Monday, September 29, 2014

Don't Take Resistant Starch Alone: Whole Real Food RS3 Expands Lean Core Microbiota Whereas High-Dose Raw Potato Starch Doesn't Appear To, N=1 (Part 2)

Black Box? The Gut is Complex

Unless one does urine and stool testing, the gut is dark, dark, dark black box, especially if you don't have contact with healthy soil and/or challenged by a health disorder or disease like any of the below which are all associated with missing microbes combined with toxic overgrowths:
--chronic fatigue syndrome  [I had this]
--hypothyroidism or other autoimmune disorder (Grave's, Sjogrens, MS, RA, reactive arthritis, alkylosing spondylitis, celiac, etc) [I had this]
--hypertension, heart disease
--diabetes, severe insulin resistance  [I had this]
--struggling with body fat, obesity  [I had this]
--fatty liver, elevated liver function tests  [I had this]
--gout, hyperuricemia
--hypothyroid, hypoadrenal  [I had this]
--poor gut health (constipation, diarrhea, loose stools, cramping, etc), IBS, IBD, CD, UC, C difficile
--broken brain-gut: foggy fatigued frazzled fat  [I had this]
--mood or mental health, paranoid/schizo, bipolar, anxiety, depression, etc

Many factors affect what goes on in our small intestines and colon. The gut environment is regulated by pH, transit time, organic acids and various gases emitted by our little zoo.  With over 1000 species in there, each has to be fed and each cross-feeds each other as well as us, the host. Populations shift quickly like based on the dynamics in there. Our colonocytes devour much of the butyrate produced and our liver and mitochondria, the rest (acetate, propionate). Hydrogen (H2), carbon dioxide (CO2), sulfur (H2S-- often smelly), and methane (CH3 -- scentless) determines the population shifting because they are actually 'food' for somebody in the zoo.

Test...don't guess.

Flint et al JAM, 2007
GUT: Black Box of Metabolic Crossfeeding

Nature Abhors a Vacuum; So Does Your Gut

Don't take raw resistant starch alone -- Consider taking the entire spectrum of fiber and cooked + raw resistant starch to feed the entire village in our gut, not just the RS2 eating ones. It takes an entire village to make a healthy host.

I love the biohacking on the gut that Tim Steele has done! His gut is really optimal in many respects I'll review. To me it is an excellent example of the power of food and food therapy. Please see his gut testing blogpost on how the uBiome test showed that with real food, cooked-cooled RS3 appeared to help more ANCESTRAL CORE MICROBIOTA TO BLOOM. The ancestral core is a great reference point because these are the core strains found in non-diseased, low inflammation, healthy European adults. His results require confirmation (the simultaneous AmGut is pending).

Nice QS n=1 Experimentation 

Gut Microbe

Genus Level

20-40g RS3
for 6 wks

Real Food
Tim's Results

uBiome Normal

20-40g RS2
for 1 year

Potato Starch
Tim's Results
F. prausnitzii
(?suboptimal, not B.longum)

Switching from high dose RS2 to real food high RS3 not only preserved the Bifidobacteria but significantly and dramatically expanded several of the big butyrate factories, lean (twin study) biota and ancestral core [based on %relative abundunce, not sheer #].
Enriched in mice colonized with or invaded by members of a Ln microbiota: 
Bacteroides uniformis* -- B. vulgatus is one of ancestral core
Bacteroides vulgatus* -- one of the 7 ancestral core
Eubacterium desmolans* -- E. rectale is one of the 7 ancestral core
Parabacteroides merdae*
Alistipes putredinis* -- one of the 7 ancestral core
Ruminococcus callidus
Ruminococcus bromii -- one of the 7 ancestral core
Clostridium symbiosum
Roseburia unclassified -- one of the 7 ancestral core
Clostridium ramosum
Akkermansia muciniphila ~~ high in hawwt, high lean mass rugby players w/low inflammation
Ruminococcus obeum
Ruminococcus sp. 14531
Eubacterium ventriosum -- E. rectale is one of the 7 ancestral core
Betaproteobacteria unclassified
Burkholderiales unclassified
Personally I think comparing uBiome with AmGut is like comparing apples with oranges -- but let's take them for face value and see if they confirm published 16S rRNA study outcomes. The uBiome did not show any significant deficiencies when Tim dropped the PS. In fact, his superior gut responded very adequately and got even better.

Profound changes on Tim's two stool tests:
uBiome (fiber, high RS3 cooked-cooled) versus AmGut (pure high RS2, low fiber)

--F. prausnitzii 1.7-fold increase (clostridia cluster IV)
--Ruminococcus 4-fold decrease (clostridia cluster IV) ~ POTATO STARCH LOVER
--Roseburia** 36-fold increase (cluster XIVa)
--Eubacteria 8-fold increase (cluster XIVa)

Benefits of Roseburia**

I'm a huge fan of Roseburia**: R. intestinalis is a Big Phat Butyrate Factory and Eats Oligosaccharides Inulin, Cooked Resistant Starch, Digestible Starches, Chitin, Beta-glucan and Much More. It is the major butyrate factory for tested humans and appears to go down 4-fold on VLC diets, with identical reductions in butyrate and short chain fatty acid production.  That makes sense, no? Starchy carbs contain RS3 and grain/legume related fiber like beta-glucan and oligosaccharides. Starchy fruit like banana contains inulin.  To me, Tim's results make sense in the context of Roseburia, Eubacteria and F prausnitzii studies. These are not big RS2 eaters so may have become diminished and overshadowed to below the normal healthy averages.

Starches, inulin, oligosaccharides, beta glucan and RS3 all feed directly or crossfeeds to Roseburia, however, it seems to prefer a wide spectrum of fiber (except RS2). This was the major jump I think for VLC'ers and starch-free, low-carb Paleo diets.  It is ironic because the whole spectrum of fiber makes us insulin sensitive and burn fat better. RS2 mildly does too but not to the high degree as inulin, glucomannan, whole (gluten free) grains, chana dal and legumes.

