flora by supporting the growth of adult gut bacteria. It only takes one bottle of formula in the first weeks of life to have lasting impact on gut flora. (NEC is one consequence. There should be no formula use in hospitals, because milk banks are healthy alternatives.)

Antibiotics and formula are costly to healthcare systems and very lucrative to the medical industry.

Sorry about my tirades. It is a sensitive subject.

Viktor said...

Hi Dr Ayers

Just picked on your previous comment on toothpaste - any recommendations for gut friendly alternatives?

Which ingredient is the culprit?

Many thanks,
Viktor

Viktor said...

Hi Dr Ayers

Just picked on your previous comment on toothpaste - any recommendations for gut friendly alternatives?

Which ingredient is the culprit?

Many thanks,
Viktor

Anonymous said...

Thanks for your response Dr. Ayers. To clarify, I'd like to know what you think about the strains in AOR Probiotic 3 (Streptococcus faecalis, Clostridium butyricum, Bacillus mesentericus) and their ability to repopulate the gut after a course of antibiotics. It seems to be recommended for that, not for constant supplementation.

Also, since you believe constant supplementation should not be needed once gut flora are repaired, is that also true for fermented vegetables? Can they be discontinued once gut flora is repaired?

Finally, if using fermented vegetables, how does one know which strains are being supplied by the vegetables? Do different vegetables promote the growth of different strains?

Thank you again!

Alex said...

Dr. Ayers,
Another data point that might interest you. My son had his C-reactive Protein measured recently. The result was 0.2 mg/L. What do you make of that?

Also, a homeopathic doctor we have seen recommends trying colloidal silver spray in my son's nose and throat. I see you think it is damaging to gut flora. Is that so even if applied topically to nose and throat - not imbibed?

Dr. Art Ayers said...

Alex,
That CRP seems fine. The silver seems off the wall toxic and inappropriate. Silver is a persistent, systemic heavy metal and is toxic to everything at low concentrations. ???
And that is applied topically. I wouldn't use it on my plants.

Dr. Art Ayers said...

AOR 3,
I don't have any experience with this probiotic. It has a strain is C. butyricum, and that may be useful in your case. If you were treated with antibiotics, you probably lost dozens of different species of bacteria out of a couple hundred species. The probiotic at best would replace one or two of the missing species.

If you keep eating homemade fermented veggies, you may pick up a couple of new species with each batch and more with different veggies and different airborne bacteria. Commercial fermented veggies will be more uniform and dairy probiotics will only be useful as the bacteria pass through. The more antibacterial products you use and the cleaner your surroundings, the longer the repair process. If you worry about the cleanliness of public restrooms, it will be slow.

Dr. Oz is paranoid about public restrooms, and that is why he still has gut issues.

Dr. Art Ayers said...

Viktor,
Other people can make better suggestions for tooth paste that doesn't have ingredients like sodium lauryl sulfate (also used as SDS in gel electrophoresis of proteins) that is responsible for mouth ulcers and canker sores, or triclosan, which is a broad spectrum antibiotic. I wouldn't be surprised if these two chemicals that provide the foam and biofilm dissolving properties of most tooth pastes don't also contribute to sick gut flora.

Rinse thoroughly after using any cleaning product or breath freshener in your mouth. Remember that all natural plant products, especially essential oils, are toxic to gut flora, since phytochemicals are natural chemical antibiotics.

WilliamS said...

"The silver seems off the wall toxic and inappropriate."

Maybe not always. Interesting viewpoint on the use of *colloidal* silver and gold in medicine:

http://www.optimox.com/pics/Aurasol/nanoSilver/SilverGoldPlat.htm

Jenn said...

Thanks MaryBeth.

My email is jennex@hushmail.com. I'm interested and excited to hear from you.

Marybeth said...

Dr. Ayers,
How does one know if they have improved their gut flora without having your fecal matter scrutinized under a microscope?
Thanks,
Marybeth

Lulu said...

