Friday, March 14, 2014

Gut Microbiome Biohacking Basics; Mild Havoc? Or Unmitigated Upheaval?

Linkin Park
Roads Untraveled

Roads Untraveled?

More and more studies are pouring into our collective knowledge about the microcritters in our 'forgotten organ,' the humble gut. The latest making the rounds is a stunning article on how one of the first antibiotics created by Eli Lilly in the 1950s was used as a 'digestive aid' in livestock (like ?cocaine in COKE? or ?nicotine in tobacco once plugged by physicians or ?gliadin in modern hybridized wheat plugged by govt juggernauts) .They were used to put on fat and poundage to cattle and livestock by a 3-FOLD magnitude. In those war and post-war days, the population was skinny and desired 'fat'. In modern times, we've flipped. The majority are overweight/metabolically deranged and desire 'thin.'
Source: Big Tobacco led throat doctors to blow smoke (Stanford)

Do Antibiotics Make Us Fat?

"On the Point" with Tom Ashbrook has a new podcast that interviews the author of the new NY Times article linking agricultural use of antibiotics in animal feed decades ago with the new diabesity epidemic, Pagan Kennedy. Dr Ilseung Cho is also interviewed, gastroenterologist at NYU and gut microbiome researcher. Dr. Cho talks about the potential gut effects of antibiotics.

Dr Cho is from Marten Blaser's lab which recently concluded in their study "Infant Antibiotic Exposures and Early-Life Body Mass" that YES antibiotics are highly correlated to higher 'fatness' in babies who received antibiotics before age 6 months, and older as well but the effect was less consistent apparently after babies start to crawl around (Trasande et al 2013).

Clearly there are multiple factors that go into becoming fat. Clearly we have ignored the gut microbiome for too long. 100% of everyone that I know has had at least a single course of antibiotics if not double digits. As a child of a physician, I've had my share. For many fevers and sniffles, I got the 'pink liquid'. Partly I went into pharmacy believing that drugs were not only good, but life saving.

Can antibiotics actually be life altering and life stealing? Bringing on autoimmunity? Triggering UC, Crohn's and IBS? Ushering in the storms of autism, diabesity and allergies that are seem inescapable and epidemic? Before I had kids, I once had Shigella. It was awful and Cipro did cure it -- but did it impair my gut? Should I have taken measures to protect the commensal populations?

My oldest daughter was born ~14 years ago via emergency C-section. Despite breast feeding her, she had 2-3 months straight of inconsolable crying and colic (age ~6-9 months), endless ear infections (6-12 months), then later developing reactive asthma (1.5-10 until we started vitamin D) which required middle of the night treatments, nebulizers and urgent care visits. We have never had asthma in the 'family'. It certainly didn't appear 'genetic'. In hindsight, I suspected that her atopic hypersensitivities be related to many things not excluding the (lame gut) legacy that I handed to her, C-section birth and formula at age 6 - 18 months.
How important is the maternal microbiome bequeathed to the baby? Did my firstborn inherit a gut with major deficits secondary to the 15-20 courses of antibiotics during my life (which of course did save my life a few times, including a large third-degree burn)? In light of the new data emerging from 16S rRNA sequencing technology, all these questions are being illuminated and even answered.

ONE THE POINT PODCAST: Antibiotics and obesity. Whether it’s possible that antibiotics plump up humans the same way they do animals, livestock. American farmers commonly feed their livestock grain laced with antibiotics because it makes bigger animals. Heavier. Fatter. So what about the antibiotics we humans take – for the ear ache, the strep throat, the sinus infection. Could those make us heavier? Fatter? No one argues that diet and exercise – or lack of it – come first. But could antibiotics be a scale-tipping X-factor in American obesity?

From Tom’s Reading List
New York Times: The Fat Drug – “In the last decade, however, scrutiny of antibiotics has increased. Overuse of the drugs has led to the rise of antibiotic-resistant strains of bacteria — salmonella in factory farms and staph infections in hospitals. Researchers have also begun to suspect that it may shed light on the obesity epidemic.”
Mother Jones: Can Antibiotics Make You Fat? –”Are we being exposed to tiny levels of antibiotics through residues in the meat we eat—and are they altering our gut flora? It turns out that the Food and Drug Administration maintains tolerance limits for antibiotic residue levels, above which meat isn’t supposed to be released to the public.”
Nature: Antibiotics in early life alter the murine colonic microbiome and [INCREASE] adiposity – “Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we proposed that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities.”

Intro of our Gut Characters

Here is the line up. They originate from life -- mom, diet, foods, dust bunnies, soil exposures, pets, kissing, hugging, licking doorknobs, etc.

Source: Ch 2 The Commensal Microbiology of the GI Tract
Manson, Rauch, Gilmore 2008

Intro of Some of What Our Gut Characters Do [Caveat: If We've Got Them]

They eat and poop, and we eat their secretions (vitamins, amino acids, SCFA (short chain fatty acids)) and then poop then out. Half of our dry poop in weight is in fact them. Their DNA exceeds ours by 150-times. Basically their microbiome complements our human genome with 150-fold more genes. Our Homo sapien-derived double helixes don't alter (much, debatable here). Their's is contrastingly plastic. They can sweep up lactose digestion or antibiotic-resistant plasmids or DNA from their environment or via microbial-sex. In evolution, they appeared first and will likely appear last... "Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. (Thomas et al 2011)" When diet resource allocation or subpopulation neighbors shift, so do their gene expression. They shift to the diet provided. Additionally, they can control our gene expression. Bacteroidetes thetaiotamicron (one of our vital omnivorous commensal symbionts, Roberfroid et al 2010) has been shown to turn on/off over 400 genes in the host, thus altering molecular architecture and body functions (Heselmans et al 2005). Indeed, our microbes may maketh the man, woman and child (and all animals, insects, plants).

Your response to fiber, RS, g banana/plantain flour, potato starch, probiotics and food all depend on what is filling your zoo cages, the pre-existing microbiota. Do you have vipers or voles? Electric eels or earthworms? Is your apex predator for the ecosystem EXTINCT. Does excessive flatulence blow you to the moon and clear the room?
Source: Fermentation of non-digestible oligosaccharides by human colonic bacteria
Gibson et al, 1996


No one who lives in an industrialized country is exempt. Broad spectrum, potent, synthetic antimicrobials can permanently damage the gut characters originally present many new studies besides research from Cho and Blaser's work. Jansson et al discovered that for a single 7-day course of antibiotics, gut testing showed that even TWO YEARS OUT WTF, THE SYMBIOTIC GUT CHARACTERS WERE GONE. The former fingerprint and diversity were extinct. Diversity means resilience -- the ability to bounce back and be robust against inevitable changes, shifts and hurdles. Michael Pollan, author and eater of all things fibrous and fermented, stated that after a 'precautionary' course of amoxicillin antibiotics prior to oral dental surgery, his intestinal commensal populations plummeted. The healthy blooms disappeared (Prevotella), replaced by noxious Proteobacteria (NY Times, My Best Friends are Germs 2013). Antibiotics and their drug-resistant DNA are also found in feedlot poultry, pigs, cattle, dairy and eggs. It is hard to escape these chemicals even if your dental surgeon or pediatrician are not eager to whip out their blank Rx pads.

Why Do Antibiotics Do So Much Damage and Can Lead to SIBO/SIFO?

Here is our gut below -- the  intestines are long and when splayed open have a large surface area equivalent to a high-piled terry cloth towel as large as a tennis court. The small intestines are 6-8 meters and colon ~1.5m. The small intestines are significantly longer: 4-5-times longer than the colon. This is where disease can begin. The interface between the outside world and our immune system and blood supply are separated by a single layer of cells. Many microbes actually attach to the intestinal cells in the small intestines (eg SFB, segmented filamentous bacteria) and eat from our bodies directly. These are the same organisms recently shown to prevent or cure T1D model in rodents. Most of the other gut characters live in the interior of the tube (lumen) or in the slime (mucous) along the length of the whole intestines.

Functional Ecology of the Small and Large Intestines
Source: Martin F P et al., J Proteome Res 2009;8:3464–74

The Russians have studied bugs far longer and in a more integrative manner when compared to Pasteur or other micro-phobes. Some of our best probiotics (Natren), yogurt strains and gut-healing protocols (GAPS) are from Russia. Korshunov et al has been studying how gut microbes can be protected with Bifido and Lactobacillus probiotics after chemotherapeutic induced dysbacteriosis (antibiotics). His studies revealed that SIBO (small intestinal bacterial overgrowth) occurs almost instaneously. He didn't study the mycobiome but it's not unfathomable that SIFO (fungal overgrowths) occurred as well. The small intestines are vulnerable because the role of the microbes there is one of protection, immuno modulation and symbiosis. Once the ecosystem is perturbed, all health can change. Extraction of nutrients is just one single function of the small intestines. The immune system lines the entire gut from mouth to anus, and particularly in the small intestines the job is intimate and foremost. When the ecosystem is complete, our commensals + gut do the job of:
--maintaining tight junctions
--prevent permeability
--stopping breaching or bacterial/fungal translocation to other organs or blood
--allowing tolerance for other commensals (Toll receptors, toll='fantastic' in German)
--decreasing allergic reactions and hypersensitivities (asthma, eczema (Heisenbug), food intolerances (gluten/dairy -- me), sinuses (Richard N), etc)
--tagging pathogenic strains, protozoa and parasites as foreign invaders for elimination
--secreting antimicrobial peptides (AMPs) to limit the growth of unsavory characters (the commensals are the 'apex predators' of the gut ecology)
--modulating mood and behavior by facilitating neurotransmitter and hormone synthesis (HPA-thyroid-genitalia-GUT axis)
--other than the spleen and bone marrow, create immune cells necessary for host health

There are a ton of factors for dysbiosis and unbalanced microbiota -- but antibiotics seem to be at the core, like here and here. Without commensal symbionts guarding the gut due to potent pharmaceutical antibiotics, the minor population of pests and vermin strains are left alone and un-mitigated. When there is plenty of food around, they will bloom or double overnight (or sooner). Korshunov et all called this 'contamination of the small intestines,' in other words SIBO/SIFO. It is indeed a common clinical feature in modern medicine as new human gut microbiome studies are revealing, yet largely undiagnosed with no modern medical solutions. The 7 steps for the ultimate gut health restores the commensal populations to a level that allows the gut to recover stability, diversity and optimal health.
[Characteristics of experimental antibiotic-induced dysbacteriosis]. [Article in Russian]
Martynov AI, Grinevich AS, Korshunov VM, Pinegin BV. Zh Mikrobiol Epidemiol Immunobiol. 1982 Jan;(1):48-54. 
Changes in the microflora of the large and small intestines in mice and guinea pigs after the oral administration of canamycin (a hardly absorbable antibiotic) and ampiox (an easily absorbable antibiotic) in different doses. The administration of these antibiotics in different doses (therapeutic, subtherapeutic and over therapeutic) led to an increase in the number of opportunistic microorganisms and the contamination of the small intestine by these organisms. These changes were also well pronounced in guinea pigs, normally having no enterobacteria. After the administration of the antibiotics was stopped, opportunistic microorganisms were gradually eliminated from the small intestine. The rate of decontamination depended on the administered dose of the antibiotic: the higher the dose was the longer the process of the decontamination of the small intestine lasted. An increase in the amount of opportunistic microbes in the large intestine and the decontamination of the small intestine occurred simultaneously with the decrease in the amount of lactobacilli and bifidobacteria in both the small and large intestines.  

OTHER MICROBIOME KILLERS = Atkin's, VLC, Ketotic, Low-Fiber Diets

There are many ways to kill your gut besides antibiotics. Dietary changes make profound changes to the gut. Diet is in fact one of the primary drivers of diversity and populations in the gut. As we know with Darwin and his finches, diet drives evolution of morphology and anatomy. The main gut characters that produce the anti-inflammatory BUTYRIC ACID and other SCFAs are also the same ones often associated with longevity in centanarians, better health and less fraility (Roseburia, F prausnitzii, Ruminococci, Bifidobacteria). The preferred diet of these butyrate-producers is fiber + RS. These 2 groups: (1) Ruminococci (Clostridium cluster IV) and (2) Roseburia (Clostridium cluster XIVa) munch on mostly RS, not inulin, other fibers or meat (eg other a bacteria eats bacteria world LOL). They do not appear too diversified in their culinary palate, yet they comprise the great majority of gut characters in healthy, disease-free, cancer-free individuals. Ruminococcus bromii assists all of the other gut inhabitants by being an enthusiastic and primary degrader of resistant starches, making carb by-products that can be utilized by others lower in the ecosystem. When these 2 groups 'bloom' in the colon, gut pathogen populations go down, gut inflammation is reduced and even horrific diseases completely and 100% reverse in new research trials (C diff antibiotic-induced colitis, UC, IBS, autism, etc).

Butyrate drops precipitously with a low-carbohydrate, low fiber/RS diet in a study by Duncan et al 2007. The anti-inflammatory gut species took nosedives (see below) -- Roseburia, F prausnitzii, Ruminococci, and Bifidobacteria. Subsequently, butyrate in the stools became only 1/5 to 1/4 of the maintenance diet amount. Butyrate trended with Roseburia (Clostridium cluster XIVa) populations. The prime fuel (70-80%) for colonocytes is butyrate from microbial fermentation (the next best is glutamine from skeletal muscle, then glucose). An energy crisis occurs when they are not supplied well.

Human gut characters prefer and need indigestible carbohydrates. Indigestible to Homo sapien but digestible to microbial amylases and a consortium of enzymes that break down all configurations of fiber and RS starches down. These butyrate-producers are not as carnivorous as other species (Bacteroidetes). This is likely from millions or perhaps I suspect billions of years of co-evolution where our gut species took advantage of the environmental bounty and abundance of plant fibers. The biomass of earth is 75% plant carbohydrates;  microbes blanket the earth, air and water.


Source: Karen Scott PhD ROWETT SLIDES
Duncan et al (2007) AEM 73; 1073-1078


Bea said...

Have never left a comment but have read your blog for quite awhile. I am completely baffled why all the low Carb bashing lately by you and RN. LOW CARB IS NOT LOW FIBER. Why it's trying to be painted that way I don't know. When you go low Carb and drop all the refined products you fill the void with lots of vegetation. Typically the higher the fiber content the lower the carbs. Visit any low Carb blog its mostly vegetable recipes. You have to get creative with them because they make up 3/4 of your diet low Carb. Sorry don't want to eat white rice. There is a reason S. Korea has one of the highest rates of diabetes. Also don't want to drink the potatoe starch koolaid and brag about my 3 massive poops I had
today and how great it felt. The major group starving their gut biome are the sad eaters but for some reason it's the lc group that has become the whipping boy.

George Henderson said...

I don't know that the microbe changes on VLC bear any comparison to those on antibiotics. On VLC the species are all still preserved, they are present if you want to feed them. But if they have been troublesome (perhaps as a result of antibiotics) you can suppress them a bit with VLC. Excellent if you have arthritis, spondilytis and so on.
It doesn't make sense that a diet people use because it heals their gut issues and restores their digestion is "killing" their gut.
The healthiest people are also the people least likely to get sick in future.
In any case, Atkins was all about non-starchy veges. Fibre. I would be suspicious of an institutional Atkins diet, but I would not expect a wild-type Atkins diet to be low-fibre.

Bea said...

Please somebody show me where in any Atkins book he said to restrict fiber. I did have to go on a low residue diet once very short term. It was nothing like low Carb. A short time after I had a stool test that showed low bifidobacterium. I ate asparagus for 2 weeks and retested it had shot way up into the high normal range. Just from asparagus.