Fermentation of RS2 (green banana flour/version B or raw potato starch/version C) will be spread completely through the entire colon if taken with insoluble and soluble fiber. What counts? A fiber rich diet of 15-25 or more grams daily of rainbow foods (plants and fruits with diverse color polyphenols and antioxidants known as proanthocyanidins). Psyllium. Steel cut oats. LEGUMES OR WHOLE ROASTED POTATOES (which are paleo foods imho). Inulin rich foods are asparagus, artichokes/sunchokes, onions, chives, shallots, leeks, garlic, chicory, endive, many roots, and yacon. Every geographical area on earth has easy access to cheap inulin (fructan) rich foods. The natural human diet might be a FODMAP- and RS-rich diet for perfect gut health. Chart of FODMAPs.

I'm also a huge fan of Tim's guts. It superior in many respects.
--full spectrum of ancestral core present which are seen in the healthiest, non-diseased in Europe (Julien Tap's work); many of these strains I see 'missing' on many reports. He's got them.
--awesome stool pH
--no yeast
--no parasites
--no pathogenic bacteria (Shigella, Salmonella, Neisseria, Yersina, Proteus, Serratia, Kleb pneum)
--high butyrate and off the chart SCFA production (personal communication)

He can feed his gut prebiotic food and see many low frequency strains flourish and easily thrive. Perhaps certain guts are more reliant on certain strains than others. Every gut is different and testing is really the only accurate way to determine what's inside.

He reported GI/TMI problems on just food only, without supplementation of extra gut bug food (potato starch). After losing 100 lbs of fat and reversing every modern disease (Hashimoto's, diabetes, gout, fatty liver, obesity), his gut seemed suboptimal despite an awesome high RS3/fiber diet and years of weeding with frequent use of a high antioxidant botanical tea. I think Tim's gut maybe have felt the 4-fold drop in Ruminococcus bromii, just as VLC'ers had an observed 4-fold in Roseburia and subsequent vacuum of butyrate.

I think supplementation is good in this respect, even for a potato farmer with routine access to chicken coops, poops, manure compost, muddy root vegetables, homemade kvass and kefir!
"I will say that at about 2 weeks on the 'no PS' diet I noticed some changes in my digestion. I again had some minor smelly farts, my 'TMI' was a bit 'looser' than I like, and I was not quite as regular as I had become accustomed to. By the end of the 6 weeks, I was feeling fine digestion wise, but things were a tiny bit different--not bad, but different. I tracked FBG intermittently and found no big changes. Sleep stayed great.

After the experiment, I went back to taking 2TBS of potato starch daily and within just a few days I was back to normal in the TMI department, nice, well-formed stools, and the gas went from 'silent but deadly' to 'loud but friendly.'"


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


You mentioned the wonderful dandelion greens which I'm envious of! Certainly I think there is synergism between probiotic+fiber as well as fiber+RS so combining all the different RS and fiber spectrums was ancestral and yielded such an enrichment of the 'core' that gut researcher Julien Tap studied in healthy Europeans.

I concur -- the testing is still in its infancy and discrepancies are not uncommon:

(Mr Heisenbug discussed thoroughly as well -- I am looking forward to his own uBiome being posted soon)

All your self experiments are fascinating! Inulin is awesome! Thx for sharing what you've done. I'll do one soon but I'm afraid t won't be even a fraction as diverse, robust or resilient as yours!! I've seen quite a # of testing GDX, ubiome, amgut and functional med labs -- no one looks as superior as yours, from your perspective.

Dr. B G said...

BTW what do you guesstimate the daily (fiber) NSP intake was for the 6wk RS3 experiment? Was white rice the only grains? How many servings of 'slow carbs' per week (lentils, legumes 1/2cup=1 serving)?


Viktor said...

Hi Grace and many thanks for a great blog!

Would you mind outlaying which test your recommend doing and, if you or any of your readers have the information, how to practically go about doing these test if you reside in Europe.

I am a long term sufferer of seborrheic dermatitis and I am convinced that there is a gut-link in this condition (also noted in some research papers). If you have any additional input on this particular condition I would be very thankful.

Kind regards,

Dr. B G said...


Glad you enjoy it!

Most modern conditions are all missing bifidobacteria and all of our soil organisms.

You can't go wrong imho following the 7 steps and using version B of bionic fiber. Most people however also have yeast. Ashwin and several commenters and I discuss several methods to weed candida down while raising the good gut symbionts

Please let us know what questions you have and your progress!

After I added what I was missing and lowered the yeast/fungi, I saw success rather quickly. You need to target what is high+low. lol

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


Thx!! Black rice is great, eh!! Yeah green mung beans cook fast -- I found out the hard way too! My dad used to make a sweet soup and chill it every summer. In Asia they like to put mung and 4-5 other beans and croix (boiled) on shaved ice in the summers. The topping is sweet evaporated condensed milk (I have to tell the ladies to scoop only half).

I think you said the 1 year experiment with 20-40 g Bob's Red Mill PS daily was also high fiber but was it as high fiber as this n=1?

Did you notice any other physiological or anatomical changes?
--more lean, less lean?
--better brain-gut, less?
--better muscle gains, less (lifting or farming)?
--any before- or after lipid, thyroid or A1c panels?

Sorry to be nosy! in the name of SCI-ENCE.

Excellent summary -- sounds very much like the 7 steps and rich in RS3, soluble and insoluble fiber and immunoprotective oligos.

List of RS3 rich foods (written by Tim Steele)

Arabinoxylan -- whole grains, psyllium

Arabinogalactan - a storage carbohydrate of trees and many plants (carrots, radish, black gram beans, pear, maize, red wine, tomatoes, sorghum, coconut meat)


Glucomannan - found in the cell walls of certain plant roots and wood, also a component of bacterial and yeast membrane. Konjac roots contain 40% by dry weight and are a great source of glucomannan

β-Glucans - found in oats, barley, whole grains, shiitake, oyster, maitake, mushrooms, dates, yeast

Pectin - found in avocados, berries, citrus, fruits, vegetables

Gums and mucilages -- found in grains, legumes, seed extracts (guar, locust bean), tree exudates (gum acacia, algal polysaccharides (alginates, agar, carrageenan), psyllium

Anonymous said...