I have just discovered your blog during a search for more information regarding resistant starch. Your ideas about ferments and replacing the bad with the good gut flora have filled me with hope.

I have been dealing with autoimmune problems for 4 years now. Diagnosed with interstitial cystitis, fibro, post viral syndrome, chronic migraines, POTS, some acute neurological impairment. I did over a year of doxy and over a year of valcyte (not simultaneously). I have done SCD, Whole30, variations of paleo and vegan.

The more I have researched, the more convinced I have been that inflammation is a huge problem for me. I have a serious sleeping disorder and I know the lack of sleep contributes. I think it is a vicious cycle.

I recently came across info on resistant starch and its ability to improve the digestive biome. Until my home ferments are ready, I have been drinking red miso and kefir. I am careful not to overheat the miso (I mix the paste with cold water and then add warm water). I have taken some probiotics-Jarro-dophilus.

I am having a lot of gas and some mild neuropathy, which I haven't experienced for a while. I can't tell if it is a herx reaction or my body telling me something isn't right.

Here is my morning shake:
2 TBS unmodified potato starch
1 TBS golden flax seed
1 TBS chia seed
1 TBS Carlson fish oil, lemon flavor
1 scoop lemon neuro-mag
1 TBS diatameceus earth
2 TBS spirulina
2 TBS hemp powder

Trying to drink three cups of miso a day.

Night:
2 TBS Potato starch
1 cup kefir
little local honey

Until my ferments are ready, can you suggest anything else I can do? I am sure my gut needs a lot of repair (although, to be clear, I do not have IBS or those kinds of symptoms).

Anonymous said...

Hi Dr. Art,

Thanks for the very informative post.

For someone suffering with IBS-Constipation, how long do you think it'll take to fix the issue with eating homemade fermented veggies? Is this a process that will take weeks, months, longer?

Also, once fixed, does one have to continue eating fermented veggies every day? Or will the gut bacteria have established themselves, only needing the occasional serving for maintenance?

Thanks.

Steve said...

Would you be kind enough to tell me if these locally produced fermented products would be beneficial, under your guidelines/recommendations please. They seem to be naturally fermented by local farmers via lactic fermentation.and not industrially produce thank you.
http://www.realpickles.com/process.html

antonio sabarro jr said...

Is there anything to be said for oceanic bacteria as a means for rebuilding gut flora? ie swimming in the ocean, eating raw seafood/sea weed. I do not live by the ocean but noticed a great improvement in bowel activity/ gut health after swimming in the sea for several days when on vacation. It would be interesting to see if the American gut project finds better flora among costal people.

Ms.Pearl said...

"If you worry about the cleanliness of public restrooms, it will be slow. Dr. Oz is paranoid about public restrooms, and that is why he still has gut issues."

As usual, Dr. Art, you continue to crack me up with your insight.

As I mentioned in earlier comment above, I grew up in the American South, and food was left out all day. I regularly had "stomach flu," and since then I've rarely had it as an adult. I don't have the hygiene mentality that is so common today. That being said, I do take precautions when preparing food for friends because I don't want to expose them to something that might make them ill when I would remain immune.

I noted one comment above decrying your friends who are writing a book on fermentation because they suggest scraping off mold and going forth.

I've been doing this a long time with my ferments. Some of them were questionable: one batch of my preserved lemons comes to mind. That batch smelled like purex and had a horribly grotesque mold growing on top. The intrepid me scraped the mold and a few superficial layers off, and poof! the problem was solved. I've been eating from that jar for 3 years, and I'm still here.

Dang. I guess I'm not paranoid enough.

judy

Steve said...

I eat a fairly decent amount of white rice (that is usually reheated) and reheated waffles (that are made largely from potato starch and rice flour, then frozen). I have a smaller amout of total fiber intake (around 24 gms per day) from dark chocolate, fruit and veggies. i regularly eat small amounts of fermented veggies. I seem to have a very robust digestive system, averaging 3 good size BMs per day. i've always wondered how this is possible, since I don't eat that much fiber. Would the reheated rice flour/potato starch waffles and reheated rice add a significant amount of resistant starch leading to more stool production? thanks!

maria said...

