Thursday, December 4, 2014

Latest American Gut Results

Apparently the American Gut Project (also now available in England!) must have gotten a burst of energy recently.  Several people have told me that they just got results back they've been waiting nearly a year for. I also just got some results from a sample I sent them in July.

I'd like to show you all my most recent report and compare it with one from almost a year ago.

First, I'd like to say that you have to take this all with a grain of salt, because what you are about to see is simply a snapshot of what my gut looked like the morning I procured the sample, and my interpretations. Also, as we well know, fecal microbiota is not the whole story...there's also microbes that live in the mucous layer and may not be accurately reflected in a fecal sample. That said, I think that you can infer quite a bit from an American Gut Project microbe analysis.

And, as I showed in the Comparison Blog Post, some of this could be completely misleading because of the test methods or sampling errors. I wrote lots more about my first AmGut test last year on FTA as well.

I wish that I had a complete 'before' report from when I was eating a VLC type diet and not enjoying such good health as I am now, I think it would look much different, but the American Gut Project was not available back then.

These two reports represent different eating styles.  The most recent report was after about two months of a fairly high carb intake, probably 200-400g/day, from starchy carb sources like rice, potatoes, squash, plantains, gluten-free grains, seeds, and yams. I was also eating large platefuls of leafy greens and especially fresh dandelion leaves and roots, kale, chard, spinach, onions, and garlic. My goal during this time was to eat about 50g/day of total fiber with none of it coming from supplements. This way of eating was a distinct diversion from my normal way of eating, which is more represented in the potato starch supplemented diet.

Last year's report (bottom) is more the way I normally eat.  I really find myself feeling less hungry and perfectly fine eating one or two starches a day...maybe a baked potato at lunch and some rice with dinner.  My pantry is full of all kinds of cool grains, though, and I eat them often (teff, oats, quinoa, etc..). I try to get a salad or some fruit every day, which is a bit more difficult for me in Winter when I must rely on "iffy" supermarket produce. Summertime I am a fresh veggie eating machine as my garden pumps out homegrown vegetables and berries hang from every bush all around my house.  I use potato starch, inulin powder, glucomannan, dried plantains, alone or in combination, most days, to increase my fiber intake. I'm not religious about it, and rarely if ever have taken 4TBS of potato starch since I did that first test over a year ago. Usually it is more like 1-2TBS/day of potato starch and a spoonful of some other fiber. I usually try to prepare my starches so they are 'cooked and cooled' to maximize RS3.  Again, not religious about it.  I just try to get in the habit of being mindful of fiber. I think I get 20-50g of fiber most days and 100-200g of "carbs" but I don't count carefully.

Protein and fat-wise, both diets were similar.  I eat meat...lots of fish that I catch myself, moose that I harvest, eggs from my chickens, and also some store bought, conventional chicken and beef. I have never bought grass-fed meat in a store intentionally.  I think the idea of grass-fed over grain-fed is great, and if you do that, wonderful. I use Kerrygold butter sparingly, some olive oil or coconut oil in cooking. If you haven't guessed, I don't fret over macro ratios!

I have had no antibiotics in at least 10 years.  My health is great and weight is stable.  I'm not overweight or underweight.  Just right, I think.

 Here are two American Gut reports.  The top one was from a sample collected in July 2014 and the bottom from a sample collected in June 2013. In the bar charts, my sample is on the far left, and compared to other groups of people who have submitted samples, some 16,000 I believe.

Here's what jumps out at me on the reports above...

The Bifidobacteria, a general marker for health, was highest on my potato starch supplemented diet (11.3%), and well above average on the whole-food diet (4.8%).  Most people have less than 1%.

The Firmicute:Bacteroidete ratio is completely swapped between the diets. Many studies reported that a micriobiome with a greater percentage of Bacteroidetes is more likely to be associated with obesity and inflammation, in this respect, the "Potato Starch Supplemented Diet" would be considered "inflammatory" and "obese-causing."  I'm not worried, though.  This correlation has since been disproven numerous times and may only be true when no other factors, such as increased Bifidobacteria, are considered, as this paper explores:

Both the scientific literature and the popular press have heralded the association of obesity and the relative abundance of Bacteroidetes vs. Firmicutes as a robust finding. However, several recent reports question the strength of this association. Two large studies found no association between obesity and the Bacteroidetes: Firmicutes ratio. Furthermore, several publications actually report a higher ratio of Bacteroidetes to Firmicutes among obese individuals, in direct contradiction with the original findings.