Which lab do you recommend to be tested for dysbiosis and parasites? I've been tested through Diagnos-Techs before and they showed yeast, blastocystis hominis, and several pathogenic bacteria, as well as very low SIgA. I'd like to be tested more thoroughly for parasites because my adrenal fatigue slipped into CFS six years ago after a trip where I went tubing in a river and stayed at a house with two pets.

Dr. B G said...

What did DiagnosTech say you were low in? Bifido? Was lactobacilli high or low?

Well B hominii and yeasts are a good place to start!

GDX had parasite testing using 3 days of sampling

Biohealth too and both reliable IMHO

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


Can you believe I'm pushing the off-white powder? lol I do prefer leek soup though!

I love seeing your numbers which make me giddy -- the A1c shows a wonderful trend and improvements in overall sensitivity! It must mirror the health of the gut too. In Shanghai at the peak of dysbiosis (because I didn't know but I had parasites, M.morganii and yeasts), the HgbA1c was 5.4% and I was eating too many almond flour based 'breads'. lol I stopped these and within a few wks it was back < 5%

Numbers are the biohacker's best tools, with the right context, s/sx and vision.

BEAR SLOBBER AND POOP!!!! ~great!!!! Frozen is better than nothing for probiotics

Galina L. said...

There is a bid taste difference in the buckwheat bought inside any American store and the type sold in Eastern European stores in US. American type is over-roasted or raw and turned into mash when cooked.

Dr. B G said...


Why is that? I had some in China that was apparently organic dark and lighter buckwheat that fell apart too quickly. My Russian friend grew up with buckwheat porridge everyday (and there are studies showing Russians have the most strongest, longest um colons) so I tried it and it is a little like oatmeal.

Do you soak? Soaking makes them fall apart faster

Galina L. said...

In my opinion in American stores buckwheat is roasted to a higher degree, and it taste much worse than the one eaten in Russia and sold in Eastern European stores in US, plus turns into much instead of still stay like grouts. Just buy another kind and you will notice huge difference. On the top of it, in ethnic stores it is also cheaper. It is too late now, I will write with more details tomorrow.

Anonymous said...

So I tested and found blastocystis. Any thoughts on oregano oil or other weeding protocols? My doctor wants to use metronidazole but hoping to take less drastic measures if possible. I've been doing the 7 steps prior to testing and have been having really good digestive results (thank you)! All that's left now is a nummular eczema rash...

Dr. B G said...

There are many things that 'squeeze' out B hominii but also need to start with as healthy a gut and less yeasts/Candida. Yeasts always co-exist with pathogens. Sorry -- your doc is wrong, need to target both. And if metronidazole is used, residual lactobacilli strains will get decimated (sometimes that's good if all in the small itnestines causing fat/foggy/fried) along with good soil and bifido bacteria. This leaves even MORE yeasts/fungi unless antifunals/botanicals exercised concomitantly.

It's not as easy as rx = metronidazole without long term effects evaluated

Galina L. said...

Good quality buckwheat shouldn't fall apart quickly, groats should keep shapes well while being nutty and fluffy inside. Some people soak buckwheat, some don't - groats absorb water well, if you pour 2 cups of water into 1 cup of groats, in a while water will be absorbed, and buckwheat will be cooked in a shorter time. Actually, it will be complitely eatable after soaking, but not fluffy inside. I usually don't do it. It is a normal practice to reheat a pot with a kasha several times before meals while keeping pot in a refrigerator or on the top of a stove between meals.It doesn't get spoiled easily. Morning gruel is most often made with a cut groats, whole ones are used for a side dish, hot groats are also consumed with a cold milk and salt.
I don't think that Russians colons are long due to eating a buckwheat. People also consume huge amounts of cold sauerkraut, beets and pickled vegetables, mushrooms, root vegetable salad with beets Vinegret is very popular. Do you want cooking directions? It contains root and fermented vegetables and dressed with a mix of oil and a brine.

Dr. B G said...


I appreciate your thoughts -- what other high fiber foods do you think Russians and other northern Euro ate ancestrally? Millet, amaranth, rye, barley, wild rice, spelt/wild wheat?

Those are awesome fermented root salads! YUMM ;)

The poor ate a lot of buckwheat, is my understanding. They contain AX (arabinoxylan) which are superfoods for our gut (psyllium has AX; version A of bionic fiber).

During the intermittent ice ages and aridification -- these grains became more tolerant of the flux of weather. AX may've been selected to buffer the drought and cold/heat stressors.

I suspect our gut bugs adapted as well lol. And grew longer um colons. Beans adapted too - they grew more oligosaccharides which are super nuclear fuel for our flora too

Carbohydr Polym. 2014 Feb 15;102:557-65.

Effect of heat and drought stress on the structure and composition of arabinoxylan and β-glucan in wheat grain.
Rakszegi M et al

The effects of heat (H), drought (D) and H+D (from 12th day after heading for 15 days) on the dietary fiber content and composition (arabinoxylan (AX) and β-glucan) of three winter wheat varieties (Plainsman V, Mv Magma and Fatima 2) were determined. Results showed that H and D stress decreased the TKW, the β-glucan contents of the seeds and the quantity of the DP3+DP4 units, while the protein and AX contents increased. The highest amounts of AX and proteins were in the H+D stressed samples with heat stress also increasing the water extractability (WE) of the AX. However, while the content of AX content was generally increased by all stresses, drought stress had negative effect on the AX content of the drought tolerant Plainsman V. Fatima 2 behaved similarly to Plainsman V as regards to its drought tolerance, but was very sensitive to heat stress, while Mv Magma was the most resistant to heat stress.

john said...

Although it is "insoluble," fiber from coconut might be worth a try. I've made unsweetened macaroons, but of course you can just eat the meat or creamed coconut. Other recipes with coconut flour should be good too. PubMed has a few supportive studies.

Galina L. said...