Dr. Art what's your take on seeds? I know seed oils (omega 6) are dangerous and are definitely a no, but what about sunflower seeds, chia seeds, flax, etc? Are any seeds good?
I have Hashimoto's I don't know if that makes a difference on including them on my diet. Thank you.

Sally Leone said...

Dr Ayers,

You've posted that since our guts can handle plant toxins we should be ok with what man made toxins we come into contact. What is your take on the radiation of west coast seafood from the Fukishima reactor. Can our guts handle that?

la femme natale said...

Dr. Art Ayers,

I am once again greatly entertained and educated by your blog and its commenters.

I haven't eaten fruit in years, and I recently wanted to give it a try. Although I regularly eat starches and homemade sauerkraut, the fruit just blew me up. How would one get the necessary microbes to digest fruit without fermenting fruit into alcohol?

Thanks.

la femme natale said...

Hahaha, now I've just read your post "Phytochemicals, Natural Antibiotics and Antioxidants" where you basically say to juice fruit, throw out the juice, and eat the fiber. Disregard my fruit question!

Out of curiosity, have you read about the
Kitavans and their diets?

Dr. Art Ayers said...

la femme natale,
I am familiar with Stephan's discussion of Kitvans. I think that the important point is the meaning of "carbohydrates." I think that the Kitavans have a low glycemic diet and most of the starch that they consume is resistant to pancreatic amylase (RS), meaning that it is actually soluble fiber used to produce anti-inflammatory butyrate by colon gut flora. I would call this a low carb, high fiber diet. I assume that their gut flora is rich in the Clostridium spp. That stimulate Tregs and reduce autoimmune diseases.

Dr. Art Ayers said...

Sally,
The levels of radiation are vanishingly small. I am much more afraid of antibiotics, wheat flour, vegetable oil and fructose than environmental toxins and radiation.

Health is 90% diet, gut flora and exercise. Personal genetics, environmental toxins, etc. contribute a few percent each.

Kay Dee said...

There is one big thing this that Blog doesn't treat:
stress, and stress Hormones up-down-regulation.
-
Cortisol pushes on blood glucose, so up regulates insulin.
Cortisol shuts down immune system activity.
So "immune-system/microbiome" continuous modulation is disturbed.
Cortisol blocks fatty acids release from cell membranes, so blocks eicosanoids production, so blocks inflammation modulation.
Cortisol impairs Thyroid activity, so slows metabolism, so impairs immune activity, slows gut motility, so interferes dramatically whit micro biome.
-
Just to say they I'd love to read a post on stress.


Thank you for sharing your science Dr. Ayers.
Kay Dee.

WilliamS said...

"I think that the Kitavans have a low glycemic diet and most of the starch that they consume is resistant to pancreatic amylase (RS), meaning that it is actually soluble fiber used to produce anti-inflammatory butyrate by colon gut flora. I would call this a low carb, high fiber diet."

Interesting thought. I'm curious how you arrived at this since the Kitavans reportedly eat lots of tubers and fruit, which I'd think would provide quite a bit of digestible starch in addition to their soluble fiber.

Anonymous said...

As you start to add fermented foods to the diet, would digestive symptoms such as heartburn get slightly worse at first?

Asim said...

Hi Dr. Ayers,

Richard mentions tubers a lot these days and how primitive societies spent their time going for the portions close and in the soil, according to my understanding. This seems to blend well with what you have always been saying in relation to gut diversity and eating the bugs, and not being excessive in terms of cleanliness. The tubers provided the resustant starch to which the critters in the soil looked to eat, so while primitive man was eating plenty of resistant starch, they were eating the bugs attached to the tubers within the ground as well. The more I read what you say, the more it makes sense. It doesn't necessarily have to be about the type of food you eat, such as a magic food pill like a particular nut, but consuming foods like resistant starch with the flora attached to it, thus the idea of eating locally and off the ground or through fermentation. Everything else is really irrelevant.