 Faecalibacterium doubled with real food only.  I love Faecalibacterium! This genus has only one species..."prausnitzii." We can call this line item F. prausnitzii, then, [plus, it's fun to say: "Fee-cali-bacteri-um prows'-nitzy."]. Why do I like it?  Easy.  It's a real workhorse, and we all seem to have it.

Faecalibacterium prausnitzii is the most abundant bacterium in the human intestinal microbiota of healthy adults, representing more than 5% of the total bacterial population. Over the past five years, an increasing number of studies have clearly described the importance of this highly metabolically active commensal bacterium as a component of the healthy human microbiota. Changes in the abundance of F. prausnitzii have been linked to dysbiosis in several human disorders. 

 Is it problematic that my F. prausnitzii was cut in half when supplementing with potato starch?  Probably not. It seems that the trade off was maybe more Bifidobacteria!

Family Lachnospiraceae doubled with real food only. This family contains 19 different genera of gut bugs. This family of microbes is undoubtedly a sign of health, and the home of the Clostridia Clusters that Mr. Heisenbug loves. They are protective of C. diff infections. If you are missing these...look out!  The fact they were cut in half does not bother me one bit, as even at 50%, I have more Lachno than the other groups of dieters!  Had they disappeared, I'd be singing a different tune!

Order EC94 20,000x enriched on real food only!  What the hell is this?  Turns out, even weirder than you could imagine. 

...EC94 accounts for 99% of sponge-derived sequences but is absent from seawater. This enigmatic OTU is only known thus far as a coral-associated clone and has only 90% similarity to the next most closely related sequences which are from sponges and thus may be true symbionts of marine invertebrates and whose unknown function is intriguing.

It looks like I haven't developed "Hamster Gutz" as some have speculated...I am turning into Sponge Bob Square Pants!

Tim Steele?
What the...? 

Let's look closer. This seems to be legit, reading up on EC94, it is a very unique microbe and not likely to be an error. But how did I get it in me?  Well, I do spend quite a bit of time deep-sea fishing.  I have been known to eat raw fish pulled fresh from the ocean.  I have never drank from an aquarium, but I have gulped seawater while snorkeling in the coral of Hawaii.

Is it worrisome?  Not to me.  At .04%, this means that I have maybe a tiny colony the size of a pinhead somewhere in my large intestine. The 20,000 times enrichment probably means I am the first person to show this microbe. Who knows?  Maybe it gives me super-powers like Sponge Bob.

Let's take a closer look at the bar chart:

Lack of Proteobacteria.  You'd never guess, but Proteobacteria is the second largest group of bacteria. This phylum contains 1534 species or 32.3% of all known bacteria. This is also where most known pathogens reside.  One poor person I know had an AmGut report that contained almost 40% of total Proteobacteria...and she was a very ill person.  Seeing almost no Proteobacteria makes me very happy.

Diversity. As almost every American Gut profile shows similar numbers of the "Big Two" (Bacteroidetes amd Firmicutes), I like to look much closer at what is living in the smaller section of the charts.  I think this is where we see how much diversity we have.  A recent study came out describing the gut flora as a "King" and his "court."  It excites me to see some signs of diversity in these reports, but I think it only shows that you harbor a nice court for the king, and not much can really be speculated about this from my point of view.  Maybe some day this area under the magnifying glass will expose some true gut protectors.

"The diverse spectrum of glycans, which is present in the human colon, is derived from the diet (resistant starch, arabinoxylans, inulin) or the host (mucins). To construct a microbial network unit for these specific glycans, one needs to consider the concept of a king and his court. First, there is the specific primary degrader or keystone species for this glycan (‘king’). For many of the diverse spectrum of glycans that are present in the colon, such keystone species have been proposed. As an example, resistant starch requires the presence of Ruminococcus bromii, arabinoxylans are specifically degraded by Bifidobacterium longum and Akkermansia muciniphila seems a crucial species for the initial breakdown of mucins. To produce an industrial product, i.e. an effective microbial network unit, one also needs to provide the primary degrader (‘king’) with its cross-feeding microbes (‘court’)."

SAD Report:

For comparison, here is a recent American Gut report of a person who has taken many antibiotics, is on PPIs for GERD, and eats a fairly typical SAD diet.