Buckwheat was not the food for poor people (rye bread was, together with lentil and barley), people from all levels of society loved it, many festive foods of very rich contained buckwheat. Suckling pig or goose staffed with a buckwheat or on a bed of buckwheat are good examples. Also, Orthodox church rules keep many days meat-free, and a buckwheat with sauteed onion and mushrooms were and still is a popular lent dish.
Millet gruel is still loved and popular dish, especially baked with pumpkin pieses, before 20-th century a dish called kpupennik was very popular among low-classes and fishermen in a nature setting. It was a cross between a soup and a gruel, often based on a broth from small fish and craw-fish(fish stayed), with added onions and potatoes, with millet cooked in it, when a krupennic was ready, a salted pork fat made into a paste with garlic or onion was added before eating. Nowadays people use the term "krupenic" for a buckwheat or millet puddings. I guess the worst ingredient in Russian cooking is a sunflower oil which is added everywhere. Unfortunately, butter and pork fat are not allowed during lent and lent days, but sunflower oil is fine. I am absolutely not a religious person, but a national diet is always influenced by a prevalent religion. I use olive oil on occasions when Russian people use sunflower oil except cooking.

People in Russia don't eat amaranth or spelt, as far as I know, rye bread was and still is very popular. People consume a lot of raw onion and garlic, it considered to be a preventive measure against a viral infection. Out of fiberous foods black radish has been frequently consumed since well before potato times. Grated reddish with grated carrots,sour apples, garlic, vinegar and oil is frequently eaten as a winter salad.

Recipe for a Vinegret- mix together chopped cooked potatoes, beets, carrots, add chopped raw onions, salt, oil, keep it in a refrigerator, before eating add chopped pickles and/or sauerkraut and brine. If you put fermented veggies and a brine right away, your Vinegret will turn sour next day, which tastes as a spoilage. I eat a LC diet, my personal version of Vinegret is modified, but my son and husband follow a traditional Russian diet with a lot of buckwheat and potatoes not out of patriotism, but because it is what we like to eat. I also bake a sourdough rye bread for my family members.

Jacquie said...

Does cooking vegetables reduce/diminish their fiber benefits?

For instance, most nights I have 2-3 cups of fresh cooked vegetables with supper. A mix of broccoli, cauliflower, zucchini, carrots, mushrooms, onion and garlic is typical, simmered/boiled in about 1/4 cup of veg and/or bone stock, for eight to ten minutes (half that time for broccoli). Everything in the pot is made a part of my meal.

Also, does anyone have any idea why eating raw garlic (a clove or two, crushed) would cause some of my toes to swell, discolor and itch? Having the garlic with olive oil makes the reaction even worse. I'm wondering if it might be an antimicrobial effect of the garlic--though I can't detect any infection on the affected toes...

Cat said...

I was raised on an Eastern European diet very similar to the Russian one. My favourite bread is wild yeast fermented rye bread; most breads use a sourdough rye and then just wheat flour, but pure rye and wild yeast is so much tastier. Best thing to do would be to find an Eastern European store.

Re: the buckwheat. I find that buying raw groats, soaking, then roasting them yourself (I just do it in a pan on the stove) makes for a much milder and nuttier flavour. But that's just down to taste preference I think, because many people enjoy unsoaked roasted buckwheat, aka 'kasha', just fine. Soaking after roasting doesn't do much, but prior to roasting it really improves the flavour and probably the nutrition, due to phytase activity (or so I'd assume). It's not the traditional way though, so it will likely change the effects of the buckwheat on the gut flora.

I also wanted to add that despite a robust Eastern European diet, cod liver oil use, OK Vitamin D status from pickled herring and lard consumption, raw milk, and use of her own garden veggies + eating berries and other plants w/o washing, my grandmother still developed an H. pylori infection she could not beat without antibiotics. My diet/lifestyle was not as perfect, but still very good, and I was not protected from gut dysbiosis either. A lot of Paleos come from the SAD, so ill health is not surprising; for me it was unexpected. Genetic vulnerability is probably the best guess. Traditional diets only get you so far, then you need to personalize. Totally agree on your emphasis on testing, Dr. BG; it's the only way to know what's really going on. I need to get on that testing! (I'm not American, so I'm not exactly sure what's available to me . . will be researching.)

Galina L. said...

Jacquie , your reaction on garlic looks like an allergy. Stay away from it. As a person who has multiple but well controlled allergies, It looks like that essential oils are not benign, I remember having worsening of an allergy after eating too much cilantro.
In my culture frequent garlic eating especially with hot soup during cold months is very popular, but I abstain from it when I feel like some of my allergies could be on the rise. I avoid spicy foods in general for that reason.

Karen said...

Thanks for your thoughts on blasto. Interesting that you mentioned yeast because I have suspected them for my daughter and I. I did a CDSA (per my doctor) which only showed the blasto and NG of bifidio and lacto and no yeast but you recommended an OAT test which I'll ask my doctor and ped for (unless I can work with you)! I am by the way, feeling fat/foggy/fried -gained 7 pounds over the last year which is odd as I've been the same weight since forever - never has been an issue. Should I test for SIBO too? I have no digestive symptoms at all with the 7 steps - in fact only way improved TMI (no more constipation) excellent sleep, and a nice, even mood. If I digress (fall off the wagon with a weekend of parties and such), I pay for it big time - way too easy to get back to square one;)

Dr. B G said...

THx Karen -- awesome results and buffering of GI distress (D*MNF*KCING PARTIES, BOOZE AND BAKED GOODS!)!!
Yes CDSA won't culture yeasts. It's retarded -- when yeasts go 'agressive' and pathobiont, they don't grow on their media. Yes contact me if you need more help.

Dr. B G said...

Yes makes sense to dry and roast after soaking (removing antinutrients and getting fermentive action to increase protein and RS bioavailability). MMmm fermented rye sounds good. Isn't that the funny thing that WAPF fermented rye diets are probably healthier than a no grain paleo?

Thanks for the cultural context! I was repeating what my Russian friend and dad had told me -- who grew up in the Ukraines. YOU ARE MAKING ME DROOL. Krupennic sounds absolutely divine!

Dr. B G said...


Well for RS3 cooking/cooling 24hrs will enrich 'fiber'. For inulin, overcooking will degrade it a little and change to digestible carbs hence 'sweetness' upon roasting or stewing

That is an odd reaction and as Galina, noted, sounds histamine related like an allergy. So cooked garlic doesn't cause swelling, itch etc?