Dr. B G said...


Plug your food into fitday or somewhere and tally the fiber. Resistant is 'zero'. A large salad perhaps 5-10 grams.

The longer someone is on VLC and ketotic, physiological insulin resistance raises BG and further creates 'carb sensitivity'. It's not really that carbs immediately massively raise BG, but the feedback because the gut is trained to suck all the carbs since it has been de-conditioned for a period of time.

I love VLC. It is therapeutic and brings nearly 98% of health metrics to decent levels after SAD damage. However for long term I question both its sustainability and gut consequences. From all that I've presented on this post, what do you disagree with, Bea?

Absolutely -- all the Asian countries are now suffering Western, industrialized gut effects from refined carbs, high fructose corn syrup (Koreans love this sh*T), fast food, gluten gluten glute, pesticide residues, and less exercise. Whole organic barley is probably rarely eaten there now. Rice is likely GMO like the rest of the world. China, Japan, India and Russia mimic USA guts now.

I don't advocate that much white rice... have you seen my low glycemic index soaked whole grains, lentils, legumes, tubers and heirloom veggie list? White rice unless cold, reheated, fried rice doesn't have that much RS (fiber) and thus raises BG compared to other sources.

The funny thing is that the more RS a person consumes, the higher the insulin sensitivity.

Tom Naughton has had improved and lower fasting BGs with using resistant starch despite the same diet. He gets a healthy dose of DIRT from his farm, I believe. It will be interesting to see the rest of his health trajectory but it is aligned with the clinical and scientific data on fiber and RS already.

From FTA Richard N:
Tom got interested in resistant starch. He's tried it. He was also just on Jimmy Moore's 100th episode of his Low-Carb Conversations with Friends. Tom spoke exclusively about resistant starch the whole 10 minute segment, beginning at 1 hour and 27 minutes into the program. Go give a listen, hear what Tom has to say, what Jimmy thinks, and what Jimmy might be trying after his book project is done. (Easiest way to be able to advance to the spot is download the Mp3 and open it your own player.)

Dr. B G said...


Thank you for your thoughts. Arthritis is often a manifestation of the gut microbiome because like AK alkylosing spondylitis the small intestines are frayed and microbial translocation has occurred to the joints and peripheral organs. A diet that doesn't feed the small intestinal occupants can help but will not necessarily heal. Sometimes these occupants are parasites, fungi and/or protozoa (as I have seen in clients) and require botanicals with antiparasitic, antifungal and antimicrobial spectrums to gently weed them out.

I think finding the root causes yield better than results starving the microbiota. Just my opinion.

We are not agreeing on 'fiber'. Resistant starch is a fiber indeed because it is indigestible by us, only fueling and feeding the microbiome so they can do their wonderful job. I've seen a few references on Hep C and autoimmune arthritis. Gut pathogens are all implicated.

I used to have Hashimoto's (my sister Grave's). It is the same exact story. Gut pathogens are implicated, SIBO present, microbial translocation into blood and circulation, autimmunity ensues, human host organ attacked (thyroid; Yrsenia, Klebsiella, etc molecular mimicry), organ fails or is sick.

I believe the early 'starch free' diets really worked but long term if the person recovered health, they should be able to return to consuming these foods with no problems (except gluten I would advocate). Starch free is pretty exclusive when the largest molecular problem is gliadin which binds the zonulin unit that opens up the gut, increase permeability as well as inflaming the gut, raising stress/cortisol, thus decreasing commensal populations while increasing the pathogenic strains. Antibiotics rush all the above by wiping out the protective commensal populations.

These 2 caught my attention

Gut. 2010 Jan;59(1):88-97.
Gut microbes define liver cancer risk in mice exposed to chemical and viral transgenic hepatocarcinogens.

Reumatol Clin. 2013;09:229-38 - Vol. 09 Num.04
Of Bugs and Joints: The Relationship Between Infection and Joints

Dr. B G said...

George, Bea ~

Have you read the brilliant DuckDodgers insights about the long term observed effects of VLC that are not published or in an Atkin's book? Our guts host our immunity. For me, it is unthinkable that they can do their job if they are starved of the fuel which preserves and helps them thrive.

Root causes -- dig deep. IMHO you'll find the gut microbiota. The best diagnostic testing is currently from Genova Diagnostics which runs 16S rRNA sequencing testing, accurate parasite/pathogen evaluation and urine testing for bacterial and fungal dysbiosis biomarkers. We can track the buggers LOL!

DuckDodgers // Mar 12, 2014 at 22:01

"Cool. Glad to hear we’re finally discussing details! Although Dave defines “zero carb” as literally no carbs, “zero carb” can also be defined as anything below 50g of starch/day. And many people consider any carbs from non-starchy vegetables to be negative net carbs (you burn more energy digesting them than you get from them).

Here, take a look at this:

Dangers of Zero-Carb Diets, II: Mucus Deficiency and Gastrointestinal Cancers

Paul Jaminet dissects the “Optimal Diet” in that link. The Optimal Diet was developed 40 years ago and it was 60 g protein – 180 g fat – 30 g carbohydrate per day. It’s considered to be a “zero carb” diet. And after 15-20 years, the people who ate that diet came down with alarming rates of gastrointestinal cancers. Even the president of the Polish Optimal Dieters’ Association came down with stomach cancer. Massive glucose deficiencies and mucus deficiencies.

So, Jaminet recommends 150g of starch/day for virtually everybody to maintain gut health. And what we see with the PHD is that people’s guts heal very nicely. It appears to cure a wide range of ailments and diseases. You don’t see that kind of recovery with the Bulletproof Diet because that’s not what it’s trying to achieve. The Bulletproof Diet is mainly about brain hacking, not overall health.

As Paul put it:

It’s plausible that a zero-carb diet that included at least 600 calories per day protein for gluconeogenesis would not elevate gastrointestinal cancer risks as much as the Optimal Diet. But why be the guinea pig who tests this idea?

It’s a good question. You are braver than I."

George Henderson said...

Dr B. G., I wonder if all ancestral diets supplied similar amounts of resistant starch. Potatoes, bananas, rice didn't grow in Scotland. Other fibres - and lipids - are bifidogenic; almonds, for example. And Bea's asparagus.
So if you were committed to VLC, you could probably still find a way to feed the troops.

I don't doubt the RS benefits, the advantage of having extra butyrate etc. But I think something is missing when this is used as a criticism of VLC or Atkins.
If you read Dr Atkins' Diet Revolution, he doesn't just feed patients fibre, he reintroduces carbs after ketosis.
ALL the carb-lovin', potato-eatin' paleo peeps you've mentioned - every last one of them - went VLC first.
As far as anyone knows from their stories, you might NEED to go through a period of ketosis and a weeding of the microflora to get those benefits.
It is certainly going to help in very many cases.
I think we need a narrative that tells the whole story, of a binary, two-phase intervention.
You have made a very good and useful post here by the way.

Dr. B G said...


My problem is that Atkin's has had a 're-education' and it doesn't include whole soaked non-gluten grains, lentils, legumes, tubers, corms or bulbs. Besides potatoes, there do exist other forms of underground storage organs that are edible and sustainable.

VLC will always have a place but we are probably disagreeing on time frame. For some individuals (like me), VLC was damaging. The high cortisol state from having to burn fat and generate glucose and ketones took a toll for me. There are comments from a ton of n=1 stories that VLC and Atkin proponents tend to want to ignore, I think. Both Richard and Tim developed clinical T2D when their BGs fasting shot up > 120-130 mg/dl after extensive VLC. Personally I feel that this is not conducive to longevity or ultimately optimal gut health.

Are you Scottish? The moors, peatlands, and marshlands of Scotland and northern Europe were very similiar to the paleo nutriscape and terrain during the transition from Ice Ages to mega C4 grasslands. I suspect our ancestors consumed a pretty heady diet of RS and fiber because sedge tubers/corms (like tiger nuts), cattail bulbs, water chestnuts, wild carrots and other roots were common and found in C13/C14 isotope density studies from enamel and other remains from 1-3 mya.

AG Brown et al
Site Distribution at the Edge of the Palaeolithic World: A Nutritional Niche Approach

This paper presents data from the English Channel area of Britain and Northern France on the spatial distribution of Lower to early Middle Palaeolithic pre-MIS5 interglacial sites which are used to test the contention that the pattern of the richest sites is a real archaeological distribution and not of taphonomic origin. These sites show a marked concentration in the middle-lower reaches of river valleys with most being upstream of, but close to, estimated interglacial tidal limits. A plant and animal database derived from Middle-Late Pleistocene sites in the region is used to estimate the potentially edible foods and their distribution in the typically undulating landscape of the region. This is then converted into the potential availability of macronutrients (proteins, carbohydrates, fats) and selected micronutrients. The floodplain is shown to be the optimum location in the nutritional landscape (nutriscape). In addition to both absolute and seasonal macronutrient advantages the floodplains could have provided foods rich in key micronutrients, which are linked to better health, the maintenance of fertility and minimization of infant mortality. Such places may have been seen as ‘good (or healthy) places’ explaining the high number of artefacts accumulated by repeated visitation over long periods of time and possible occupation. The distribution of these sites reflects the richest aquatic and wetland successional habitats along valley floors. Such locations would have provided foods rich in a wide range of nutrients, importantly including those in short supply at these latitudes. When combined with other benefits, the high nutrient diversity made these locations the optimal niche in northwest European mixed temperate woodland environments. It is argued here that the use of these nutritionally advantageous locations as nodal or central points facilitated a healthy variant of the Palaeolithic diet which permitted habitation at the edge of these hominins’ range.

My ancestral background is Chinese and our diet is heavy in RS but our amylase genes tend to be high-copy compared to non-grain heavy populations. Our RS 'RDA' may be higher than yours if it's northern Euro.

Most of our common ancestral foods are very low glycemic index, high fiber and contain greater than 10 g RESISTANT STARCH per 100g-cooked serving:
--potato (20g RS)
--yams (25g RS)
--taro (18g RS)
--red bean (15g RS)
--silverweed cinquefoil (15g RS)
--pumpkin (12g RS)
--long grain purple rice (12g RS)
--water caltrop (12g RS)

Dr. B G said...

Sources and intake of resistant starch in the Chinese diet

Anonymous said...

Hallo Dr. BG,

thanks for your interesting blogpost.
In one of the comments you wrote "I used to have Hashimoto's"... so you don't have it anymore? Do you still take thyroid hormones?
I suffer from hashimoto, so I'm always searching for success-storys.

Bea said...

You can very common sense wise eat lc. It does not if you so choose exclude any of those foods.
Just had a beautiful pumpkin sqaush. I simply choose not to eat corn, white rice, white potato. Stay around 50- 75 grms of carbs. Day for many years. Never developed high fasting blood sugar.I raise sheep, goats, pigs, horses, chickens,. Veterinaries are way ahead of doctors in the gut bacteria. My horses are on low starch , sugar diets. Nothing will blow a horses feet out faster than undigested starch
causing a bloom in gut bacteria in the hindgut.
I do think resistant starch can have its benefits.It is definitely used as a panacea, per Dr. Ayers, in the livestock world to try to prevent, reverse, cover up the ills of poor and unnatural living conditions of the animals. I never grain my animals. It is very unnatural and only used to fatten rapidly. I've seen too much death from excessive high energy, high starch, high grain. Bloat, enteritis, founder, diabetes.

Bea said...

I guess my whole point in this discussion which might be getting lost because of my slight annoyance of lc bashing is Feed your gut sensibly Ala Dr. Art Ayers. You want to nurture your critters . Meet your own personal glucose needs. Mine are not high. 54 yr. Old woman. Messed up glucose control thanks to the low fat 1980's. Be very careful over doing probiotics and potato starch. Happy in control critters good, Out of control excessive blooming and fermentation can be very bad. Rashes, bloating, foggy, lethargic
might be a sign it's all too much.

Bea said...

Just wanted to address some of your points you brought up before I head out to tend me critters.Never got high fasting blood sugar even during the times I did zero or very low Carb. I had the exact opposite my blood sugars just kept slowly getting lower to where I was waking up with blood sugars in the high 50s. So I adjusted up to where they would be between 70-90 in the morning. Which was around 50 gms. I'm not married to that number sometimes its higher. I developed sibo from probiotics at one time so I am very Leary of them. I'm sure many people are just
fine with them. I've had my share of gut issues mostly before lc. Tried many protocols. Went to the famous Witteker Wellness Center in Ca.
What I have learned for my body. What it told me loud and clear was" Leave me the hell
alone". I bought the potato starch and told myself why are you messing with your body again it is healing on its own with what it needs. TIME, healthy food and not alot of it. Not eating after 2;00pm has been a major healer for my gut it just doesn't want to be a constant sewer. Colonoscopy is a major one that damages the gut. Not a properly designed lc diet Ala Dr. Ayers. Last test gut bugs are great. Still love your blog.

Tim Steele said...

Horses and cows don't do well on starchy grains because that's not what their gutbugs want--they evolved eating grasses. Pigs, however, evolved eating roots and starchy tubers and do really well when they get a good supply of RS in their feed.

Humans evolved eating starch.

Here are a few thoughts from commenter 'PaleoPhil' on Mark's Daily Apple today that fit in with the comment about starch in Scotland:

The fact that they enshrined pease porridge in a nursery rhyme that they taught to all their children suggests to me that they knew it was beneficial, at least originally. The words (pease porridge cold ... nine days old) also suggest to me that they often ate it cold for breakfast. If they didn't eat too much sugary stuff with it, that would mean that their blood sugar wouldn't have spiked in the morning, so that the overnight "fast" would have been maintained, or nearly so, despite eating breakfast. Given the BG suppressing effects of RS, they probably could even have had some honey with it without spiking the BG much. Lots of Paleo dieters skip breakfast in the morning to maintain the overnight fast and keep BG low for longer, but this isn't necessary if the breakfast contains mostly food substances that don't spike BG--RS, fiber or fat. Maybe a RS-rich breakfast is better than skipping breakfast, because the RS generates energy later in the day and for an extended period, by feeding the bacteria that then generate food for us during the day, which our ancestors could then have used to hunt and gather.

Have you noticed that many traditional breakfast foods contain at least some RS, especially when eaten the 2nd, 3rd, ... 9th, ... day? Here are some more examples: oatmeal, boxty (potato pancakes aka poor-house bread), pratie oaten, hash browns, home fries, helmipuuro (potato starch porridge - Helmipuuro - Wikipedia, the free encyclopedia), hominy grits, maize meal porridge, corn meal bread, poi, congee (rice porridge), baked beans on toast, kosai (bean cakes), black pudding (containing oats in sausages prepared one or more days earlier), water chestnut cake, idli (lentil cakes), corn flakes, muesli, .... See Breakfast - Wikipedia, the free encyclopedia and for more.

"Peasemeal brose, also commonly known as brosemeal, is a traditional breakfast dish in the North of Scotland." Pease pudding - Wikipedia, the free encyclopedia

Here's another folk rhyme:

Boxty on the griddle,
And Boxty on the pan;
The wee one in the middle
Is for Mary Ann.[3]

Boxty on the griddle,
boxty on the pan,
If you can't bake boxty
sure you'll never get a man.[4]

Boxty on the griddle,
Boxty on the pan,
If you don't eat boxty,
You'll never get a man.[5]

Bea said...