It has lots of Akkermansia, which seems to be a key species. Most people have a little bit of Akkermansia, but it seems to readily explode when the gut is not right. It's a mucin-degrader.  Seems to me that maybe it likes to eat gut tissue that is not healthy. This study on colorectal cancer shows elevated levels of Akkermansia:

In this study we used stool profiling to identify intestinal bacteria and metabolites that are differentially represented in humans with colorectal cancer (CRC) compared to healthy controls to identify how microbial functions may influence CRC development. ... There were no significant differences in the overall microbial community structure associated with the disease state, but several bacterial genera, particularly butyrate-producing species, were under-represented in the CRC samples, while a mucin-degrading species, Akkermansia muciniphila, was about 4-fold higher in CRC . Proportionately higher amounts of butyrate were seen in stool of healthy individuals while relative concentrations of acetate were higher in stools of CRC patients.

Not sure if you caught that...healthy guts are filled with butyrate producers.  Unhealthy guts are filled with mucin degraders.  Butyrate producers come along for the fiber!  Akkermansia shows up when the gut is unhealthy.  Maybe it's trying to help us.  I wouldn't call it a "bad" microbe, but I wouldn't want to see much of it on my report.

Nothing special to see!  Aside from the Akkermansia, this antibiotic ravaged, PPI riddled gut has basically nothing much to see.  It contains the Bacteroidetes and Firmicutes that everyone has, no Bifidobacteria, no Proteobacteria (maybe a good thing?), and hardly anything in the small area at the bottom.  This is a gut that has produced autoimmune skin disorders, a liver tumour, a teratoma, and many years of diarrhea, heartburn, indigestion, and upset tummy. This gut prevents its owner from enjoying most foods, so she eats the things that don't hurt. Unfortunately, this means no fiber, few veggies, little fat, and lots and lots of refined carbs.

F. Prausnitzii.  Remember mine were 10 and 20% on the two diets?  The SAD diet clocked F. prausnitzii in at 3%.

Family Lachnospiraceae.  Mine were 7 and 15%.  The SAD diet netted 5% of this important family.

Final Thoughts

I think all I would like to leave you with is, "EAT LOTS OF FIBER." If you've clicked around here, you know I'm not talking about Metamucil or FiberOne Cereal. 

I like the way my American Gut report looks when I was eating real foods, but to be truthful, it was a handful eating like that. It was way more servings of carbs that I normally eat and it was quite a chore to find (and eat) so many high fiber veggies. If I could eat like that all the time, I would.  I do many days per week eating tons of fiber and don't supplement with powders every day.

Do I take this as "Potato Starch Kills our Guts!" No. I think a typical, healthy, diet supplemented with potato starch, inulin powders, or other supplemental fiber types is perfectly fine and very healthy. 

I'd like to see everyone eating like the Hinds Cave Paleo Indians who consumed 135g/day of fiber.  But unless you are eating what they ate...good luck!  Variety is the key, I believe.  And consistency. 

For people with truly messed up guts...SIBO, GERD, all that.  From what I hear, supplemental starches are not working too great, and therefore you probably want to stick with cooked and cooled starches and other fibers easier on your weakened digestive systems. Animal Pharm is looking into this and Dr. Grace AKA the Gut Goddess, has some great ideas for you over there if you fall into this category.

If anyone would like to see the full taxa reports for these three AmGut reports, they can be viewed here in Excel:
High Fiber   Potato Starch Added    SAD Eater

I hope this was easy to understand.  It got a little bit longer than I intended.



  1. Interesting on the sea going invertebrates showing up, I was just thinking about what may be gained from Ocean Based Organisms (OBO) to go along with the benefits from the SBOs. Perhaps there's a whole new world of salty water supplements we should be drinking also?

    1. Funny you say that. I was recently reading that there is more diversity in a spoonful of ocean water than in an entire human gut!

      Here's a good article explaining what is in ocean water:

  2. Very interesting!

    Jeff Leach speculated on Akkermansia recently too.

    "My shifting levels of Akker is interesting when you consider the gut bacteria of fasting/hibernating animals like squirrels and periodic-eating pythons is dominated by Akker – or at least Akker increases during periods of reduced nutrient availability."

    1. I like to think tha Akkermansia is one of the 'good guys', but it seems to be present in every sample I've ever looked at. So I don't think one can eat a certain way to increase it. In both of the AmGut reports above, my Akkermansia was just in the fractional percentages. I've seen it as high as 17%.