Dr. B G said...


coconut fiber (if you're not allergic) is great and a wonderful low carb, gluten free flour is coconut flour.

Dr. B G said...

Galina and Cat

What about Jerusalem artichokes as part of the ancestral diet from your geography? The inulin content increases from North to South but it is consumed by many countries like Russia.

Galina L. said...

Jerusalem artichoke is a complitely new food in Russia, first time I tried it in 90-s, only garden enthusiasts grew it back then. When I visit Russia now, I can see that plant in stores, but it is still a novelty, like quinoa in US.

You are welcome, Dr.B.G..Self-cooked traditional food doesn't keep everyone complitely free from modern health issues, but I think we, who practice it, are better off anyway. I was a chubbiest child in my class at school (1967-1977), but since no one was fat, I was fine as well. Now I see more and more fat people when I go to Moscow, and fat children are not rare. I blame for it intensive commercial campaigns which promote sugared fermented milk products, grain mixes and juices as healthy super foods. In my young days eating between meals , especially for children,was a major dietary sin, but now Russia is picking western healthy advice and pattern of eating.

Jacquie said...

Galena -

Thank you for sharing your thoughts re garlic allergy. I really like garlic and eat it, cooked, practically everyday, without the foot swelling and itching issues, but I do have wildly fluctuating energy levels and frequent lower abdominal distention (seems like fluid, definitely not gas). I'll try staying away from it for awhile and see whether I see/feel a difference.

Grace -

And thank you for your reply re cooked vegetable fiber. I do eat a lot of legumes, tubers, and whole grains, cooked and cooled. I was just wondering if I might be enjoying some fiber benefit from the dinner vegs beyond the micronutrients.

As I just replied to Galina, while I don't get the extreme foot itchiness and swelling from cooked garlic, I do have unexplained lower ab bloat and fatigue. I've never considered garlic as a potential cause. I'll be interested to see if avoiding all garlic makes a difference. For what it's worth, years ago, olive leaf extract gave me the same trouble with the itchy, swollen toes.

You have a terrific blog. I've been following it for years and greatly appreciate the info you and your readers so generously share.

Galina L. said...

Allergy is very tricky, sometimes you can have milder reaction, but lack of sleep+another sort-of allergy-promoting substance like strawberry or alcohol could make the manifestation stronger. Probably, my interest in medicine and food came from frequent attempts to decipher what was going on . With a GI discomfort there are several possible causes, but swelling and itching is unlikely to be something else than histamine reaction(like Dr.BG said),and swelling is more serious symptom than just inching and hives . Me and my husband both have an asthma,which at that point doesn't require meds, sometimes the signal something is causing an asthmatic reaction is a fatigue.
You may stop eating garlic , then to re-introduce at first cooked and see how you are going to feel, and without other potentially problematic ingredients like tomatoes, especially cooked.

Dr. B G said...


Funny how all our foods are now global, as are infectious gut microbiota and antibiotics.


Olive leaf extract particularly is strong for its antifungal properties, much like garlic actually. In Chinese medicine, the meridians for the big toe and other toes sometimes line up to the body's anatomy. You might want consider looking at that for the fun because for me my life-changing titanium implant lined up with new onset hip problems during running and with weird pains in my big toe. These all resolved the second the implant was surgically removed. And it was all yeast related as well (was on fluconazole for 1.5 yrs to maintain life).

If you've had any # of antibiotics without adequate probiotics, soil and fermented foods, consider yeast and candida overgrowths in the gut and elsewhere (sinuses, bladder, vag, hardware biofilms).

Galina L. said...

" Having the garlic with olive oil makes the reaction even worse"
I guess you are having a reaction not on all ingredients of a garlic, but on a on a volatile compound which could be dissolved in olive oil but will evaporate during cooking overwise. The culinary practice of making a paste of bacon/pork fat and garlic before adding it to a soup (like borsh or krupenic) or stew or mashing and grinding together garlic with herbs and olive oil has a purpose of trapping volatile essential oils which would escape with a steam over-wise.

Dr. B G said...


Isn't it amazing how ancient practices are informed by some innate chemistry or food science? Garlic also increases antioxidants as it 'ages' after cutting.


Here's my bud, a fellow gut guardian, Matt Pepin. I told him I'm just gonna copy n paste is best stuff here!

12 Signs Your Flora is F*cked
by Matt Pepin on July 22, 2014 • 0 Comments
Your body likes to give you signs when you might be having issues. Usually we like to blow them off and expect them to turn around. Maybe they will. What happens when they don’t? If you have these chronic conditions it maybe time to check in with a doctor to sort these out.

1. Bloating
After having a hearty meal, especially after a bit of an over indulgence, you might have to loosen the belt buckle. Your food baby awaits your attention. It feels like you have no control. When did I put this fat suit on?
The problem with bloating isn’t just the unsightly view of an over inflated belly, it’s the fact you have fermentation happening in the wrong portion of the body! All that gas and air should be produced in the large intestines. If the body is unable to break down the food properly in the stomach, it leaves undigested particles for the small intestines. Thus the bacteria in the small intestines starts to feast off these larger pieces, leading to the production of gas and your food baby.
2. Constipation
Just…a little….HARDERR…..
The dissatisfied look on your face is totally warranted. What happened?! Multiple factors could be going on, the foods that you have eaten are absorbing a lot of the water in your digestive tract making it harder for it to slide on through to the swimming pool. Not having enough water can be the other problem. If it is chronically a problem, it’s most likely due to gut dysbiosis, or an imbalance of gut bacteria in your large intestines.
Instead of the proper gut bacteria producing short chain fatty acids, the imbalanced bacteria are feasting on the mucus lining of the large intestines along with the foods that have passed into the large intestines. That mucus gives the stool the easy passages along your colon. No mucus, and you have yourself a stool trying to pass along sandpaper. Friction is not your friend in this case.
3. Diarrhea
Travelled to a different country? You probably had a bout of traveler’s diarrhea. What about that raw sushi? Usually if you have diarrhea it’s not for very long. A day or 3. Those with IBD or IBS have it every week. If the body accidently digests a colony of bacteria foreign to it, its natural defense mechanism is to purge that bacteria out. This happens out of either end. Fun times to be had for all. If this is chronically issue, you may be able to point the finger at an imbalance of poor bacteria. The decreased transit time is most likely caused by the toxins being released by an overabundance of the bad bacteria. This forces the body to release these toxins immediately, which makes for unformed stools.
A huge problem with the short transit time is the body missing a huge component in the large intestines. Short chain fatty acids are produced during the fermentation process in the large intestines. These are essential for a healthy human body to function properly. This fermentation makes the stool become solid by the time it is excreted. Without any SCFA being produced, your body is missing components needed to function properly.