My pigs are not fans of raw tubors. Maybe because they are not wild. They absolutely love pumpkin though. You throw one in the pen and they go wild. I totally agree resistant starch is good for your gut. Don't agree on the necessity of high gi " safe starches". This maybe a weird question but all this talk of excessive flatulation just doesn't sound good to me. Too much of a good thing maybe a bad thing. I spend alot of 1 on 1 with my animals as I have a petting zoo. Horses and goats and sheep are fermenting farting belching machines. Have yet to here a pig fart. I think the excess gas some people are proud of is
not normal healthy gut fermentation. Any thoughts. Sorry if that was just weird.

Tim Steele said...

Bea - The fart reports are interesting. For me, it was a couple weeks of increased flatulence, then back to pre-RS levels with the added bonus of then not being noxious. I responded very well to an increase in RS, but many report the gas just stays and stays, although now that we've become more aware of the part probiotics play, people who were having gas problems are reporting that it goes away after a few weeks of probiotic support.

I give lots of credit to my resilient gut to all the dirt and animals I am in contact with. Not everyone has that advantage. Your petting zoo certainly gives you a big advantage, too.

On the 'High GI Starch' issue, I agree and rarely eat safe starches except for rice, potatoes, and even beans that have been cooked, cooled/frozen, and reheated. Doing this increases RS dramatically and lowers the GI of the food, plus it makes things easier. I make up big batches and freeze until ready to eat, much more convenient than making fresh every night.

The Potato Starch has only ever been proposed as a way to get a targeted, therapeutic dose of RS. Not everyone likes or wants it--no problem. Get your RS from food. Easy to do.

Bea said...

Thanks for your response. I think low GI real food sources of rs are the only way for me. I just think the whole gut bug conversation is very interesting and important but think alot of low carbers are leaving RN and this site because we are becoming almost like laughed at, made fun of and demonized on these 2 blogs. Just because you didn't leave with the one that brought you to the dance don't talk smack about her now. That is why I look at Cooling Information site more now. Thank you Tim for your thoughtful responses. Off to do ponyrides now.

Dr. B G said...


I appreciate all of your thoughts and horse and pig insights. Horses are vegetarian so I hate to limit comparisons with them. Laminitis is however similar to our gluten reactions and sibo responses I believe strongly.

You said "Be very careful over doing probiotics and potato starch. Happy in control critters good, Out of control excessive blooming and fermentation can be very bad. Rashes, bloating, foggy, lethargic might be a sign it's all too much."

To me this indicates clearly there is some SIFO/SIBO occurring with likely pathogenic and/or parasitic overgrowths in the small intestines. These are abnormal responses and significant. I hope you figure things out.

My main problem with VLC is that it breaks metabolism and breaks the gut simultaneously or in a staggered fashion. Most people recover or others still deal with broken metabolism (adrenals/thyroid), very analogous to 'yo yo dieting'. Gonadal hormones get sacrificed (testosterone, progesterone, DHEA, etc), oxidative stress increases, and I betcha longevity is seriously compromised.

For me I turn to successful ancestral societies and what they are doing eg Okinawan, Belgium, Crete, etc. None of these eschew
--meat or saturated fat
--high fiber carbs (low-mod GI)
--bitter greens
--plant based eating (I eat 70% plant based FYI)
--fermented foods and bevs
--exercise (again another bashing against VLC but another day)
--communal symbiotic collaborating
--rest, relaxation, siestas
--superb adrenal/gonadal health and hormones

Personally IMHO we are disagreeing on only a few things. My net carbs is probably 100-150 g/day (total carbs 200-250g/day). I eat more than you because I'm younger and I rev my metabolism like my ancestors through movement, strength training and cardio exercise and try to tend to fragile adrenals.

Bea said...

Dr. B G

You said "Be very careful over doing probiotics and potato starch. Happy in control critters good, Out of control excessive blooming and fermentation can be very bad. Rashes, bloating, foggy, lethargic might be a sign it's all too much."

To me this indicates clearly there is some SIFO/SIBO occurring with likely pathogenic
and/or parasitic overgrowths in the small intestines. These are abnormal responses and significant. I hope you figure things out.

Sorry if I wasn't clear but I do not suffer from any of those symptoms but have read others
Report those symptoms using potato starch.

You are right we are mostly on the same page
and my glucose needs are probably less than yours although I am fairly active.

Meat and fat.....check
High fiber carbs.....check
Bittergreens(grow them and eat right out of the dirt).............check
50 percent plants w/berries and
apples.....check by choice
Everything else....check
Lots of hiking, walking, horsebackriding, best husband. Friends
So why is lc supposedly killing my gut critters?

Bea said...

I have big doubts about Paul Jaminets glucose deficiency killing those Polish OP dieters. It just doesn't make any sense. Where did he arrive at his figure of 150 starch grams a day or you dry up and get gastric cancers. Poland is number 47 in WHO list of countries ratings for stomach cancer. The top 10 in this order are
Not exactly glucose deficient countries. In fact
high rice eating countries. My opinion is
H.Pylori is the major factor not mucin

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


To put it mildly, you logic regarding the PHD is flawed. Jaminet provides a strong argument for causation and you are using an unrelated correlation as an attempt to negate. Regardless of one's personal beliefs, do you find this tactic to be intellectually satisfying?

In case you have not actually read Jaminet's work, or reviewed it recently, listed here for your convenience is a place to start:

G said...


It sounds like you are EXXXTREMELY active~. I think what applies is somewhat different given perhaps your activity level. I misunderstood you -- sorry I thought you had referred to your symptoms.

In the VLC world (except Bernstein, Attia and Volek) exercise is eschewed. For many chronic cardio is eschewed. Forgive me if I'm incorrect. The New Atkin Revolution was written by an endurance Iron Man triathlete/physician but my understanding is that he carbs up pre-race (though I could also be wrong).

Exercise can protect against the damage to the gut microbiota induced by a fiberless or fiber restricted diet. Below is a rat study demonstrating this.

In restricted eaters, we have found a significant increase in the number of Proteobacteria, Bacteroides, Clostridium, Enterococcus, Prevotella and M. smithii and a significant decrease in the quantities of Actinobacteria, Firmicutes, Bacteroidetes, B. coccoides-E. rectale group, Lactobacillus and Bifidobacterium with respect to unrestricted eaters. Moreover, a significant increase in the number of Lactobacillus, Bifidobacterium and B. coccoides–E. rectale group was observed in exercise group with respect to the rest of groups. We also found a significant positive correlation between the quantity of Bifidobacterium and Lactobacillus and serum leptin levels, and a significant and negative correlation among the number of Clostridium, Bacteroides and Prevotella and serum leptin levels in all experimental groups. Furthermore, serum ghrelin levels were negatively correlated with the quantity of Bifidobacterium, Lactobacillus and B. coccoides–Eubacterium rectale group and positively correlated with the number of Bacteroides and Prevotella.

Don't want to complicate things but we want Bifido, Lacto and Clostridium cluster XIVa (E rectale). These are our friends. All are big butyrate producers and guards of the gut/immunity. Lacto even reverses a lot of metabolic disorders when used as a probiotics in animal/human studies. Excessive Proteobacteria is highly associated with disease, dysregulation, and disorders.‎

Anonymous said...

Dr. BG,

So glad you posted again!

I'm freaking over my son. He's developed red, rashy cheeks, light colored stool and eczema patches on his neck recently and I don't know how to help him.

Would you be able to work with me? I'd love to do a stool test through you.

Please let me know. Thanks!

Bea said...

Thank you for the link. I do own the PHD book. Sorry I don't have a PHD but hope its still OK to have my own opinion. Tatics are for war. That is not my intent:-)

Bea said...

Good Morning Dr. B G

Just wanted to clarify before I before quit hogging this post ( farm humor:-) Love the blog. Learned alot and so appreciate the time you put into it. I learn stuff from all the blogs I peruse.
PHD- 3 eggs a day
Art - I enjoy apples again(pectin)
You - cashews, tarro are sources of resistant starch in the Chinese diet. I eat those. Sounds like my active lifestyle is helping nuture my friendly gut bugs.(Forgot to add to the list cleaning stalls, feeding, picking up kids and walking the ponies at parties, wrestling sheep) Peter -butter is goooood. PUFA bad
I don't think I'll ever go up to 150 starch carbs a day as I only eat twice a day and if I ate 75 grams per meal I would have to take a nap after every meal. I did that for too many years on the sad diet. Hope you have a awesome day!

Bea said...

Oops, Meant 150 grams of starch. Really specifically white rice is what I'm referring too.

SK said...

1. What amount of fermented veggies per day are you recommending?
2. Is this an ok source? Looks good to me; your view?
3. What is your current dietary recommendations? Seems a bit unclear as to amount of starch/ non veggie carbs you recommend per day?
Also, fruit?
4. I ask this as you previously recommended VLC- and in particular for CVD Plaque reversal? Have you re-thought plaque reversal recommendations?

Jan said...

Dr BG great post! Wondering what you recommend from Natren for gut repopulating? Also, what do you think about Dr Ayers recent post saying basically that dairy probiotics don't really work or help with a broken gut? I have Hashis/SIBO and eat a nutrient dense diet (PHD) plus a good amount of RS/PS added in. I can't tolerate fodmaps and don't digest raw veggies and fiber basically plugs up the works. I'm trying to find what I need to repopulate my gut. I eat fermented foods, take Prescript Assist and probiotic mix. I'd appreciate any suggestions. :-)

dr j said...

Hullo Grace! Konjac john here!

Did I send this exquisite horse diet document some time ago?- it set me on the path of linking chewing after meals with focusing on the likely care of my own "hind" gut.

I love this statement " This may run counter to the schedules of many current horse owners." Much like humans.

He's linking a carb type (fructan) to time of day to season to drought/good rains impact on the plant-horse interface and the consequent risks and advantages to the horse diet .

We are nowhere there yet, we prefer to buy any vegetables, mainly determined on price , but pay a fortune for a costly meal of whatever prepared by an egocentric chef.

An example...

Good Grazing Management

Good grazing management will lower the consumption of fructan and reduce the incidence of colic and laminitis. Good practices should include:

Limit grazing on high fructan grasses – less than one hour a day for susceptible horses.
Use grazing muzzles when necessary.
Don’t overgraze pastures – fructan is higher in the lower few inches of the plant (Watts and Chatterton 2004).
Fructan is lower on fertilized fields - the plant is less stressed, less fructan.
Graze early morning – fructan is higher in afternoon/evening after a sunny day
After a sunny day and a cool night, limit grazing in the morning – the plant has not used up its energy store of fructan during the night

This type of knowledge i have only seen in cattle drovers who have spent a lifetime of watching animals on the move from one farm to another over vast tracts of land here in Australia.
You're a beacon!
all the best

G said...

Tim ~ Thanks!

Anon ~ Hallo, yes had Hashi's when I was 18 after a lot of cafeteria gluten, late nights/vampire lifestyles, not enough sun/vit D, family stress and starting college. But it healed somewhat gradually over the next 5-10 years with sunlight exposure, exercise, laughter/friends and eating Chinese food (less gluten). I do take some Nature-throid but I have some residual mercury and hope to eventually titrate off or down at least when I evenutally finish chelating.

David ~Enjoyed your comments. Paul is brilliant. I'm in the first edition LOL and the new version has been on my bed stand (borrowed from Myrick)

Gen ~absolutely! Email me

G said...


Anything that says 'raw' is likely to be unpasteurized and retaining all the live bacteria! They are a great SYNBIOTIC = bacteria + fiber

Yes for plaque reversal I'd consider aiming for metabolic improvements via focusing on gut health, hormonal health, eliminating toxins (mercury, PCBs, etc) and mitigating mental stress... so then VLC is out the window unless it doesn't impact thyroid/adrenal health. That would be fine for some people temporarily or transiently and not a bad tool but now so many other tools may exist that deserve some attention imho.

Unknown said...

Dr. BG: I sent you an email message. Ping me back?



David said...

Posting again with correct info.

Dr. BG: I sent you an email message. Ping me back?



G said...


Actually I love all the natren products seriously. The Gyn-Natren was the best thing and was intro'd by my lil sis who used to have endless yeast infections (from endless Strep and endless antibiotics). It cured me too after Candida after a titanium implant and tetanus vaccine (mercury).

For Hashi's, have you considered a full gut rehab and evaluation if you don't see complete success with the simple interventions? It is not uncommon for parasites/pathogens to prevent 100% gut healing. Once a pathogen establishes in a disturbed gut, I have found that they are difficult to dislodge.

Have you considered g plantain or g banana flour? These are the 'NEW' version of the 7-steps optimal gut plan...

Step #4.
VERSION A: Green banana flour 1-3 Tbs + Raw PS (potato starch) + high ORAC green powder in 2 cups water
VERSION B: Raw PS (potato starch) 1-3 Tbs + Psyllium (if not allergic) 1 Tbs + high ORAC green powder (I like Amazing Grass, LOL) in 2 cups plenty of water

I really like g banana flour -- it has soluble fos and inulin and other oligo fibers which propel off pathogens that adhere to the small intestines and help them to be eradicated. Please consider it. Also FOS and inulins feed Bifidobacter more than RS can feed Bifido. We need Bifido -- it is a potent anti-pathogen protector in the gut. It competes for binding sites and helps to aggressively eliminate the more resistant and pathogenic strains that are left behind after rounds of antibiotics.

G said...

David ~ Yes I'm behind and will respond soon. Thank u!

Bea and dr j ~

Thank you for the discussion. I love my readers -- YOU GUYS ARE SOOOOO SMART!!!

The horse biology is fasinating I had no idea.

I wonder how much of the grassheads appear during the spring? Some, right?? Then basically the animals are getting gluten in their diet and perhaps their zonulin is as fragile as humans, opening the gut and causing permeability and inflammation/sibo.

Prior to 10-20kya and the massive grasslands overtaking the earth as the Ice Ages subsided, the C3 grasses (barley, rye, wheat, oats) were frost-tolerant and store a lot of fructans and starches efficiently. Some researchers believe these starches behave as an molecular ANTI-FREEZE (much like I suspect RS in USOs, understand storage organs LOL haa!).

Something like 95% of plants on earth are still C3 so we will not get away from these -- they truly are weeds and will grow anywhere and everywhere because of the cold and CO2 selection factors. For prevention of laminitis ('gout' in horses) the experts advice among many things is to avoid both C3 cold-weather grasses -- oats, barley, rye and wheat and high sugar C4 grasses. It's funny 'safe pastures' is just like PHD safe starches ahah.

"Dangerous C3 Grasses for Grazing

Ryegrass, fescues, cocksfoot, brome, paspalum and barley grass
pastures, as well as common cereal grain grasses, such as oats, wheat
and barley, are most likely to have the highest NSC content as they flush early in spring or after summer rains. These grasses continue to produce fructans and NSCs for growth under favourable conditions. Many native species of grasses have lower levels of NSCs and sugars, but they are often grazed out or competed with by more vigorous C3 or C4 grasses."

Doesn't this sound familiar like my WAPF-ey 7-steps??

"Soaking hay in water may
reduce some of the NSC, but shouldn’t be relied on as left over sugar concentrations may

Other fibres (structural carbohydrates) feeds for laminitis-prone horses can be hulls, such as soybean and lupin hulls, and fibres foods such copra meal and beet pulp. They are not
used as a full replacement of traditional roughages but more to supplement the diet to increase
fibre intake."

Are you guys familiar with how successful horse manure is as fecal transplants to cure GI problems in horses? Yes -- smart vets, they're all so brilliant.