      A funny thing, the two reports that I've seen with the highest Akk, were both from people who are skinny and have been their whole life, eating whatever they want to eat. I can also relate that 'being skinny' doesn't equal 'healthy.'

  3. "But unless you are eating what they ate"... and moving as they moved. ;-)

  4. You've got more F. prausnitzii than me!
    I had 19.66% earlier this year (with uBiome, so as per your last post, we can't really compare) but that was right after abx. In my case it is probably just one that is resistant and took advantage of others dying off, though that doesn't make it bad in any way, but it's a survivor.

    I had lots of Akkermansia before I developed ulcerative colitis, and much less after (abx again) right after UC so the jury is still out for me on whether it's a bad sign to have it high. But I'll have to see what it's like when I next test after almost a year of high fibre and natural food. Interesting that it is high in CRC though, because of CRC's link with UC. Maybe it being high set me up for a fall.

    1. The very worst gut report I've seen, the one with 40% Proteobacteria, still had 5% F. prausnitzii. Yes, it's a survivor. One thing I'd like to point out that is easily overlooked, lots of these microbes can live on different food sources. Probably F. prau has many foods it can choose from. And it also seems that when fermenting different foods, they produce different compounds, as expected.

      I don't think we can condemn Akkermansia. Perhaps it's high when we need it the most, as Gemma showed in her comment above. I cringe when I see the suggestion to implant Akkermansia in 'fat people' to help them lose weight. I just can't see it working that way.

  5. Just found another weird one...maybe I do have SALMON GUTZZZ!

    An archaea, Nitrosopumilus, .04%:

    "Nitrosopumilus maritimus is an extremely common archaeon living in seawater. Gene sequences suggest that the Group 1a Crenarchaeota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. This organism was isolated from sediment in a tropical tank at the Seattle Aquarium by a group led by David Stahl (University of Washington)."

    As Nitrosopumilus only has one species, we can be sure this is what they found.

    I was in Seattle recently, but I did not drink from any aquariums! Swear.

  6. hmm, just pinged american gut AGAIN. Still awaiting results from September 2013.

  7. Did you log-in and look? I found mine by accident! They have not notified me yet.

    1. Okay, finally got it. Looks a lot different from yours.

  8. Dr Grace no longer believe that supplementing potato starch is a very good idea, and that it might suppress beneficial bacterias as well as diversity. I tend to agree with her, and I struggle to find evolutionary justifications for consuming such large quantities of rs2. Have your opinion on the matter changed?

    1. I've been loose in my opinion of potato starch from the beginning. I co-authored a 3-part blog saying real food better than supplemented starch last spring (Read Here)

    2. Whoops, hit send too early.

      There is no ancestral justification of eating a low fiber diet supplemented with high dose potato starch.

      I have never recommended that, or anyone, that I know of. Lots of low carbers who get little fiber have asked about it, and I think that some potato starch in their diet is better than no fiber, but not as good as a variety of fibers. Make sense?

      But, the amount of potato starch I talk about frequently, 4TBS, is the amount found in one smallish potato. So it's not an unnaturally large amount. 1TBS of pectin or psyllium that is unnatural! You'd never get that much in real food.

      People have eaten raw yams 'forever' and still do in some parts of the world, same as green bananas, raw potatoes, and some other raw foods that are high in RS2.

      I do NOT think that RS2 consumption is unnatural by any means.

      In fact, the more I look into it, the more I see it is completely unnatural to NOT have it in our daily lives.

      What is VERY unnatural is a low fiber diet, guts that cannot tolerate many foods, antibiotics, and excessive sterilization. I think that some potato starch, if needed to boost fiber intake, is doing a world of good for many people. Way more good than 30 years of Metamucil, Benefiber, and the recommendation to "eat 30g of fiber per day" from the USDA withno mention of fermentable fibers and resistant starch.

      There is still a lot to learn, but I think we are making headway into the whole gut health puzzle. Whether the savior will be potato starch, cooked and cooled foods, or some other fiber type is what this experimentation is all about.

      And I don't think potato starch "suppresses" diversity by any means! Possibly if fed to mice as a sole source of food it may suppress diversity, but included as a natural source of fiber in a natural amount...why would it? Makes no sense, and there are tons of papers to show differently.