Dr. B G said...

(cont) 4. Heartburn / Acid Reflux
Eating fried/spicy/processed foods are widely known culprits of causing heartburn. And for good reason too! Our guts aren’t meant to handle the artificial nature of these foods, thus making them essentially foreign! Bile and acids in the stomach try to break down these foods, but the normal amount of acid cannot properly break down the foods, leaving partially digested foods entering the small intestines.
Pressure from the foods being fermented in the small intestines allows the valve in our stomach to open. From this opening comes the acids and bile remnants into our esophagus. Hot stuff! Those painful burps and warming sensations are just another sign that your gut is out of sorts.
5. Seasonal Allergies
Pollen counts are being tallied on your local news. Spring is just around the corner. It’s gonna be a rough day for those with allergies. I don’t think our ancestors had to rely on pollen counts. Even when we are young, we never had a problem with allergies, but we somehow grow into them? Why are seasonal allergies so wide spread now? The modern human is constantly producing histamine due to poor diet.
Histamine is what gives allergy suffers those itchy eyes, post nasal drip, sneezing, coughing, and feeling of being just plain miserable. What is producing all this histamine? A poor gut flora could be a potential problem. Eating a poor diet gives the bad bacteria food to hang around. And like a stray cat, they just won’t leave. As they are setting up shop, they are chomping on your food and they are producing toxins. Some of these toxins cause the body to respond by producing histamine.
Your body can only handle so much histamine, until the symptoms of an overburdened body cannot handle it any more. Add pollen to your system and you have just created a histamine tsunami.
6. Acne
Getting acne when you’re past your teens is not the best look. A pimple here and there is normal, but when you have a full outbreak, you can feel like those Lepers from the Ten Commandments. When I was a kid, they used to tell me that what you ate didn’t give you acne. Science today tells us otherwise.
Again, poor diet habits or the imbalanced flora will give the bad bacteria a chance to thrive. If they pounce on this opportunity, they have the ability to produce toxins. The liver is put underneath intense stress, from its daily functions, and now with this new load of toxins being funneled in. If the liver can’t bear the load, it passes back into the blood stream. It then finds its easiest way out of the body: through the skin. Bad news for us, our pretty little faces end up being the toxic waste land in the form of acne and blemishes. Seriously liver?!
7. Skin quality
Foods are eaten to give us the fuel needed to complete the proper functions throughout the day. They give our body nutrients and those nutrients go to our organs and we are able to perform our everyday activities. What happens when those nutrients never get to our organs? What if another organism is harvesting it all and not playing nice and sharing. The smoking gun maybe a gut that has a colony of bad bacteria being greedy and using the nutrients for their own well-being. Not cool bad gut bacteria. Our skin being the biggest organ of the human body suffers. Dryness, bumps, scaly, are signs that our skin might not be getting the proper amount of nutrients needed to give it the glow our skin deserves.
8. Nausea
Stomach pains and feeling nauseous are clear signs that you might be getting sick or eaten the wrong food. By wrong food, I mean a bacteria laced edible. That nauseous feeling is just your flora battling back against that overflow of bad guys. Sometimes, you’re able to weather the storm. Others, the purge is needed. Welcome the purge, it’s usually a sign of victory for the good flora. Score one for the flora!

Dr. B G said...

(cont) 9. Food intolerances
Milk, eggs, nuts, cheese, tomatoes, fish, and the list goes on. How does all of a sudden we get food intolerances after years of eating with no issue? A bad flora means there is probably inflammation in our guts. This inflammation can come in the form of stomach pains, nausea, itchy eyes, dry throat, etc. Enzymes maybe suppressed that help break down these foods. Or could it be that a particular species of gut bacteria is no longer colonized in your gut. Or worse, another bacteria is using these foods as its own, and it’s by products are now essentially giving you these symptoms?
These are questions that need to be answered by more science, but in some cases food intolerances can stem from a poor flora.
10. White tongue
Unless you have been having ice-cream or a white Russian, your tongue should not have a white coating covering it. It’s best to check the condition of your tongue upon waking. A little bit of white isn’t anything to be too concerned about, but when you have a thick layer you might just have yourself a yeast infection. This could be your only symptom, but if it goes untreated, other not so fun symptoms could pop up eventually. Yeast is a part of a normal flora, but if they begin to grow out of control, they can destroy the flora and making your life miserable and cause a host of other problems.
11. Get sick often
Yeah the seasonal cold should be no big deal, but when you start experiencing one after another, or just can’t kick that hacking cough, your immune system is comprised. Just so happens your gut is responsible for around 70% of your immune system. With a good flora intact, pathogens don’t have a chance to wreak havoc on your body. Without the good flora, the common cold can mess you up for a week. Blowing into tissues and hacking up mucus isn’t how I like to spend my time. Fixing the flora helps prevent these nuisances.
12. Antibiotics
You got sick and the Doc gave you a prescription for some antibiotics. Short term they might help you out; long term you just dropped the atom bomb. Remember that flora you had in your gut? Well, they just got nuked. Zapped. Obliterated. You get the picture. But you say, “I eliminated the bad guys too.”
Yes, but let me paint this scene that I heard on a podcast/blog: Say you’re the king of the castle and you have invaders coming in. They have infiltrated, and your army is kinda weak. Instead of building up more troops, you decided to set the castle a flame. Everyone dies. Mission Accomplished? Unfortunately, more bad guys show up…and now there is no resistance. They rebuild the castle. They now own the land. This is what happens if pathogens come into your gut after taking antibiotics.
The pathogens will have no resistance, and could put you in a world of hurt. Not saying to not ever take antibiotics, they are essential for preventing infections when applied properly. Just don’t take them every time you get a sniffle or a small cold. Protect the flora.