Asim said...

Even in one of his latest posts, referencing carnivorous cultures and people like the Eskimos who live in cold regions, where access to soluble fibers from vegetation is limited, he mentions the notion of the 'fiber' within raw meats and consumption of organs that were not cooked and had the guy bugs attached to it, fed by polysaccharides which you mentioned in the past in brief as well, when talking about things like glucosamine. As long as your eating the bugs and giving them food and getting your basic nutrients, whether veggie or meat, avoiding things like industrial oils in large amounts, health should come.

Asim said...

It's almost as if the real issue is phobia to dirt. Modern society, everything has to be sanitized in some way. As a kid growing up, eating fruit off the tree or veggies on the ground were common. Chewing grass in your mouth while playing outside was nothing.

Anonymous said...

Dr. Ayers: in many of your blog posts, you recommend the consumption of soluble fiber. Other than apples and onions, could you provide some other foods that provide good amounts of soluble fiber. Also, it is correct to assume that if I consume fermented carrots for example, then I would be building the appropriate bacterial colony for proper digestion of raw or cooked carrots. Thanks for all you do. Ron

LeonRover said...

Due to blogger reload error I was left with Cool Art's latest post at the top of my list.

I glanced thro' the comments noting that there were 2 references to Lindeberg's Kitavan research.

Here's a link to a Lindeberg paper I have on open FireFox page.
(Am J Clin Nutr
1997:66:845-52. Printed in USA. tO 1997 American Society for Clinical Nutrition
845
Age relations of cardiovascular risk factors etc.)

cn.nutrition.org/content/66/4/845.full.pdf+html?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=lindeberg&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT

Table 1 shows:
Yam, sweet potato, taro 1200 g/d CHO 300 g/d
Fruit 400 g/d CHO 50 g/d

This from an estimate of 2200 kCal/day for a 38 kg person. Lindeberg does not state the tubers have been processed; the inference I take it is highly fibrous. Refined CHO I estimate at 25 g/d glucose, 25g/d fructose.

Elsewhere Lindeberg states that much fruit is left to rot.
Sláinte

Anonymous said...

Good discussion. A lot of this information is speculative. Not saying it is bad advice, but where is the experimental data to back up all these claims? Seems ridiculous to be concerned about potato starch.

Sally Leone said...

Dr. Ayers,

Thought you might like this post and discussion over at Norm Robillard's site 'Digestive Health Institute'
regarding resistant starch. http://digestivehealthinstitute.org/2014/03/24/resistant-starch/
My take away was if you have a really sick gut RS may or may not help you. But if you are relatively healthy and looking to increase butyrate producing bacteria then RS is probably a good source? Your thoughts on the post would be appreciated.

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Anonymous said...

Hello,
My daughter has moderately severe psoriasis/eczema. Could this be related to gut dysbiosis? I plan to try your suggestions re: resistant starch, veggie ferments, etc, but wondered if you had any other suggestions? She also has low T3/T4, with extreme fatigue, and is now on thyroid meds. She is only 13. Could all these problems be related? Thank you so much for any insight!-Laura

Anne Clive said...

Hi There - what an amazing site -such knowledge -I am 57 -very active and generally well -I have had rosacea for years but seem to be improving somewhat -due to recent 2 yr paleo plus dairy -diet -which I love -BUT what I thought to be anxiety turns out to be a high histamine problem -self diagnosed -but fairly obvious -hilarious loading with tuna and anchovy or chicken soup spending days in the fridge -I hate waste and so my food lasted ages -no more -I eat fresh -huge difference -so I had 2 sorts of flushing face -and can watch certain foods gang up on me -strawberries instantly -I've never thought of myself as sensitive to anything -but it seems I'm sensitive to loads of things -now I understand why red wine makes me flush-and gives me a headache - which I thought was the rosacea -and probably is -but its also high histamine -
ALSO -4 yrs ago I had dental implant work over 2 years and had disastrous amounts of anti biotics -I have always had lousy teeth -loads of abcesses -root fillings and finally 6 implants -I now have the cleanest mouth ever -have really got the hang of mouth hygiene -and hope I've stopped the downward spiral of disappearing teeth -also in the past I have had amoebic dysentery and giardia -in India - and again loads of antibiotics -so my poor gut flora over time -although I will say I eat ludicrously well now -and have finally given up dairy -I knew I had to one day -and cheese is riddled with histamine -so - my bowels seem to work really well despite all the insults -I've often used acidophillus which I now see was pointless - my real question -after all that history is -fermented anything is high histamine so how do I repopulate my bowel with all those beneficial bacteria you suggest by fermenting vegetables ?