POOP = ultimate probiotic

(granted from healthy donor, no pathogens or viruses or diseases)

G said...

dr j,

THx for the link!

You might like this -- evolutionary background and it's from AUS...

dr j said...

G,thats really neat...typical..takes a grrrl from Shanghai to find an excellent C3/C4 overview published in Oz with deep input form a caring horselover from the USA.


Jan said...

Thanks @Dr BG. Love the info and yes, I'd love to get help! I feel like I'm so close! How can I reach you? I know you're busy!
I am doing your 7-steps but can't handle any FOS or inulin. It feels like knives in my gut and/or completely constipates me. Right now, I'm using Heathers Healthy tummy fiber, acacia Senegal and I can handle 1/4tsp in the morning "drink". I also take Amazing Grass powder, PS, and my probiotics with that drink. I've ordered banana flour from amazon. It's on the way.

Thanks so much!

George Henderson said...

@ David, the PHD theory of carbohydrate essentiality had little to do with bacteria (other fibre can feed those) but with ideas about the uses to which colonic cells would put glucose itself. There seems to be some truth in this, based on the metformin model.
But it does not prove essentiality of any particular sugar or other fibre. People have lived on meat alone, and meat fibre (collagen etc) is also prebiotic (carnivores have normal gut health, humans to survive have had to live as carnivores for protracted periods - even if this is not the preferred ancestral diet, it is not a diet that causes the death of humans).
Resistant starch and other pure prebiotics are empty calorie fertilizers for gut bacteria. My sister-in-law uses molasses to feed bacteria in soil, this is because they benefit from the minerals - bacteria can make some vitamins, but need minerals. Fertilizers have their place, but organic gardening of microflora ultimately means wholefoods.
In this metaphor, antibiotics are Roundup, probiotics are seeds, prebiotics fertilizers, and VLC dieting is weeding and trimming your garden. Good food is organic compost.
They all have their uses, but some strategies are more "natural" than others.

I know oats in Scotland are a relatively recent crop, not sure if pease porridge plant grew wild or was later cultivar. Hazelnuts and acorns and wild roots seem most likely starches.

dr j said...

Dear George,

Sometimes i despair at the Cinderella status of the host colon : your statement "Resistant starch and other pure prebiotics are empty calorie fertilizers for gut bacteria" is a tad dismissive to the colon itself if we are to build an integrative picture. The colon is not a stoney faced Easter Island static tube - if your frame of reference is that of a colon itself,it is a dynamic, regenerative entity. Just one example- , the csiro autopsies of pig colons that gave numbers of increased length of 20 to 30% in 2 weeks when RS was added to the diet. To me, that's profound growth, even more extraordinary than the regenerative properties of your beloved liver!

dr j said...

and if we follow along the line of duck dodgers in terms of glyco-conjugate chemistry, this recent abstract suggests that colon mucus chemistry pressures microbiota ecology-

"A functional mucus layer is a key requirement for gastrointestinal health as it serves as a barrier against bacterial invasion and subsequent inflammation. Recent findings suggest that mucus composition may pose an important selection pressure on the gut microbiota and that altered mucus thickness or properties such as glycosylation lead to intestinal inflammation dependent on bacteria.... the effects of mucus glycosylation on susceptibility to intestinal inflammation, gut microbial ecology and host physiology. We found that TM-IEC C1galt (-/-) mice did not develop spontaneous colitis, but they were more susceptible to dextran sodium sulphate-induced colitis. Furthermore, loss of core 1-derived O-glycans induced inverse shifts in the abundance of the phyla Bacteroidetes and Firmicutes. We also found that mucus glycosylation impacts intestinal architecture as TM-IEC C1galt(-/-) mice had an elongated gastrointestinal tract with deeper ileal crypts, a small increase in the number of proliferative epithelial cells and thicker circular muscle layers in both the ileum and colon. Alterations in the length of the gastrointestinal tract were partly dependent on the microbiota. Thus, the mucus layer plays a role in the regulation of gut microbiota composition, balancing intestinal inflammation, and affects gut architecture."

dr j said...

And if one had cholera, the use of cornstarch might be a godsend

Mechanisms Involved in Governing Adherence of Vibrio cholerae to Granular Starch

"Such adhesion may contribute to the beneficial effects observed following administration of granular starch-based oral rehydration solutions to cholera patients".

Tim Steele said...

George - If you come here and throw around gardening analogies, expect some feedback!

Weed-Seed-Feed as Dr BG is developing is an integrative approach to gut health, and her 'Feed' step is the most unique among gut health 'programs'. Tell me how, on a VLC diet, feeding of gut microbes is accomplished?

To use your analogy of gardening, a VLC diet is the same as trying to go grow a crop of big juicy red tomatoes and fertilizing them with your brother's molasses...yes, the molasses may provide a few missing nutrients, but tomatoes are nitrogen hogs, so without a hefty dose of nitrogen, preferably from well-composted manure, the tomatoes will grow--but they will look pale and set fruit poorly.

If there is no ready supply of well-rotted manure, a handful of man-made nitrogen fertilizer will supply the nitrogen these tomatoes need, and you'll see them quickly respond (as long as they are still not missing P and K). BUT, rest-assured, pouring more and more molasses will do little for the languishing tomatoes.

Another way to get nitrogen in the soil is to grow plants that have roots which attract microbes that make nitrogen. The nitrogen-fixing bacteria will create soil rich in anything planted there the following year will find ample nitrogen thanks to some lowly microbes.

OK, so in your VLC scenario, you are just outright starving your gut microbes. Not ALL of them, no, you will surely still have the microbes needed to make poop, digest animal collagen, and work on the plant fibers you may or may not be ingesting. The result will be a gut full of weeds. This diet does not preferentially grow anything. It does not produce lactic acid and butyrate. It does not foster the growth of bifidobacteria, the pH will be wrong, ammonia will be produced, and the microbial profile will show species that are adept at degrading mucin, sulfurs, and methane and not ones that degrade plant matter.

This situation not only leaves your colonocytes starved of butyrate, their preferred fuel, but forces them to survive on glucose from your blood. In your haste to avoid eating glucose, you force your gut into a glucose burning factory instead of a fat-burning factory. The colonocytes now behave differently. They no longer self-destruct when they should and they do not form highly efficient Peyer's Patches where T and B cells created, trained, and stored. This is your immune system starting to fail on VLC. Your gut is also ripe for a hostile takeover by the first pathogen to arrive.

Tim Steele said...

NOW, if Dr BG's advice was "Eat a VLC diet and include 4TBS of pure potato starch daily," that would be pretty lame. It would probably be a bit better than the standard VLC diet, but it would not create the flourishing gut microbiome we all deserve.

Instead, she recommends doing a 'soil test' to find and deal with pests, then repopulates the gut with microbe containing foods, probiotics, and naturally found microbes on organic veggies and in dirt. Then she wants us to fertilize the garden with the food it requires: resistant starch, inulin, FOS, pectin, mucilages, gums, and the micronutrients found in real foods.

This diet will grow a gut full of 'big, juicy, red tomatoes' just like we want. The colonocytes will be flooded with butyrate, bifidobacteria will flourish, lactic acid producing bacteria will be pumping lactic acid and create a pH favorable to beneficial microbes and inhospitable to pathogens. The immune system will improve and overall health will improve.

The attack here isn't on VLC diets, it's on any diet that starves the gut microbiome of the fertilizer it needs to produce a healthy garden of life. The SAD diet actually has more gut fertilizer than the standard VLC diet, even one that is 3/4+ plants. If those plants were onions, garlic, leek, chicory, and green bananas I take that statement back. But, if the plants are the ones found on a normal salad bar, it's not going to be enough.

It's possible to eat a VLC diet and maintain good health health if one focused on getting ample low carb, high fermentable fiber plants. Some seem to have cracked this code, but unfortunately most practitioners of LC/VLC diets do not. They rely on protein, fat, and non-starchy veggies without any thought to RS, inulin, FOS, pectin, gums, mucilages, and other gut bug foods that leaves their gut in a rut.

It's estimated we need about 40g of fermentable fiber per day to produce the butyrate we need to fuel our colonocytes...without RS, that is hard to do. Two pounds of raw onion or a pound of garlic or 1/2 pound of chicory root would be required. Any other plant you try to eat, you just can't physically get enough prebiotic fiber from to make the butyrate you need unless you ate pounds and pounds a day, but then you start getting other problems.

OK, sorry for the novel. Us farmers get excited over this to tend my crops.

Tim Steele said...

dr J - nice to see a fellow farmer here!

There is a similar study on the adhesion of microbes to other raw starch granules and it's not just corn starch that does this! Potato starch, green banana starch, and rice starch also are effective at removing pathogens. I assume just about all raw starch granules will attract microbes to some degree.

Matt said...

How do I get an email notification with the latest post from this blog?

Tim Steele said...

Matt - You have to sign in with an identity, then you get the option.

Most people use a Google Account for this, pretty easy.

Bea said...

Dr BG and Tim

My last gi test was
Bifado-7.6 . The graph didn't go much higher. It almost pegged the right side. The test before this I was trying to starve some probiotics out of my upper gut and bif was very low. Asparagus is the only thing I added to my diet before this test a few weeks later. It's great vege for the critters. A staple in my diet now. Hope that can help someone else. Tried some PS and my mouth burned and
tingled and heart raced for about 5 min.

Tim Steele said...

Bea - I was trying to add you and your asparagus into my lengthy dissertation, lol.

Asparagus is a great food for gut bugs! Full of inulin and FOS. When I was growing up, we picked wild asparagus for a few short weeks in the spring along with dandelion greens. This, after a long Winter of few fresh veggies must be a welcome sight to your gut bugs.

There are certainly going to be many pieces to the whole gut health puzzle; genetics, stress, lifestyle choices (smoking, drinking, etc..), sleep, geography, and age all play a big part beside the diet.

Potato starch is not for everyone, it was only ever presented in the first place as a source of RS. You are not alone in not liking it. Green Bananas and g banana flour are a much better source of prebiotics, though maybe not quite as high in RS, they are high in RS, inulin, FOS and a slew of other stuff that comes along with a whole food.

Glad you have the insight of several gut tests to see what's actually growing in you. Most people are missing that crucial key. I just sent off a sample to the Genova Labs for a Metametrix GI FX 2200 report. It will be interesting to compare that with my American Gut report of 6 months ago.

I've seen several other Metametrix reports that showed people have fairly high bifido. I'm not sure that the result on their bar chart (7.6 as you indicate) means that you have really high levels of bifido, only that you have high levels compared to a baseline of the population.

The Am Gut report shows your actual numbers in percentage, not percentile, and in comparing the two reports, I'd have to say that being in the 50-90th percentile of Americans for bifidobacteria counts is still pretty low as most people hardly have any bifidobacteria in their guts.

As shown on our Am Gut reports, my wife, eating a pretty clean SAD diet, had no detectable bifido. The sample population of several thousand people showed an average count of about 1.5% bifido. My report showed I had 13% bifido, which was the highest ever seen as far as I know. My diet at that time included daily servings of cooked/cooled rice and potatoes, dried/raw plantains, and 4TBS of potato starch. No probiotics or yogurt, but a good bit of sauerkraut. And probably 1 pound of meat daily.

The pig studies I was reading at the time predicted my high bifido count almost to the letter. Pigs who were switched to high RS diet increased bifido from 1-2% to 10-12% in a few weeks time.

What's funny about bifido, they don't even prefer to eat RS or inulin, they eat the byproducts of other microbes who do the primary degrading of RS and Inulin and produce chemicals that bifido thrives on.

So, Bea, the fact that you had good levels of bifido tells me that you have a gut full of good microbes that took advantage of all the plant components in the asparagus and produced butyrate and other gut bug fuel that ended up supporting a good population of bifido. Not everyone can do that. Be glad that you can. Do you mind me asking what you past history with antibiotics is? I know you work around animals, so I suspect your proximity to novel microbes helps you as well.


David said...

I'm ready to order the Metametrix GI FX 2200 and came upon something interesting. This guy:

uses two tests in his practice, Metametrix and BioHealth BH #401H. The linked page shows comparisons where Metametrix missed some things that were picked up by BioHealth and vice versa.

Thoughts? The #401 test, no "H" as in "pylori" is quite a bit less expensive. Belt and suspenders, overkill...seems like a good idea but I'd like to know if others have gone down this road, etc.

Link to the BioHealth page:



Bea said...


On the sad diet I ate over 5 years ago I could digest anything. Was fat and unhealthy though. The beginning of my descent into gi hell started with a colonoscopy about that time ago. Everything I ate ran right thru me after that. Took probiotics BioK drink etc. Developed massive upper gut fermentation with those. Everything I ate was fermenting up high in the small intestine. It did stop the runs but my small intestine was now a colon. Hence my aversion to probiotics and even ferments. Self took amoxicillan to try to kill the probiotics. Helped but was right back. Found a gi that would give me rifaxamin. Felt much better. But my poor si was just wracked. It was so inflamed they thought I had blockage and went in laprascopically. Ice cream, only hagen daz, became my friend. So guess who now appears. Yeast/fungas. Now I'm tingling. Can't sleep. Didn't know what it was at that time but lactose was it's friend. Even went
Cedar Sine a in LA. They went in diagnoses vascular profusion in the si. Dr. talk for inflammation. Last time there it was 100 degrees and the air was broke on the car. Drove home with the windows down crying eating ice cream. It was the only thing that didn't feel like it got stuck in the si and at that point I still wanted to live. Bed ridden for the week after. Was losing sensation up my arms and legs. Pretty much ready to give up. My mom called 1 day. I was watching this show and sounds like candida. Called my GP begged her to take that day. Gave me nystatin and I was out shopping in a few days. Of course it wasn't that easy but it told me that was what was going on. Went back to Ceder Sinae and they said your right it could be yeast as rifaximan pretty much cleans out the si. OK why don't they tell people no sugar when you take it? Where I am today is probably still have inflammation but much better. Learned from Cedars to give the si a break and leave ample time for it too cleanse. 2 meals before 2:00 has been a great healer for me. Time, time, time . It's really almost perfect the last 6 months. Don't know if I will ever get a colonoscopy again. I know I can't take probiotics. But sometimes I think all of that got me to here which is pretty great now.

Tim Steele said...

Bea - And now we know...the rest of the story.

Keith Bell said...

Tim, nice prose, especially the part about Peyer's Patches. But wouldn't an effective diet depend on current microbial balance? For example, in the last blog about the autistic child with "buttloads of butyrate" where too much butyrate is a bad thing, wouldn't the ketogenic diet be helpful in bringing balance due to very low carbs?

Most people believe the ketogenic diet is about raising ketones, but some studies show ketones actually lowered over time on the diet. And that makes sense considering the building block of ketones is butyrate. And the most basic ketone, acetone, is product of clostridium bacteria. But the ketogenic diet is apparently a good thing for many imbalanced people including in cancer, I believe due to flora shift. In these people, the diet you're advocating would seem to be adding fuel to the fire. Speaking of fire, there's also the theory of acetone build-up as cause of spontaneous combustion in humans. Best to wear loose-fitting clothes.

Tim Steele said...

Now, Keith, how can I take you serious when you don't provide a single study or link?

Just kidding! I hear you about ketosis and it's place for some people. It certainly has therapeutic value, I just don't think it's a good strategy for the healthy, though.

Keith Bell said...

Actually, even for the unhealthy, there may be reason for revision of the so-called ketogenic diet to include your plan. It would fall more in line with the GAPS diet which isn't necessarily low carb, but addresses the same population (autism, epilepsy, etc.).