By Matt Pepin

Kira said...

I am still trying to understand the effects of cooking on the various sources of insoluble fiber. For example if I made a creamy soup with Jerusalem artichokes, would the inulin be completely degraded? What about pectins. Are there any left (in a useful for the gut form) in steamed apples or carrots? Would cooking, cooling and then reheating affect how digestible the fiber is?
Are you aware of any papers that look into this for non RS2/RS3 fiber?

Dr. B G said...


Great questions -- I dunno but as foods 'over cook' their digestibility increases. For foods containing starches, then the SDS (slow digesting starch) will gradually become RDS (rapidly digesting starch) which will contribute to raising blood glucoses.

RS1 is the starch embedded in plant seed, grain and legume covers and structural parts. I think with cooking and chewing RS1 becomes digestible but again this is not evaluated and probably contributes actually little.

As far as I know cooling only enriches RS, not pectin, inulin or other fibers because RS3 is a crystal structure and gram for gram, RS3 is a more potent prebiotic than RS2 in studies. This is probably why Tim has seen metabolic and glucose sensitivity despite consuming a substantially higher carb (low GI) study imho. The whole food like cooked J artichokes and steamed carrots contain iRNA and other messages that our genome can actually 'read'. Perhaps our gut microbes do too ;) lol

I couldn't locate much on inulin loss from cooking but for tequila production inulin from agave cactus is concentrated down into more simpler fructose for fermentation -- step 1! ahaha

Crit Rev Biotechnol. 1995;15(1):1-11.
Tequila production.
Cedeño M.

Tequila is obtained from the distillation of fermented juice of agave plant, Agave tequilana, to which up to 49% (w/v) of an adjunct sugar, mainly from cane or corn, could be added. Agave plants require from 8 to 12 years to mature and during all this time cleaning, pest control, and slacken of land are required to produce an initial raw material with the appropriate chemical composition for tequila production. Production process comprises four steps: cooking to hydrolyze inulin into fructose, milling to extract the sugars, fermentation with a strain of Saccharomyces cerevisiae to convert the sugars into ethanol and organoleptic compounds, and, finally, a two-step distillation process. Maturation, if needed, is carried out in white oak barrels to obtain rested or aged tequila in 2 or 12 months, respectively.

Galina L. said...

It is amazing how people found out by just practicing healthy ways to cook food and to heal a body. The China's medicine is one of such wonders.

Cat said...

Dr. BG,
I don't recall ever eating Jerusalem artichokes, so I think Galina is right. It's some sort of sunflower, though, right? My grandmother grew sunflowers and used the seeds in her rye bread. I remember buying a sunflower head as street food.

I looked up inulin on wiki to see if I could recognize anything . . dandelion was definitely used, but I'm not sure to what extent it was eaten as a salad green versus used to make some type of alcoholic beverage (lol). But I know other Europeans who eat it in a salad. Onions are used in everything; it's a major flavour agent, and considered medicinal. Garlic as well, but not as prevalent I think. I remember being dosed with raw garlic in a teaspoon as a child, the same way people use cough medicine. I also remember bitter, bitter chicory. We didn't have it a lot, and wiki tells me it's used in German cuisine.

A lot of the plants we discuss are already used in many cuisines, and can be found in the store. But many of the plants my grandmother, and even my father, grew up with, were ones they foraged themselves. Mushrooming is some type of national pastime in my country, apparently. So many varieties, and by the time my father was a young adult/teen, he could already recognize the edible varieties versus poisonous. My grandmother also picked new, wild greens for her salads and soups (like baby greens), and had all sorts of herb/spice blends she made herself. A lot of that specific regional knowledge of plants has probably been lost, though I remember seeing a paper on it, so perhaps someone managed to record it.

Foraging isn't very typical among North Americans (outside of the Natives), but everyone in my father's generation did it . . perhaps this was also a way to get beneficial soil microbes, when they ate some of it on the spot without washing, just rubbing on your shirt. I've only had wild blueberries and apples a few times, because my parents immigrated to Canada and are not familiar with the regional plants to feel secure about foraging. But I know people who forage and then wiki the plants to see if they're edible . . not always a good idea, and there have been some issues with throat swelling . .

But in general, the way you describe eating for beneficial gut flora is very similar to what I grew up with (prior to some Westernization; and I should also add that Poland is known for its sweet tooth and love of alcohol, so WAP would have found many, many cavities): potatoes, grains, beets, carrots, parsnip, horseradish, so much cabbage, beans, peas, many mushrooms (pickled, cooked), nuts, berries, apples, plums, honey, etc. It's nice, because it means there are already so many cookbooks and cuisines to try.

Galina L. said...

Cat, I spent some time in Canada before moving to US, and when I lived in Edmonton, my friend told me about her experience working in the archive of the Museum of a Ukrainian culture as a volunteer. The archive contained a lot of records of whole families of early newcomers being poisoned with mushrooms they thought were eatable because it looked like eatable ones in their native country, but were poisonous in Canada. She told me since then the habit to forage went out of a wide-spread practice.

Dr. B G said...


Yes that happens with migrants in California I've heard too -- several people will lose liver or go on the liver transplant list. It's like Tylenol overdosing.

Plants have ways of mimicking and surviving. FUNGI have been here billions of years before us ;)

Where are you from? How about any of these roots or plants? Galina -- sound familiar from childhood?

Elecampane -- mountainous herb and root -- rich in inulin

% inulin fresh weight (YUMMMM~!!!)

Onion Bulb 2-6
Jerusalem artichoke Tuber 14-19
Chicory Root 15-20
Leek Bulb 3-10
Garlic Bulb 9-16
Artichoke Leaves-heart 3-10
Banana Fruit 0.3-0.7
Rye Cereal 0.5-1
Barley Cereal 0.5-1.5
Dandelion Leaves 12-15
Burdock Root 3.5-4.0
Camas Bulb 12-22
Murnong Root 8-13
Yacon Root 3-19
Salsify 4-11

Galina L. said...