you might need a lie down after reading all that

Thanks for such a brilliant site

Anne

Ann said...

Anne (nice name!)

Two other blogs you may want to visit regarding gut health are Animal Pharm and Free The Animal. Big discussions going on there about gut health and probiotics right now. Also many great professionals posting there and answering questions.

I had many of the same problems as you. Poor gut flora, histamine issues, skin problems, etc, etc. When I started fermented foods I had headaches EVERY DAY. It was obvious cause/effect. I would eat something fermented, and within 1/2 hour I'd get a headache. Also many food intolerances and seasonal allergies just getting worse and worse as years went on. First I was having problems with gluten, then dairy, then potatoes, then oatmeal, coffee, chocolate - the list got longer and longer. It seemed like the foods I COULD eat was shorter than the list of foods I couldn't.

I started taking probiotics with "soil-based organisms" seven weeks ago, and within two or three days the headaches from the fermented foods were gone. Also other benefits as well - stools improved, skin improved, more energy, better sleep, and improved tolerances to some foods. I had been completely unable to eat regular potatoes for about the past year, but after a few weeks on the probiotics I was eating potatoes again. Still some issues with dairy - mild depression and anxiety, mild asthma symptoms when I consume daily, and my seasonal allergies are worse this year (but so are everyone else's it seems - I live in the Pacific Northwest - apparently THE epicenter for mold and plant pollen allergies)but I have every confidence that will get better this year.

The probiotics I'm taking are Garden of Life Primal Defense Ultra, Prescript Assist, and AOR Probiotic 3. All have different organisms in them, so I cannot tell you which ones are helping the most.

I am also taking the usual obvious acidophilus and biffidus strains. I take one probiotic called "Theralac" which has six strains considered to be "colonizing" strains.

I've been using a "carpet bombing" approach with probiotics this year, reasoning that if I bombard my gut with enough different strains, some will stick and crowd out the bad guys. So far so good, and I'm feeling better all around.

Hope you have improving health and good luck!

Ann

Alex said...

Hi Dr. Ayers,
Just wanted to give you an update on my son with the enlarged tonsils/adenoids and resulting mouth-breathing/sleep apnea. His vitamin D level was 45.3 ng/ml in mid-April. He plays in mud frequently - we have woods with a creek nearby.
Getting him to eat homemade sauerkraut has proven to be quite difficult so I have been giving him Ultimate Flora kids probiotic and more recently some Prescript-Assist. I do mix a bit of juice from the sauerkraut in with smoothies or applesauce but don't know what kind of dose that gets him. His tonsils are as enlarged as ever and the sleep apnea continues. If homemade fermented foods are to work, how long should I expect it to take before I see results - are we talking days, weeks or months? With Vitamin D normal and CRP normal, along with a likely good omega3/6 balance, is systemic inflammation still suspected? Thanks again for your enlightening blog.
Alex

Sally Leone said...

Hi Dr. Art,

Found this meta study showing correlation of fermented food intake with increased esphogeal cancer risk in certain countries. One conclusion was the certain fungi release carcinogenic chemicals. I wondered what your thoughts were? The study: http://www.nature.com/bjc/journal/v101/n9/full/6605372a.html. I did a search on your site but couldn't find anything. Thanks.

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