I especially like the idea that RS attracts microbes in the small intestine, basically cleansing the small intestine, possibly via targeted biofilm-busting amylase production. Perhaps origin of the "buttloads of butyrate problem" is the small intestine where overgrowth shouldn't take place.

That's the problem with PCR stool testing, not knowing where the overgrowth is . . . the only real way to know is via biopsy such as this new study where tissue samples were taken:

But the PCR tests are better than shooting in the dark. Are you sure you're Dutch and not Russian?

Bea said...

Yes there is always more. ..... to a story:-) . My lingering symptom is an inability to digest lactose
But probably best because me and Hagen Daz were like a fatal attraction. When it was good it was soooo good and then he tried to kill me. I still look at him in the store. Think of the good times and move on. To the meat and PRODUCE dept.

G said...

Keith, George, Tim ~Thanks for your replies!

Bea ~ HA aha. I knew it.

Have you considered that you got yourself an iatrogenic infection from the colonoscopy?

Look at all the things you can get???!

G said...


Oligos, inulin, FOS are great too (as you know, like breastmilk the perfect SYNBIOTIC -- microbes+GOS)

Studies with Inulin-Type Fructans on Intestinal Infections ...‎

Soluble Fiber Viscosity Affects Both Goblet Cell Number and Small ...‎

Soluble plantain fibre blocks adhesion and M-cell translocation of intestinal pathogens. J. Nutr. Biochem. 24, 97–103. Roberts et al


Dr. B G said...

Dr J

You know I love that "POOISAZOO"

And this one is WOWOW neo-classic "The colon is not a stoney faced Easter Island static tube - if your frame of reference is that of a colon itself,it is a dynamic, regenerative entity."

Bea said...

Dr. B G

So, what is your recommendation regarding colonoscopies. Are they really necessary? The whole thing just felt so wrong. I have a girlfriend that thought it was no big deal. For me the drinking that crap. Up all night cramping and crapping. Arrive exhausted. Wake up destended and gassy. Am I wrong to never want to go thru that again? Even if you don't get an infection what are the effects of washing you colon out like that? Duh! Dumb question. I lived it.

Dr. B G said...


If medicine actually did a outcomes assessment like they did for mammagrams and found essentially no benefit -- I betcha they'd find the same with colonoscopies... If they did it accurately and analyzed the cost-benefit-risks with these iatrogenic infections. They don't list C difficile but I thought recently I saw contamination and subsequent infections as well. FUN.

Your experience is obviously rare but I hear ya. YOU ARE THE ONE AND THAT CLEARLY SUCKS, I'm so sorry again. Hey I'm the person who takes my kids to the dentist and say
--no fluoride
--no silver fillings
--no fillings period (we do butter oil and CLO)
--no Xrays or radiation
--or no Xrays without the d*mn THYROID GUARD
--no antyhing LOL


Yes biohealth is awesome... It seems like the GI FX 2100 was more accurate for pathogens and parasites but I guess they have changed to microscopes (I think). Thank you for your thoughts!

Karen said...

Dr. BG

Thanks for sharing your kids stories. I have two, a daughter (10) with ADD and a son (7) who is very likely to be ADHD. Yep, both were exposed to antibiotics a few times in their earlier years - maybe 2 courses each but sounds like it doesn't take much. I have had many courses over my life - sadly, I've likely passed on the aftermath. Our naturopath is suggesting following the GAPS diet but wondering if this protocol would be just as therapeutic as GAPS? Also, we're testing for yeast so if positive, would the RS and probiotics/ferments still be applicable? Appreciate your thoughts!


Michael Frederik said...


I know you asked Grace, but I will add this on colonoscopies: I think they are a terrible idea. I had quite a few myself, but I now refuse to have any more. I think the risks -- not just in wiping out the entire digestive tract which might be worse than antibiotics -- just don't outweigh any benefits.

Some interesting discussion here:

Bea said...

The doctor told me to repeat in 2 years because of a small polyp but I've had others tell me their doctor said 5 years. My diet is so different now I don't imagine I would torture myself like that again. I used to eat alot of popcorn and Ezekiel bread. I blame it on that. I sounded like a cat with a Hairball trying to get those little husks out of my throat. Must have been a lot of scratching going on in there. I have looked at the roarofthewolverine. Poor guy. It is so sad when something they tell you is going to improve you life destroys. I have another horror story about cholesterol lowering that
took a couple of years to recover from. I will never have it tested again. Pretty much avoid doctors these days.

Bea said...

Dr B G

I have pretty much figured out a routine that keeps my Post BS # under 120 . My BS is usually in the 70's in the mornings so my Carbs are eaten then. If it goes up 50ish points I'm still good. Second meal of the day has the non starch veges. My question is in regards to the BS #s posted by RN at FTA. Give him credit for putting them out there but do you feel these are healthy numbers? I would not feel well with those #s. Is the ultimate goal to improve those #s. I know he was having high fasting #s . But aren't the post #s the most telling? When I see it said that when you lc you crash and burn because you loose your tolerance for carbs. OK, this is how I feel about. Your opinion is greatly appreciated. I crashed and burned a long time
ago. I just developed a tolerance for living in
a diseased state. There were probably bells, whistles and sirens going off at first and waned as my body got used to the feel of high BS. A random gtt test and BS was 200 at 2 hrs.
It all felt so normal. When my body now lets out a 5 star alarm when my BS goes over normal I am glad. Glad it no longer accepts an abnormal state as normal. Wishing everyone well on there journey to good health!

Natasha v. Potato said...

Hi Bea and Grace,

Grace replied to me on R. Nikoley's blog. I want to give RS a try. I have also come here via low carb.

I have great appreciation for Dr. Richard K. Bernstein (Diabetes Solution), he has done a terrific job of introducing Blood Sugar (BS) monitoring on individuals. He was the first non-medical professional (he later became an MD) to have a meter at home. Before Dr. Bernstein, Diabetics (1 or 2) had to guess at where their BS was. With Diabetes Type 1, Dr. Bernstein can easily set a base of very low carb. He does also teach how to adjust for higher levels of carb intake.

However, not everyone has an the obvious defunct metabolism of a Type 1 diabetic and this is where things get murky for the rest of us.

Some people can tolerate lots of carbs, and some cannot. This is do to the fact that there are various stages of tolerance and corresponding metabolic function. Here on this blog we are refocused on the gut, and the various levels of its health.

I really think it is un-necessary to bash or unduly criticize the low carb community. It does a lot for some people. But it all depends on the problem! Thus, the many "experts" who outline specific amounts of allowed carbohydrate are correct *if* your personal level of metabolism function matches theirs. But what if there is more wrong...

So, I have been stuck. Low carb and LCHF has been really good for me. I experienced healthy BS for the first time in years! I learned that when I feel shaky, I wasn't low... I was actually getting high. Some times when I felt miserable, I would test and yes, I was high again. I got my MD to do the tests, and he says "not diabetic". Not helpful! :-( If I try to eat "normal" food or increase my carbs, I have brain problems, shakiness, etc. When I feel good or had a good sleep, I check my BS and it is perfect. Feeling good and sleeping well is essential to quality of life. If I can only get that through low carb, then the zeal is understandable. No normal person could actually say "I like restricting my carbs". OK, if necessary,

So, I am here to improve myself. My weight isn't shifting and I feel that something is missing. I will keep what works, like monitoring my blood sugars. I would dearly love to eat more carbs and not have to be a zealot for any diet... But we will have to see, if doing RS will heal my gut and help me to metabolize foods better. So many in my family have type 2 diabetes, NASH, hypoglycemia, and one was on insulin for T2D and diagnosed with porphyria and died of NASH - her case was like this horrible train wreck that I could do nothing about. Then my personal history of CFS/ME. I am dental amalgam free, no RX, LCHF, etc. But at 5'6 and 190 pounds, I am not satisfied with the status quo.

Thanks Grace for the Blog and all your research. I have more to read. I bought kefir today (never had before). Also bought some PS - which I may or may not try...cause I have problems with potatoes. I am looking forward to your comments about my potato issue because quite honestly, I would love to eat potatoes again.

Thanks! Natasha

Kieran said...

Great post. Some new information here for me. It also confirms my past experience. A brief stint with a strict paleo diet resulted in atopic skin issues and increased stress and inflammation. I wasn't eating enough carbs (no fault of the diet, just the execution). I suspected I had altered my biome in way that resulted in the skin changes but I didn't know the specifics. Thanks for fleshing it out.

Bea said...

Natasha v. Potato

Your comment really touched me. I feel your pain. I don't why but lc has allowed me to effortlessly maintain a 40 lb. Weight loss. If I over do the fat it just doesn't stick to me like refined carbs. I have to include white rice, tatos, beans, etc in the no bueno list. Some freaky exception for me is white flour does not spike as bad. Don't make it a habit but if I want a a decadent croissant or something I can eat it in the morning. I have to say and I
realize I may be
a total freakl but "I Like Restricting Carbs"
Because better than food I like, walking, running, sleeping without sweating, getting back up on a horse after many years, fitting in to size 8 jeans(formally 16) being up for anything. I was always the no person. I don't
feel good
BS roller coaster. I don't feel I'm starving my gut in any way. Breakfast today chicken with
cold cooked carrots, greenben s and asparagus. Usually always berries with cashews. Lets just say the poor things were starving sorry they are taking one for the
team. Example 2 parents high cholesterol. Mom fine 80. Stepfather 2 major heart attacks. Variable mom great glucose control. Stepdad rice, beans, tortillas. Not diabetic, pre
maybe, but bad control. I don't think rs can unbreak older broken people. There is a down side to feeling so great at 54. I need to find some younger friends.

Natasha v. Potato said...

Dear Bea,

Thanks for your reply. I am thrilled that you are a size 8, 54 year old who feels great! :-) I am turning 40 in the next few weeks. I have some good days but I want to feel good all the time.

Today, is not a good day... Last night I thought I would try having some fried rice. I ended up with a blood sugar of 202. :-( It was probably a little higher than that as I tested 1.5 hours PP, and I meant to test at 1 hour. It didn't come down until 2:00am. Had supper at 5:30pm. That's hours of high sugar. I also had a hard time sleeping - slept very light and I was very hot, actually sweating.

This morning I was hopeful, loaded up on kefir, ferment vegie, and psyllium husk. Hot cereal of un-sweetened coconut and ground flax (usually I have egg, bacon and coconut oil). Anyway, by 10am I was on a carb binge. :-( It wasn't the breakfast or the supplements, it was last night's fried rice.

I can't tell you how awful it feels to have a binge - compulsion to stuff yourself (while at work) with junk carbs. I finally went and ate my lunch (konjac noodles, homemade meatballs and 1/2 cup tomato sauce) in an effort to blunt the blood sugar rush and calm the hunger.

This proves that I need to stay low carb while adopting the RS/gut health ideals.

Binging is not emotional (IMHO). If the triggers keep being triggered, I can see where it would become an emotional trauma. But I only have these binges after deciding, "I need a treat.... I will eat this or that" or, "everyone else is eating and so I will too...". Then I pay for it the next day with blood sugar roller coaster and carb binge.

Grace, do you think this will improve after I do RS / PHD for a while? Any thought on my Potato Starch dilemma?


pipparoni said...

Natasha vs Potato

When reintroducing carbs please be sensible. Eating a breakfast of eggs and beans would not spike your blood sugar and would keep it stable for most of the morning. When I went back to eating carbs I went down the hot cereal route and eat carbs without much fat or protein, and overloaded on them, Big mistake. I felt my blood sugar drop within an hour. Now I eat balanced meals and always include fat and protein with a moderate serving of carb, (NOT HOT CEREALS) and my blood sugar stays as stable as a rock and I can go for 6-7 hours before I get hungry again..

steve said...

Dr BG:
How many probiotic 3 pills do you recommend a person take on your program? Package labeling says dose is three? Seems like a lot
Should you take this for a period of time before adding RS of some kind, or do all at same time?

Anonymous said...

@Bea & George -- thank you for reiterating the truth regarding the Atkins diet -- plenty of fibrous veggies and in later stages, nuts, berries/lower sugar fruit and even starchier fare according to one's individual carb tolerance. Atkins was also ahead of his time in recognizing the importance of pre and probiotics long before it became popular. I believe in the value of rs and pre-probiotics, but believe the needs vary amongst individuals and likely between the sexes. The over the top rhetoric ("Low carb kills!") and the idea that we have have to have a precise amount of starch rs or otherwise every day or we are walking disease magnets is just silly. Bea's words resonate with me because we're close in age and both enjoy our low carb fare. I enjoy my food and the fact that I am slim at a time when most women start gaining.I also thank George for his insights and especially posts regarding liver health. I respect the Jaminet's and but the comment about gastro cancers is a meme that was based on one woman's opinion that she posted on Hyperlipid blog. Not scientific. Also, if we are looking at statistics, why does Korea have rampant gastro cancer despite all the protective fermented veggies and rs? That's rhetorical --of course there are variables -- massive variables. Some are genetically prone to produce more or less mucin so maybe for those prone to less, the low carb diet pushes them into a "deficiency." Variables matter. But the meme re cancer and mucin deficient lc diets rages on...Middle aged lc women go even stricter to near zero carbs and engage in massive exercise and crash -- but it's the mucin starving diet's fault. Variables matter.

Keith Bell said...

Anonymous, the main "variable" is poor sanitation over generations. For example, Korea is still known to have sewage problems; it's a coprological culture consuming its own waste for generations (just like coprophagy in mice):

I stress the word "generations" because children are born imbalanced from imbalanced mothers, not simply a matter of genes, but microbial predisposition:

The bottom, ahem, line is, it's time to stop shitting in water.

Bea said...


Glad to know the lc lifestyle has worked well for you too. I know I have become a bit of an annoyance on some blogs lately defending the lc lifestyle. But I feel the bashing is a little out control all of a sudden. I also feel the advice at FTA to "Up carbs to 200 grams and quit monitering your BS" is downright dangerous. If I was on that site when I had gi issues I would be worse and diabetic. I have experienced some side effects from LC. My maturity level has seemed to decrease along with my BS #s. I have a hard time driving with 2 handS on the wheel . Now it's music turned up and dancing. Doing the robot while your driving is not safe.I COULD DIE. Teenagers will not go to the store with me as I might start Moonwalking down the aisles if MJ comes on. They are so uptight. I know probably high cortisol signalling my liver to pump out glucose to my poor dried up mucin. LC seems to have made me an opinionated twit too. No one will convince me that feeling this gooooooood is bad. Sorry:-)

G said...


No I don't think that will immediately improve -- but if consideration for low GI carbs is taken as Pip (THX HAWTNESS) then it may be far less until insulin sensitivity ramps up with fiber + RS


Awesome link. Bionic guts -- that is interesting! Wolverine's story is more than compelling. I wonder how he would do on the 7-steps?


I love you and ur poor gut. I push root cause exploration -- why is your gut fuckered after the colonoscopy? What the heck is in there that prevents proper food, fiber and fodmap processing?


Absolutely! Lactobacilli in ferments helps to control yeast. It does help to control yeast and pathogens before a ton of ferments however because these can be histamine inducing for some.

Common story. FODMAP mania was like all the rage within 1-2 years of the switching to the 'VLC' paleo-flavor of the month! And i was to blame also and fell into the low fiber trap. I'm so grateful for newer technology to do stool testing and access to food-based, natural solutions ;)

Bea said...