Sorry, no,not familiar as food sources except for rye,garlic, barley and onion. Besides berries and mushrooms, people only collected in a wilderness horseradish, sorrel and a wild onion(ttps://Черемша - I clicked on "translate"). I also know several wild medicine plants. I was told people collected chicory root during a war to use as a coffee substitute.

Cat said...

Galina, yes, this is definitely the reasons I was never taught to forage in Canada. It's still a little bit strange these things happen, because even on home turf people get poisoned, due to how similar some poisonous mushroom varieties are to the non-poisonous ones . . something I thought people were aware of, but unfortunately not. My friend who forages verifies the identity of the plant, and then only samples a tiny bite and waits for swelling/mouth tingling . . still scary lol.

Dr. BG, I'm Canadian, but my parents immigrated from Poland in their late 20s, along with one set of grandparents, so I was raised with Polish traditions/cuisine/language as my primary culture at home. We visited Poland frequently throughout my childhood though, but I really don't know exactly what we ate, outside of the common foods I recognize. And of course the food was made to be palatable to my young, picky palate, so I didn't experience everything there. I've picked up some stories about the food from my father, but it's not a lot.

Leeks I recognize, because my family just uses it excessively whenever a garnish is needed, in soups, salads, etc. It's in so many dishes. I know this, because I can't stand it lol.
Burdock my grandmother has pointed it out to me on nature walks, I think, but I don't recall eating it. It's possible it was eaten in Poland, though, since UK cuisine uses it and there are many similarities across European cuisines.

The random plants (esp herbs), I don't really know them. They're regional, and we sometimes get packets of them from friends and relatives, so maybe there's something in the spice/herb cabinet.

Jaime said...

Okay....I am a bit confused now.... I used to have really poor digestion, hormonal balance etc. All of that is 'mostly' under control now with dietary changes (paleo-ish). I still have food intolerances though that present as very rapid bloating to gluten and corn/potato starch, and skin issue (psoriasis?) on my hands if I have too much dairy (more than a serving/week). Everything else digestion wise is fine, just the annoying bloating. My confusion is in whether following the 7 steps will help resolve some of this? Or should I try to get more resistant starch from food sources rather than supplements? A couple of days of trialling some potato starch have resulted in bloating from 1 tablespoon. Start with less? Start with another source of resistant starch?

Dr. B G said...


7 steps will help but you need to identify and fix the root problem
--what's missing
--what vipers are still present (relative term -- could be good guys but in the SI)

Good luck and try enlisting a consultant to help ur confusion

Hoppy said...

I'm the anonymous from 9/30 at 9:56 am.

My last Gi panel was done in March 2013. It showed:

-a few red blood cells
-many yeast
-many blastocystis hominis

-mixed gram flora absent (expected moderate to heavy growth)
-moderate streptococcus salivarius (pathogenic)

-low SIgA: 23 (normal is 400-800)
-intestinal lysozyme: borderline elevated
-chymostrypsin: 8 (normal >9)
-gliadin antibodies: borderline high (been GF for 7 yrs)

This was the third stool panel from Diagnos-Techs I've done. The blastocystis was there in 2009. Other results were similar, just with different pathogenic overgrowths. This was the first time with yeast or red blood cells.

I've been gluten-free for 8 years (became much stricter about cross contamination after the above results came in) and dairy free for most of the last six years.

Eating grains often makes me bloat up within 30 minutes. Is it safe to assume this is SIBO? Should I follow the seven steps? How do I treat the blast?

Hoppy said...

Thanks for all the work you do. My integrative doctor has been somewhat helpful. She knew enough to suspect dysbiosis was the cause of my high blood ammonia levels last year instead of thinking something was wrong with my kidneys (or whatever average doctors think).

Dr. B G said...


RU celiac? those look like celiac numbers to me.

Consider some serious gut rehab. Please read the comments here:

Hoppy said...

I was off gluten from age 16-20 and then again from age 24-present (32). I've never been diagnosed as celiac but it wouldn't surprise me. My brother and dad both have trouble with gluten (not as bad as me) and my mom just went gluten and dairy free after she had lab testing showing thyroid antibodies. (Her thyroid levels are still fine. Being gluten free is keeping her hands from hurting).

I had endless ear infections as a toddler until I had tubes. Then from age 8-16 I had sinus infections over and over and strep several times, so I was on a lot of antibiotics as a kid. The sinus infections went away as soon as I went gluten free.

These days grains leave me slightly stuffy and bloated, but nothing like the sinus trouble I used to have.

Since my last stool test showed raised gliadin antibodies I have become much more vigilant about cross contamination. There is still room for improvement.

ballabolla said...

A short heads up from Holland, am not there yet but am following your posts closely!
Am stopping PS (2 weeks ago), my FODMAPsensitivity vanished, am now on 2 TBSP GBP/2tbsp tapioca, 1tbsp collagen in coconutmilk with a little maple syrup a day. I eat yellow plantain, parsnip and carrot more often ;-)
Am feeling way better and am improving slowly. My 23andme DNAtest is here the end of this month.
1 question:
What do you think about kombucha (preferably daily, icw RS and what about the histamines?)

X, Saskia

NS said...

Does anyone know the rs content for raw yacon root? Apparently, it's entirely edible in its raw form.

Dr. B G said...


Sorry I missed this one -- your FODMAP sensitivity vanished?!! You can eat and not get bloating/gas with FODMAPS now? awesome!

Kombucha is great if you can tolerate -- I think it might have some histamines because a lot of people with mycotoxin sensitivity or fungal overgrowhs don't appear to tolerate at all. Collagen is super -- just found out from Dave Asprey it is bifidogenic. It's a glycan much like the lining of our mucosal linings that feed the good gut guardians like Roseburia, Akkermansia and Bifidobacteria longum

Yacon is high in inulin -- improves fat loss. One study showed 33 lb loss after 12 wks. No RS at all; it's not starchy (ru thinking of jicama? I get the 2 mixed up lol)