There is no longer anything wrong with my gut except mild lactose intolerance. I process fiber, fodmaps, nuts. Just chose to not ride the "Safe Starch" train. It's an oxymoron to me. Thanks for the concern. Maybe you can help me with this. Why do I feel like putting a bullet in my head every time I hear that phrase "Safe Starch".?
It's so new age. It's starch. Paul doesn't have special powers to make it safe for all. Hope you'll still love me . Me bad:-)

Natasha v. Potato said...

Dear Grace, Bea and Pip,

Hello! Thank you for the lovely comments.

I am on day three, of fermented veg and psyllium husk - nothing else yet..... While I had an ill conceived overfeed of fried rice on day one, which lead into a carb binge on day two... Today was very different. I had a small breakfast and small lunch. Wasn't as hungry. I even stopped at a bakery and bought a small cookie, just one. For the first time in years and years, I could eat *just one* and felt fine. No carb binge started, no need for self control or restraint. One cookie was plenty and nice. Utterly shocking.

Also today, I came home from work and instead of being exhausted and desperate to eat, I chatted with my husband and helped him with some work issues for almost an hour. Then... I started cooking. Made us a great supper. No - eating while cooking, or "let's go out", or "don't talk to me until after I eat".

I've been thinking about Grace, Richard and Dr. Ayers,(and others on these blogs) today. How utterly BRILLIANT you all are.... To keep searching until you found this system. Knowing, learning and maturing the science to figure this out. I am just in awe - I word I have never used.

I was thinking... it is like we all have a gut, which is like a mini compost pile that we carry around with us everyday. For us to be healthy, our gut needs to be thriving. Seed, Feed and weed... So interesting!!

And, I won't have to be LC for the rest of my life. If my gut is healthy, I should be able to digest anything and be fine. Shocking.

I am so tempted to try potatoes/PS...but I can't risk wrecking this weekend. I will likely have to get the green banana flour.

Yes Pip, you are right - slowing re-introduce carbs while healing my gut. I can't stuff down food it can't digest properly. High and unsteady blood sugars mean
that I can't handle it. This is all so interesting!!

I read and read yesterday. I am still playing catch up with all of you. I will restrict myself from posting needlessly. But I just have to say - BRILLIANT. Absolutely brilliant.

Question, what experiences are there with pets? Cats or dogs? Do we "re-seed" with adult, child or animal microbes?

Natasha :-)

Anonymous said...

@ Keith,

How does one explain the tables here re colon cancer by country? The diets are all so varied but interestingly, the US with it's obesity and SAD diet did not make the top 20. Plenty of fermented food and rs loving countries did. The diets and variables are all over the place (especially pollution) so it's difficult to make sense of it all. Emotions can change one's gut biome -- again, so many variables.

Regarding babies born to mothers with unhealthy gut biome -- do unhealthy paternal gut biomes play a role? Aren't bugs transmitted via sex and sharing of food. My dentist has a big poster on his wall depicting cavity and (alleged) heart disease causing bacteria being passed via sharing of food. If this is true, then wouldn't the father's gut biome also play a role in the developing fetus' gut biome? He infects the mother etc? I wonder how true it is though given that I have no cavities, my hubby has tons of cavities plus far heavier history of antibiotic use than me, yet we happily "share bugs" regularly. When I asked my dentist about this, he said that he believes that while unhealthy mouth bacteria can be transferred to another person, there are likely other factors such as diet, genetics, oral hygiene and unknown factors also matter in terms of actual risks.

Anonymous said...

@ Keith -- sorry, I forgot the link I refer to in last post:

Bea said...


Also why do vegetarians have one of the highest rates of colon cancer.? Not just the ones doing it wrong. Also interesting to me is post bariatric surgery the chances of developing colon cancer increases 60% for the next 7 years. Read somewhere that one theory was the increase in undigested carbohydrates causing a rise in fermentation in the colon. Me thinks too much of a good thing....bad. Just the musings of a very unscientific mind.

Third Chimp said...

Hi Dr. BG;
I just tried to order some ARO Probiotic-3 within Canada (where I live) and it is apparently unavailable while they "reformulate" ! Have you (or anyone out there) heard anything about this?

Gabriella Kadar said...

Third Chimp, it's bureaucracy not efficacy. Health Canada stopped in country sales due to no DIN Drug Id Number.

Ordering from the US is also not legal. But apparently some people manage to get it back over the border.

Bea said...


OK, I promise this is my last comment and then I am gone. Your post over at MrHeisenberg made my head spin. I'm just a simple person and this all too much for me. In defense of Rye consumption you wrote of a study comparing Rye with other carbohydrates . Here is an excerpt

" In the wheat, oats and potato group. 62 genes were activated that increased oxidative
stress and the stress response. Worsened blood sugar balance and generally amplified all of the forces in the body that lead to obesity, heart disease, cancer, diabetes and Alzheimer's disease! It was 100% effect. No good genes were turned on."

Whaaaaaaaaaa. Do RN and Tatertot know this. This is why I quit listening to politics. I started feeling crazy.

Keith Bell said...

Anonymous, that is an interesting list, isn't it? Thanks for posting it. And while I agree, so many variables, there are a few factors seemingly prevalent in colon cancer:
1) Bacteroides overgrowth, including both the carb and meat-digesting bacteroides, B. fragilis and Prevotella. What causes this? Too much meat and and not enough fermentable carbs of the right type. Note potato starch (RS2) creates lower Bacteroides, but another type, manmade RS4 creates higher Bacteroides. Bacteroides are also known as antibiotic resistant mofos prone to translocation, meaning they leave the gut and make trouble elsewhere in the body such as the brain. Fusobacterium are also associated with colon cancer and they're similar to Bacteroides, but with badass toxins.
(links dedicated to Tim)

2) pH imbalance, low gastric acid creating SIBO and shifting the Firmicutes/Bacteroides ratio toward Bacteroides. Not enough RS2 to create short chain fatty acids like butyrate means Bacteroides get the upper hand because they like it more alkaline. Bea, that may be the reason one study found colon cancer more likely in vegetarians as the diet doesn't demand enough acid (avocados and walnuts aren't apparently enough to create acid). Think proton-pump inhibitor SIBO warnings and alcohol leading to hypochlorhydria. Have I mentioned low bacteria/acid allowing opportunistic fungal overgrowth associated with cancer? And look at those cold and sunless countries with low vitamin D and cold temps causing more acidic blood leading to microbial overgrowth.

3) poor sanitation where places like Slovakia discharge raw, untreated sewage into drinking water supplies. Only around 60% of households in Slovakia are connected to sewers. The highest number on the colon cancer list is Slovakian men where males are commonly more prone to imbalance due to lower estrogen needed for immune response. Women are the stronger sex.

Tim Steele said...

Keith - Bacteroides are such interesting critters. Many of these guys could be considered SBOs as they are comfy in the dirt.

Here's something you'll love to read:

Bacteroides: the Good, the Bad, and the Nitty-Gritty

Remember my AmGut sample? I had high levels of bacteroides against all expectations. Maybe because my diet was low in leafy greens, or maybe because all the RS I was eating at the time provided a feast for the good bacteroides.

I think pH is going to be crucial to maintaining a healthy gut flora. Increased SCFA activity and lactic acid from the SBO types of bacteria create their own environment in the gut, just like they do around my carrot patch in the summer. I find this stuff utterly fascinating--so many rabbit holes, so many studies, so little time to read everything.

Keith Bell said...

And, Bea, you're finding yourself doing well on low carb possibly because you've been balancing already high Firmicutes such as clostridium overgrowth illustrated in the previous blog about the autistic child with buttloads of butyrate. Diet needs to be personalized dependent on current balance. This is why injecting an autistic child with Bacteroides (B. fragilis) was found helpful and also why the ketogenic diet is effective (it's not really about ketones, it's about flora shift). But some people may be in the opposite condition and require more fermentable carbs to balance their booming Bacteroides.

Keith Bell said...

Tim, yes I've seen that one, it's amazing stuff.

Here's a recent realization: meat-eating, smoking cigarettes and drinking alcohol all result in the same flora-shift: raising Bacteroides. Last January, the U.S. Surgeon General finally classified the link between smoking and colon cancer as causal.

Bea said...

Keith Bell
Nope have none of those things and am not on a ketogenic diet. My post above yours to anonymous hit the nail on the head as to why i am lc and lovin it via DRBG. Thank you all . My main point popping in was to say lc people are healthy and have healthy guts. Probably now that I read drbgs post at MH I would say healthier. Bye!

pipparoni said...

Hi Grace ;)

G said...


I love your deep thoughts.
RE Bacteroides, recently I was on Dave Asprey's Bulletproof podcast and we were trying to bulletproof his (sad) gut. He will talk about this shortly when he airs it but the revelation is that now he tolerates RS with no problems (no massive gas, no rashes, no apparent adverse effects). It was just one dose, who knows later.

What he had was a parasitic growth and 4+ B fragilis and missing Clostridium commensals on a CDSA stool testing (I prefer 16S rRNA data from Genova diagnostics). After treatment, not only has his intolerance for RS disappeared but so was a fat gain that he could not apparently stop.


I hope this news is positive to your case. We don't have carb or odd sensitivities for no reason. Evolution would've killed our ancestors if we were so frail. Unfortunately interventions like colonoscopies and potent, broadspectrum antibiotics are all new to our species in just a blink of an evolutionary eye. We can't adapt.

You said something quite insightful that I love. UR ABSOLUTELY BRILLIANT. May I use in my writing? I forgot where you said it "the small intestines are behaving like a colon" and your body doesn't like it. I'd emphatically say your brain is working on all cylinders. Farming and dirt exposures are obviously helpful but they won't cure parasites or pathogenic bacterial infestations in the small intestines easily. It probably depends on a few things
--degree of diversity of the commensals
--probiotics Bifido or what is lacking (often I see Lacto adversely proliferating in the small intestines; maybe certain Lacto are missing like plantarum)
--health of the epithelium
--inflammation of the immune system
--toxins, etc

For Dave B frag and a parasite were overgrowing and from his symptoms, it's obviously his small intestines became like a colon. It's reversible. It takes some clinical intervention.

Third Chimp,

Get on a list -- but 3/26th should be ready!

Keith Bell said...

Grace, I'm looking forward to seeing the podcast with Dave Asprey. Glad to hear he's on the mend. Maybe it was all the bulletproof coffee raising Bacteroides, as known. So let's add coffee to the list of Bacteroides-raising activity including alcohol, cigarettes and meat. German scientists are now conducting a study to determine if stripping raises Bacteroides.
(those are for you, Tim)

G said...


Guaranteed a good time -- you'll love it. Dismantled a few bulletproof myths lol. His acetate was higher (coffee!) like that 2nd study but not butyrate or proprionate. Proprionate is a substrate for gluconeogenesis so maybe it was swayed from coffee? I don't know why there was imbalance except that that is what happens with parasites and pathogens.

Cuuul coffee finds!


Keith Bell said...

I think propionate is more a product of Firmicutes and Proteobacteria like clostridia and sulfate reducing bacteria (SRBs), known to cause problems in autism.

In previous podcasts, Dave talks about using electricity instead of conventional exercise to grow muscle mass. He may not have taken into account the antimicrobial aspects of electricity. Between that, coffee and meat, he may have stripped-away sensitive commensals. Alternatively, the electrical charges may have disabled his leukocytes (white blood cells) allowing B. fragilis overgrowth. I've read white blood cells use their own electricity to kill pathogens, then eat them.

Tim Steele said...

Keith - None of those links had anything to do with German strippers, I think you owe me a link or two!

But, very interesting about the fiber found in coffee. And galactomannans/arabinogalactins no less. Funny how a nice hot cup of Joe is the perfect catalyst for a morning 'constitutional'. Maybe it's 'cause the gut bugs are just so happy and want to reward you.

Keith Bell said...

Tim, that's prolly more about the polyphenols in coffee, see here:

Tim Steele said...

THAT's more like it!

pipparoni said...

Tim/ Grace , I notice I don't eat a whole bunch of bitter foods in my diet and I'm wondering if I should start including more, Just read a pretty cool article on w.a.p website on how good they are for digestion..

I'm thinking dandelion greens =) yuck!!! Arugala is pretty palatable but dandelion seems more medicinal


Ike said...

Is there something else that can be used instead of psyllium in step 4(b)?

Tim Steele said...

Ike - Sure, just about any of the traditional fibers will work. I'm beginning to think banana flour is the best mixer for RS. If you can't find it, look for glucomannan, FOS (or inulin/FOS), or just mix in a really green banana. A handful of cocoa nibs would work as well.

Tim Steele said...

Pip - Hell yes! Eat all those bitter greens and roots you can get your grubby little hands on! They are full of inulin and other great fibers that gut bugs love.

Anonymous said...

What do you think of this?

Thank You

Anonymous said...

Sorry i ment this one.

Ann said...

Hi Dr. Grace - I have a question I have not seen addressed here anywhere. I have been having a lot of improvements using the high orac greens, plantain flour, your top three probiotics, acacia fiber, and adding in the RS rice, potatoes, and beans, and eating home fermented foods. Seeing improvements across the board with everything except mild depressive and anxiety symptoms. Some days I feel like the food and supplement thing is dialed right in, and other days I still feel some of the mild depression and anxiety that I had almost constantly when I first started the seven steps. I'm 47, and very aware that my hormones are really fluctuating, but this doesn't seem to be following any cyclical pattern at all. I supplement with 100 mg daily of bio-identical progesterone.

My question is about using amino acid supplementation for mood support. Is it a good idea? I remember reading on the Metametrix website a case history where a man had overloaded his serotonin receptors by using too much 5-HTP. I refuse to go the antidepressant route, but feel that I could use some mood support while I'm healing.

What are your thoughts about using amino acid supplementation for mood support while healing the gut?

ruben garcia said...

can please expain what is the difference between this test.

GI Effects Comprehensive Profile - Stool

GI Effects Microbial Ecology Profile - Stool

GI Effects Mycology Profile - Stool

GI Effects Chemistries Profile

what recomend for first analisys for sibo suspicius?


Debbie said...

I want to thank Tim and Grace for this post. I'm just starting the protocol to deal specifically with lifelong constipation that has improved on a diet much life the PHD, but is still not great. But, I realize now these specific bacteria are needed for everything! I have been on this site and others for weeks - not understanding the science, but unable to stop searching. So, thank you, everyone.

Anonymous said...

Hi all,
In my local supermarket in Denmark, I found some interesting "snacks":

- marcipan bar made of:
almonds, stevia / erythritol, polydextrose, FOS, inulin, dark chocolate, salt, vanilla.

Total amount of fibers for 100g: 24g.

- gummy bears made of:
polydextrose, FOS, beef gelatin, water, pea starch, dextrin, citric acid, palm / palm kernel / coconut oil

Total fibers for 100g: 54g

So before buying, I took a look at the ingredients and they all seem like OK.

I tested the gummy bears: I ate a whole bag (90g) one evening. I felt some rumbling in my guts, increased farting but not more than that. A few days later, I had another full bag and did not experience rumbling.

I did random PS supp now and then (I eat starchy stuff in general, I am not LC), and then, had some dark chocolate with the same kind of fiber fillers. And the bam! I hit the toilet real hard one evening but it passed rather quickly.

Some my question is : can one eat too much of these fibers ? It seems like I let some bacteria strain grow too much too quick ...

I resumed eating normally with the occasional snack.

Tim Steele said...

re: Polydextrose

Polydextrose is a man-made frankenfood. Invented in a Pfizer lab in 1965 from glucose, sorbitol, and citric acid. It has been studied for its supposed prebiotic effects, and the manufacturer claims they are there, but studies show that the polymer structure rapidly degrades.

Polydextrose is in lots of foods, it allows them to call these foods 'high in fiber', but in reality, it lets the manufacturer put in less fat, less sugar, and less starch and have the same 'mouth feel' as real food for less calories and cost. Win-win for them. So-so for us. It's obviously not going to kill us, but I would be hard-pressed to tell people to go out of their way to seek out foods high on polydextrose for its prebiotic effect.

end rant

Anonymous said...

Hej Tim,

Why the rant ? I never advocated one went out of his/her way to stuff the gut with polydextrose. But really, one should not be afraid to eat something with it.

See this in vitro study:

It runs out that polydextrose was the only substrate that made B. infantis detectable. Not even FOS could yield this result.

The snacks I am having once in a while are using both PD and FOS, and sometimes inulin. I don't think it is that bad.

Anonymous said...

Tim, this one is not bad either:

Tim Steele said...

Sorry! Wasn't ranting at you, just the food industry in general.

One of my greatest motivations for highlighting potato starch and RS rich foods was to 'stick it' to the food industry who is trying very hard to make us believe that RS comes in a loaf of bread and snack foods. They spend billions on studies and billions more to figure out how to get their man-made fibers into the consumers bellies.

I won't come right out and say that polydextrose is harmful, it probably isn't. And I have no doubt that they are telling the truth about the bifidogenic effects. But it is still a food industry attempt to get us to eat their products.

Look at bottom lines of the links you provided above:

"This work was supported by Danisco Sweeteners..."

"We acknowledge the assistance of Hank Frier (formerly with Pfizer, now with Slim Fast) and John Troup (formerly with Pfizer, now with Novartis) for helping design the study..."

This stuff just scares me. I get enough grief recommending potato starch, which is just an extracted food particle.

But, still, my rant is and was against the food industry who has only their interests at heart.

Rick said...

Hi Dr. B. G.

I'm attempting to restore my gut health but noticed this paragraph in your "How To Cure SIBO, step#3."

Here is the takeaway for this blog: If you are severely immune-compromised, do not take any probiotics. They are alive. Like a live (attenuated) vaccine, probiotics are contraindicated in a severely immune-compromised individual.

I have ankylosing spondylitis. What would you do in my shoes. I've been taking primal defense, p-assist, pro-3 and 2 tbs of pstarch daily(two weeks) but just noticed that part of the write up today.

Natasha v. Potato said...

Dear Grace,

Hi! I started PS and I didn't die! I am on vacation and so I could risk losing a day. I took BRM potato starch on Tuesday evening. I did a tablespoon in water. I started to panic and so only drank half. My typical immune system reaction to potatoes and potato starch is one hour to 24 hours later (swollen, painful and burning joints, bursts of anger and crying). I took it at night, hoping to temper the reaction. I had none. No reaction. No pains. SHOCKING!!

Before trying the PS, I did kefir, raw sauerkraut, psyllium husks (seem to constipate me), and Primal Defense. Lots of home made safe starches. Also plantain.

I have to tell you, my husband is so happy that I am giving him potatoes and rice, as this has been a constant battle in our house. He is loving the homemade beans.

I can't believe the impact of RS and the SBO. I have much more to learn - about how to apply the things here to me. But I feel that finally things are starting to make sense.

THANK YOU!!!!!!!!!!!!!

Improvements so far - calmer, less anxious, less hungry, facial skin is healthier(!). However, I have very little gas and irregular bowel movements... Advice?


Tanya said...

Hi Grace,

I see you formerly used Mirena. Do you have your protocol for re-balancing your body after removal somewhere on your blog? I had one inserted several years ago. Had it removed after 4 years to conceive. Got preggo after a month, had baby and got another one at 6 week checkup. That was 1.5 years ago. So I've had one for over 5 years and am starting to wonder if that is the link to my inability to lose weight, especially in the abdominal area. I also have intense sugar cravings that take everything in me to get through and that often fails. I've been on the Bionic RS + SBO (prescript assist, saving to purchase others) for a month now and wonder if I'm wasting my time and energy since I still have this Mirena doing who knows what to my body! Working to get it taken out, husband is going to schedule vasectomy but may just do natural planning till then because I am so desperate to get this removed. Sadly, I didn't put the pieces together until I started reading your wonderful comments on this blog. You and Tim are brilliant and I look forward to all your future research and discoveries!

Keith Bell said...

Tim, have you ever considered why people of the Pacific Islands suffer the world's highest obesity rates? Might it be their traditional diet of root vegetables feeding Firmicutes overgrowth associated with obesity? This would occur over generations such that children are born predisposed to obesity, a matter of microbial predisposition.

I also view the problem as one of poor sanitation shifting flora in very closed systems; islands are microcosms of the planet.

G said...

Keith, Interesting per usual! I wonder how much of their native roots do they still eat?

Anon, Renew Life appears great but they all require refridgeration.

Pip, Bitter greens are all lovely and full of omega-3 (ALA)!

Rick, AS typically has an enterotype (or phylotype) characterized by Klebsiella overgrowth, and this feeds on PS. Please update me with your progress. For any autoimmune arthritis, rash or joint aches, usually some gentle weeding whilest seeding at the same time. Perhaps it is possible to 'crowd' out the Kleb nasties with prebiotics + SBOs but I think it will depend on the condition of the gut. AS doesn't mean low white counts. All probiotics (except potentially L plantarum or Bifido) are contraindicated if the white count is low or a person is diagnosed with immunodeficiency.

G said...


Definitely have your hormones evaluated -- low progesterone/T/E2 or estrogen dominance all can contribute to mood changes. As the gut improves hopefully you'll notice that synced up brain-gut axis.

Personally I have little experience with amino acids thought I've read good things about them.

Have you had your methylation status evaluated via 23andme? Many people with genetic variants like COMT (like my kids and I), MTHFR or others need methylated B vitamins. These are depleted with gut damage, stress and subclinical microbial infections in the gut.

Have you exhausted all the below listed?

ruben garcia
All the tests you list are included in the GI FX 2200 panel, aka GI Effects Comprehensive Profile - Stool

Natasha, I'm so happy for your progress thus far! Strong work. That is nice your hubby enjoys the diet expansion as well!

Have you tried other SBO probiotics that we've talked about? I see wonderful improvements with AOR Probiotic-3 and Prescript Assist.

Have you included other fermented foods? Do you have any healthy soil or gardening exposures?

G said...

Tanya, Thank you for your comments and kind words. The mirena is super potent but that is a good sign you were able to conceive a month after removal, so hopefully the effects will be less for you than it was for me. For detox, consider liver fortification and botanicals that help remove xenoestrogens.

We use this

G said...

Tanya, Thank you for your comments and kind words. The mirena is super potent but that is a good sign you were able to conceive a month after removal, so hopefully the effects will be less for you than it was for me. For detox, consider liver fortification and botanicals that help remove xenoestrogens.

We use this

Anonymous said...

Dr Grace, you have said a few times that probiotics are contraindicated for immunodeficiency. Can you explain why? Surely the risk of proliferation of undesirable species is even greater in these cases, so the need to crowd them out with desirable species should be higher, if anything.

Low WBC count doesn't mean we live in a bubble, or even that we are overtly 'sick'.

G said...

Crowding out with desirable species needs to be balanced by reckless invitation of invasive though symbiotic species. Check out PubMed for plenty of cases of Acidophilus septicemia or endocarditis.

The safe species are few but perhaps the safest one is L plantarum as a single strain probiotic, or combined with B infantis which have been used in neonates (against necrotizing colitis), NICU, ICU, ventilator infections, pre- and post-surgery, cancer and chemotherapy.

Anonymous said...

Thanks for that. It looks like L.Rhamnosus could be even worse than acidophilus.

I will continue my probiotics, lots of l.plantarum as it happens. Always good to make decisions with open eyes.

I can see many significant differences between my situation and those of the patients in the studies. In particular, they were mostly actively ill with acquired immunodeficiency as a result of chemo, surgery and other interventions or pre-existing conditions. Whereas my primary immunodeficiency has never required treatment, and the health issues I do have are managed through diet and lifestyle rather than medication.

I can't avoid encountering risks every day. I think the potential benefits outweigh the risks in this case.

Thanks for helping my education.

Anonymous said...

Dr B G, I wonder if you or any of your readers/collaborators have thoughts on this scenario. This weekend I had a GI virus (vs. food poisoning?) that resulted in a few hours of vomiting and violent, liquid diarrhea. I was definitely "cleaned out." It's a been a few days, and my gut is definitely not right. Vague nausea on & off (regardless of eating), lower GI cramping, stools still quite loose. Previous to this I had been taking 1 tsp of PS daily (was in the process of titrating up) and probiotics. I haven't re-initiated these, thinking I should let things "settle down." Now I'm wondering if re-initiating these might actually help? Might my gut flora have been damaged by the "cleansing" diarrhea? Any input appreciated. Thanks!

Tim G. said...

Can you please email me. I lost your email.

Dr Tim Gerstmar

roadrunner said...

Ketosis and good gut health may not be mutually exclusive. Dr. Wahls of the Wahls Protocol keeps in ketosis but eats a HUGE amount of both cooked and raw vegies. I suspect she thereby gets plenty of fiber/RS.

G said...


For infectious colitis in tropical countries is common (vibrio, shigella, etc). What's effective? probiotics and BRAT diet -- g-banana, rice, apple, toast (well I wouldn't do toast LOL). Hope you feel better soon! In a way it's great to clean things out but you don't want to lose too much of the precious flora. L plantarum appears super useful to recover these after antibiotics.

Tim ~just shot you a note!

Roadrunner ~Thx I didn't know she aimed for ketosis. I'd love to see her salivary cortisol, other hormones, 4OHestrone, and 2/16 OH estrone ratio.

G said...

roadrunner ~also "cooked and raw vegies" don't have much RS tho great for NSP fiber. Carrots and other root vegetables have some but the 20-40 g/day of RS that are conducive to optimal gut health.

One can try to get to 20-40 g/day with other fermentable fiber like inulin or other oligosaccharides but again these are also from other 'starchy plant babies' like tubers, legumes and grains.

Rick said...

Thank you for your reply Tim,
I should have mentioned that I am on biologics which led me to believe that my immune system may be compromised. Yes, the Kleb part is a major issue for me/us with AS. It loves starch and destroys my back when I consume it. I've been taking 2-3 tbs PS for almost 1 month and have added pro-3, p-assist and prml dfns psylm, orac, inulin FOS. I take Gaia adrenal health, walk, destress and most everything I read that I should do here. Gas has been prolific and smells embarrassingly awful since the very beginning. Surprisingly, PS doesn't add any pain or cause any skin issues with myself or the three others with AS. We've been documenting our progress on a well-followed post, here.

As many of us with AS do, I've avoided starch almost entirely for quite some time. Recently though, I'd followed the directions on preparing starchy foods from HTC SIBO #2. I added roughly 4-5 tbs of black beans throughout the day but woke up the next morning in SEVERE pain. I am very strict AIP and the only variable would have been a bit of cooked and cooled potato(1/3 baking potato) on the same day. I had some of the same potato the day before which may have added to the kleb over activity?
Any ideas as to why my gas just won't go away? It was funny to start but not so much one month later.
PHD recommended to one guy with AS to slowly add dextrose in order to build up a tolerance to carbs and starchy foods. The hope was that it would eventually lead up to rice or some other easily digested starches(for most people). I can eat unlimited dextrose with no pain inducing effects(although I believe it causes break outs for me) but can't seem to get over the starch hump, so to speak. Is there anything you can think of that might aid in the introduction of starchy foods?
Don't know if it changes any future battle plans but I've taken several rounds of ABX. Eg. for C. trachomatis, traveller's drrhea and took a 6 month course of abx, pre-biologics, as I had a very questionable positive skin test result for TB. I went VLC for a only a short time but I think that it definitely didn't help my gut situation. I had athletes foot as a teen and on and off tinea versicolor for about ten years. I'm HLA-B27. I stopped smoking roughly a year ago, had horrible dietary habits, binge drinker and a very stressful job. I've turned that all around completely and feel like I can be superman once I conquer this starchy speed bump. It's really frustrating to constantly read about how important starchy foods are for the gut and not be able to go near them! Cooked and cooled rice sends me heavily into flares as well. I haven't tried cooked and cooled parboil rice yet but will give it a go in moderation after my flare has passed.
Is there any harm in taking this without any testing being done beforehand?
Someone asked in another post but there wasn't a specific reply.

Tim Steele said...

Hi, Rick - I'm impressed by your tenacity and what you guys are doing at, but I am completely out of my league giving you any advice other than just keep experimenting and listening to your own bodies.

You've obviously done some genetic testing, is there any chance you guys could all do some gut testing? You all could help each other out more if you knew what you were dealing with. My guess is that you've all gotten completely off-kilter microbiomes from antibiotics and diet (same as most people) but your genetics are really causing problems.

The foul smelling gas is definietely a sign of missing microbes. I doubt you can get them from any commercial probiotics. You'll have to ensure your gut is happy and presenting a good place to live when those microbes happen along in your daily life. It sounds to me like you are doing everything right considering your circumstances.

Have you thought about contacting people about fecal transplants or more targeted 'poop pills?' I wouldn't have a clue where to start or who to ask, but keep trying, maybe there are some clinical trials going on or starting up that some of your could get in.

The Microb-X Caps look like they would be fine for anyone, no microbes, just plants and herbs.There weren't any warnings. Give them a try, like it says, 'if it causes upset stomach decrease dose.'

Good luck to you!

Rick said...

You're amazing Tim! I really appreciate your response again. I've been trying to find the most comprehensive gut test/s available. I read your interview with Fat Head and noticed these tests were recommended by you and Dr. Grace BG in the comments section.
GDX 2200 stool panel
GDX ONE urinary dysbiosis panel
Would those suffice? Which Pathogen EIA add-ons would make sense in my case, if any?
I need to do it alone as my Dr.'s won't help in this regard.
For FMT's, I've only found this place which is a bit far and rich for my blood at the moment;
Any readers able to point me in the right direction regarding FMT's?
Thank you very much

G said...

Hey Rick

Thanks for finding my blog! I appreciate your comments and struggle you've been thru.

Those tests are the ones that I recommend everyone should get as a physical annually. You want to know what vipers which are in your gut because it is obvious that you not only dealing with an enormous VACUUM of missing microbes but pathogens on board that are disrupting the epithelium and translocating to the joints in AS.

Let me know after you get them. I'd love to look at them with you!

You've been through so much and an avanlanche of antibiotics and these are not without significant gut damage.

Antibiotics destroys about 90 % of microbiota functions: bile acid metabolism, eicosanoid and steroid hormone synthesis etc

Caetano L et al. Antimicrob Agents Chemother. 2011;55:1494-1503

(Hat tip Bengmark)


G said...

The 2200 contains everything you need.

Rick said...

Then the 2200 is what I'll get :)

I would be more than grateful to have you go over the results with me.

You guys are super heroes and I thank you both!

Rick said...

Sorry G, just noticed that you aren't Dr.GBG but you are all superheroes anyways;)

Anonymous said...

Hi Dr. BG--I'm saving up to take the GDX 2200 (self pay, no insurance), and like Rick no doctor to evaluate it. My symptoms are Hashi's and chronic constipation -- plus I don't have an appendix so certainly my guts are in disarray. Do the results of the test point to a non-prescription solution? In other words, will I need to find a doctor anyway? My hope is it will just tell what probiotic critters I need.

Thanks in advance! -- Kathy

Dr. B G said...

There are 2 wonderful guides for the testing outcomes -- but if you can post a PDF link, perhaps we can all review for you and post our observations including mine?

Sorry about the confusion -- those are both my ID's. 'g' and DrBG. Also sorry -- you need to add on the EIA pathogens. These aren't automatic anymore I just realized, which is assinine, no?

Pathogens (C. difficile, H. pylori, Shiga Toxin E. coli, and Campylobacter spp) (Available as EIA add-ons)

Dr. B G said...


An elevated calcitriol is odd... Marshall would argue you have an L-type bacterial infection. Are you supplemental vitamin D? Any problems when you are out in sunlight?

Fiber crowds out the pathogens. Besides resistant starch, oligosaccharides and arabinogalactan are vital.

Read more from my buddies here -- Ripley and Gestalt

You've done excellent work on the probiotics! I sincerely hope you feel better soon. Yes I took a while for the bloating to go away. I still get bloating on/off (like after clubbing LOL). But it has tremendously improved with -- charcoal and broadening the fiber spectrum. Please see below.

Yes I like the whole seed psyllium as well as husk only. Both are great if you don't have adverse effects. FYI I've taken psyllium out of the complete protocol (just version B). I favor the benefits from other types of fiber now. Avoid beta glucan high dose due to cross reactivity with yeasts and fungi. It appears you traded one fungi for another after treatment. Avoid 'FOS' it's synthetic.

GDX says this:

• Add prebiotics to feed the bacteria that are living in the
gut. Examples include: psyllium, oat bran, oligofructose,
xylooligosaccharide, inulin, beta-glucan, and/or
arabinogalactan.91 Inulin and oligofructose favor the
growth of indigenous lactobacilli and/or bifidobacteria.75
• Improve diet. Increased intake of fibers and whole, complex
carbohydrates can increase levels of commensal bacteria.
Vegans and vegetarians have greater amounts of total
commensal bacteria. Individuals on a low-carbohydrate,
low-fiber diet may experience a drop in levels of commensal
bacteria. High-fiber foods may exacerbate patient
symptoms and should be introduced gradually.7

Rick said...

Okay, I'm on the same page now :) I'm actually shocked that I even picked up on the EIA add-ons! I'm a pretty slow reader and have to go over everything about 5 times before it sinks in.
I'll get rid of the inulin FOS and hunt down some oligosaccharides and arabinogalactan in the meantime.
I know you were talking to Lissa but I visited Dr. Blainey( an advocate of the Marshall protocol) based on this video;
I mention this because I seem to have issues with supplemental Vitamin D. I had a bad attack of iritis after I started taking Vit.D. There was an asterisk in the fact that I pigged out on holiday junk food and was particularly stressed before my attack as well. BUT afterwards, whenever I take a 5000 iu capsule, I can feel what I think is described as "ocular pressure?" on the same eye. It feels as if it's pulsating and right on the verge of a break out. I've stopped taking it and the problem has subsided. Any ideas?

Dr. B G said...

Liisa~What dose of probiotics do you take? For probiotics to 'stick and seed' when significant dysbiosis exists, it requires high dosing like 3-6 caps two or three times daily, if tolerated.

Is Symbioflor available? We use the red one. Do you have any Japanese markets near you? Some of their probiotics (shelf stable) are wonderful soil based ones.

Rick~That's odd but I think anything is possible. BTW inulin is fine and I think to confuse the public, they label it 'inulin/fos' often.

Dr. B G said...

Do you have access to this?

Karen said...

Hi Dr BG
Just got my CDSA 2.0 results back and it revealed blastocystis hominis (few). No other parasites, etc. but NG of lactobacillus & bifidio. Sad. IV antibiotics after mastitis and abscess several years ago. Never been the same since health wise. My main symptoms which prompted the CDSA testing are chronic constipation and nummular eczema which started last summer after a trip to South America. My integrative doctor wants to go right to Flagyl (then rebuild) but I'm feeling reticent after my last go around with antibiotics. However, I can't seem to find much in terms of alternative options. I've been doing the RS & SBOs prior to doing the test (had to stop 2 weeks before) and just starting up again. Just thought I'd ask since you have had experience with parasites. Thanks!

Brendan Chai said...

Hi Dr BG

What is your opinion on coconut oil? Does it have the same effect on the guts as antibiotics?

raphi said...

“The longer someone is on VLC and ketotic, physiological insulin resistance raises BG and further creates 'carb sensitivity’” —> This is demonstrably false.

It is also a perfect example of a double-standard: both anecdotal evidence and strictly controlled trials are part of scientific pursuit but they’re not equivalent. You seem to be ignoring the latter and hyper focusing on the former. No one (in their right mind) denies a significant number of VLCers and keto-goers still encounter blood sugar issues - it remains a non-sequitur to conclude that causality should thus be attributed to “the missing carbs”.

Why not face the fact that VLC/keto is therapeutically more effective than any other treatment in use (SO FAR) for diabetes/weight loss…BUT, the Kitavans are an example that ‘another way’ is possible (just not in our modern context, yet). Why not explore this apparent contradiction rather than make unsustainable statements about VLC/keto/Atkins causing increased blood sugar (and why wouldn’t that cause diabetes then? Because if that's being argued, then the 1990s would like their theory back). Also, lumping all of them together…come on. I know of VLC dietS but certainly not 1 VLC diet. Do you?

I apologize if I come across as too abrasive. I want to thank you for your blog posts which are truly informative. I share your interests as regards microbiota/biome and agree that the area will be much of the medicine of the future.

Megaera said...

I've been lurking for quite a while, never left a comment before: I wish with all my heart that the assurances and promises on this blog and FTA were things that came through for me, but I've been doing the RS/SBO protocol as carefully as I understand it, for almost two months now, and except for the first two weeks it's gone nowhere. Right at the two week point I was doing fine, then I had what felt like a one day episode of truly horrid enterovirus -- or maybe food poisoning -- and after that all the beneficial effects just ... Stopped. My arthritis rolled up about 500%, constipation returned with a vengeance...I'm going to the doctor tomorrow and I suppose I can ask for a GI FX test, but if it shows heavy metals, well, there's sweet FA I can do about that, because I have hip replacements I can't exactly have taken out. I'm doing what you recommend -- kefir, kimchi, sauerkraut ... it just has to be the commercial version, not home=made, but I am trying. And I've been using banana starch and plantain starch as well as the potato starch. What has happened to me?

Natasha v. Potato said...

Dear Raphi,

Regarding the statement "“The longer someone is on VLC and ketotic, physiological insulin resistance raises BG and further creates 'carb sensitivity’”

You believe this statement to be false. Some months ago, I would have agreed with you in. Now I know this statement is true....

Despite doing LC, LCHF and VLC for the past two years, I was not having BG or health improvements.

Having switched over to FTA/Grace's Resistant Starch and Pro/Prebiotic program, I am now having normal blood sugars when eating normal food and even higher carb foods(!!).

I started in late March, and early on, eating carbs did trigger carb binges and very high BG. :-( But I became more careful with carbs and focused on RS, RS foods and pro/pre-biotics. Gradually, I could eat the carbs too - such as parboiled rice (early reactions were high BG, now its normal), levain style bread (early reaction high BG, now normal) . Yesterday, I had a "normal" meal, including a banana (!!!!) and afterwards, my BG was 102.

It seems utterly shocking, but there is "physiological insulin resistance" that comes from LC/VLC.

And, if you start reading some of the resources mentioned here and on Free The Animal, you will understand where insulin problems (T-1, T-2) comes from. Autoimmune illness. I have been reading and reading. There is nothing wrong with carbohydrate foods, unless you have lost the ability to deal with them and your immune system has gone crazy. It is the person and immune system that is the problem not normal, natural food.

LC, VLC, Atkins, Paleo, etc. Are NOT normal diets. They are extremes that deal with microbiome problems. However, they are only crutches, they do not fix. However, people are so sick that even a crutch seems like a miracle....for however long it lasts. Once people stop getting results or never get results, then what does a person do? Keeps looking... keeps reading, and you end up here.

syd n said...

Thanks much for all your great info.

I am savvy and reasonably well-researched, but I’m so confused now! I have insulin resistance and for the first time over three and a half decades I need to lose about 7 pounds. (I’m a youthful 52 yo female!) I am someone who has been underweight forever – ate like a fat-phobic, vegetarian freak (no offense, vegetarians!), though that’s been many years ago.

I also suffered from giardia and cryptosporadiasis (had to have some sort of predisposition to not fight those off) and my gut has NEVER been the same since the giardia, and that was way back in ’92. It was the damn Flagyl: I had to do a few rounds to get rid of the giardia. I have intermittent serious reactions to GF grains and sugar – like doubled over with cramps. Awful. It used to be even just fruit. My gut feels sooooo much better when I don’t eat sweets or grains or anything starchy. Also, I ate some sauerkraut and got DRUNK, and not a huge amount. I can’t even think about kombucha. I do okay-ish with kefir, though I’m better without it, and I’m not doing dairy right now. (I was doing full fat cream in my coffee. YUM!)

For the last two years, I also made ridiculous choices, eating my fill of GF goodies, as there is a 100% GF bakery right near me. I knew full well it wasn’t healthy, but I ate it anyway. That’s when the weight gain started. So, now I’m insuling resistant/pre-diabetic (per two, four hour tests for BG and insulin).

I also am chelating for heavy metals, per tests and my history, working with a great doc, so we thought mild ketosis would be good for my brain – my main symptom is severe brain zonkiness. (I shall spare you the details.)

So, I guess the question is: How do you lose weight and decrease insulin resistance and treat your gut AND keep your brain healthy? I’ve been hard core VLC’ing it for over a week, finally deciding to “get serious.” For months, whenever I bothered to do them, test strips show I was in mild ketosis, never goes to medium. (Lots of MCT oil and full fat coconut milk, etc.) But, now I’m thinking ketosis is not good. Gah!

I absolutely know there is no cookie cutter answer, but I don’t even know where to start now, or if there is a logical “try this first, then this,” etc.

Sorry if this is a bit rambling! And thanks mightily. Sooo much wisdom in your blog.

Dr. B G said...

Good for u Syd to try looking for better solutions!

My kids and I have been chelating on/off and it's imperative to restore the lost minerals because these are important for many things including making hormones and insulin sensitivity.

Yes those baked refined GF goodies are probably not ideal ;)

VLC makes people lose salt, zinc and mag quickly. Temporarily the diet is not bad but long term may starve the gut microbiota.

ck out the 7 steps... do u have access to a good farm or gardening? FARMACY helps reset the gut after giardia and Flagyl damage and devastation. GOod luck and pls keep us posted

syd n said...

I am absolutely replenishing minerals with a complex made for use when chelating. Thanks for making sure. Super important.

I'm sorry to say, I don't know what FARMACY is!

I go to the farmer's market and get all kinds of goodies. I also have oxalate issues, which I resisted believing, but after trial and error, I know I do. Green juice + almond butter mania + a round of antibiotics = hyperoxaluria for me. I have to be careful with the kinds of greens I eat. My guess is when I heal my gut and get more oxalate-"eating" bugs back, that'll go away.

I hope there's hope after my bout with giardia was soooo long ago. But, the damage is still here, I guess. My doc is also wondering if I don't have a bit of the cryptosporodiasis still hanging around.

So, I guess I'll work to get out of ketosis and look at the seven steps, which I'm assuming is also compatible with insulin resistant/gut and brain-compromised folks!

Dr. B G said...

Hey Syd

Hope you stick around! Ck out the 7 steps and soil probiotics, bifido and lactobacilli -- they all break down plant oxalates.

syd n said...

Thanks much! I'll check out the links.

About a week ago, I started taking Prescript-Assist, and had already resumed taking GutPro. I also have Primal Defense Ultra.

For right now, I can't tolerate starchy foods, as it not only impacts my gut, but makes my brain crash! And, it also makes me CRAVE like crazy anything sweet or anything that metabolizes to sugar. Once I open the grain/sugar/starch door, forget it. I'm a bottomless pit. (This never used to be the case.)

I think I'll just do the SBOs and maybe a bit of potato starch for the SBOs to munch on for now, unless there's a better modified plan. (I know that's not optimal.) I'll quit the MCT/coconut oil and stay LC, as opposed to VLC. I don't count carbs (or protein or fat), which I guess I should. That feels a bit crazy-making - for me, I'm not at all saying it isn't super useful, and probably smart, at least in the beginning.

All a bit daunting!

syd n said...

. . . and unfortunately, lots of things like potatoes, carrots, sweet potatoes, yam, and some legumes, that you mention are good for SIBO, are high in oxalates, and for right now, that would put my brain and the rest of me over the edge - even soaked and fermented. Gah!

In the past, inulin made me bloat and cramp like crazy. I could try it again. I'm up for trying anything!

Okay, I suppose that is enough rambling on! Thanks so very much!

syd n said...

I totally SWEAR I will not post ad nauseam. Gah!! For real. There's just a steep initial learning curve!

Here's a new study that says ketogenisis is good for brain health, specifically Alzheimer's, which I know this thread is not dealing with. Though, insulin and the gut is, imho, directly connected. This is why I get so confused!! Is it just that the intervention (page 5 of this study) needs to be short-term, in your opinion? Or is it choosing your battles? Or do you disagree with the finding?


Dr. B G said...


I can see your sharp cogs turning...

I love ketogenesis -- what a wonderful tool for losing body fat fast. The problem for some however is it may compromise the gut (not enuf RS or fiber) or really affect a broken adrenal/cortisol/hormone axis. Everyone is diff and gets different mileage. Some have absolutely no problems and that is spectacular as well.

syd n said...

Thanks. :-)

Dan said...

Hi Dr. BG,
Lots of fascinating information here. You (and others posting here) seem like you might be able to point me towards some helpful resources. Like Rick, I have ankylosing spondilitis. I was diagnosed by a rheum earlier this year. I have had back pain for years but pain in my SI joint got really bad after an infection in my testicle last year- I had chlamydia, and was given azithromycin plus a month of cipro. I had diarhhea for awhile after, and terrible gas whenever i ate fruit or other sugars. Itried lots of probiotics - homemade kraut, kefir, etc but they seemed to make things worse. Since then I have intense flares of pain in my SI joints roughly once a month, plus ongoing discomfort, pain, fatigue and GI symptoms.

I recently learned about the no starch diet for AS, dropped all starches from my diet and have been eating a keto diet with LOTS of vegetables for a month. GI symptoms have greatly improved. The joint pain disappeared but came back. I should mention Im celiac, GF/DF diet for 5 years. Before the recent switch, I ate a low fat diet with lots of brown rice, veg, and some meat.

I don't have the money now to pay for testing out of pocket. I am saving up to get a consultation with a functional medicine doctor, but want to take action now. All the research I've done points to some kind of pathogen plus leaky gut aggravating an immune response. I'm thinking about trying some herbal antimicrobials, probiotics, and whatever else I can do to heal my gut, dysbiosis, and get rid of pathogens like Klebsiella.

I could use some guidance, but if you don't feel comfortable with that, I thought you might know of some good resources for me to learn more about these issues. Hard to find good info on AS.

Thank You,


Dr. B G said...

Hey Dan

Post on any thread and request assistance ;) I hope you'll be greatly rewarded.

This post is for you on autoimmunity related to AS:

Look forward to hearing more about your progressive and gut journey soon!