    3. What dr. Grace wrote: "For those on high dose raw starches -- you may observe vast differences.
      •the bifidobacteria are absent or nearly extinct (except for report c).
      •F. prausnitizii which typically makes up 10-20% of healthy stool microbiota is only HALF OR LESS of 'normal' for either a hunter-gatherer Hadza or Western urbanite.
      •Bacteroides appears overselected
      •low eubacteria
      •no Roseburia/cluster XIVa"

      "What I observe is that with high dose RS2, an overselection of gut flora that specialize in raw starches and the de-selection (?suppression) of other species despite adequate consumption of other substrates (RS3)."

      She does not mention low-fiber high-rs2 diet specifically, so I assume she means that rs2 have an impact under most circumstances. Of course there is no conclusive evidence yet, but I do believe that it was a huge mistake to tout ps as a panacea for all gut-related issues (not talking about you, but some people were really sure of themselves and insulted anyone who were skeptical about ps).

    4. I think that anyone who makes 'conclusive statements' on any of this is angling for something. Beware!

      Richard at FTA is, was, will always be a big jerk. But that's how he gets people to read his blog. I don;t regret starting out there, it got a lot of attention for RS and gut health when no one else would give me the time of day.

      From the very start, my focus was on RS as an overlooked prebiotic, using potato starch as a supplement, learning how to increase RS2 and RS3 intake from real foods, and then branching into all other fibers, because I quickly learned there was a whole world of overlooked fiber sources out there.

      I hate that the potato starch aspect got so political and turned into a hot-button. It detracts from the overall message.

      As to the laundry list of potato starch crimes you posted...look at my results. I'm not seeing it.

      But the thing is...if people don;t want to use potato starch, there is still a whole world of fiber supplements and real food that can make your gut happy. I'm sure there's something for everyone!

    5. Has Dr Grace given a specific number as to what "high dose" is? 1-2 TBS is typically noted as the usual amount per "serving" based on her bionic fiber recommendations (and what I would normally supplement with), but is that a "high dose" of RPS alone or in comparison to GBF which she now recommends as an alternative?

      I happen to have RPS and GBF and will try using less GBF only for a while because why not, just curious what other think based on their dosages.


    6. To me, "high dose" would mean trying to get all of your fiber needs with potato starch and eating no other fibers.

      I think most people can easily get 10-20g of various fibers from real foods in a day. Cook and cool most of your starches (rice, beans, potatoes) and eat a greenish banana, have some onions and garlic, and a handful of nuts. 20g easy.

      I think the magic number is closer to 40g, though, at least for me. Therefore I like to take a spoonful or two of a supplement like potato starch, inulin, glucomannan, etc...

      But really, it depends on the person. If you are happy with digestion and health, just eat real foods and call it good. If you like the way you feel with a bit more fiber or are struggling with health, try more and various types.

      Just eating a regular paleo or SAD type diet, all starches eaten hot and freshly cooked, you are lucky to get 5-10g of fiber. This is the error I am trying to correct. The standard diet we have been taught to eat, paleo diets included, just don't provide enough fiber. Wheat products give the most fiber in the SAD diet.

      The Wheat Belly doc recognized this injustice and now recommends eating a small raw potato daily for fiber. That says a lot to me.

    7. Hadza women roasting tubers >>

      You're not really eating ancestrally if you're not eating RS. Our ancestors surely ate not-fully-cooked, if not completely raw, tubers. Same as the Hadza still does. 5 minutes on the fire leaves quite a LOT of RS.

    8. Meaning, they are just charring the outside, probably to make the skin easier to peel off - and I think most of the anti-nutrients are in the skin, no?

    9. "1TBS (8g) of pectin or psyllium that is unnatural! You'd never get that much in real food."

      Hadza eat 20-30g+ of pectin, a day, year round. Often higher (think 100g+ a day).

    10. Seriously? Any cites for that? Pectin does seem to be an awesome prebiotic. How are they getting so much?

      Pectin supplements are expensive! I always figured because it was hard to access.

      I'd love to explore your statement of 20-30g/day in Hadza.


    11. Tim, baobab is approximately 1/3 soluble fiber, which is mostly pectin. An additional 1/6 is insoluble. So that would translate to about 60-90 g/day of consumed baobab, which is not much. I do 12 g/ day approximately, which about 2 tablespoons, and I am obviously not using it as a major source of calories.

    12. That is very interesting! I've just searched a bit and nothing jumped out at me other than websites selling baobab powder and saying it's high in pectin. Has anyone come across anything more compelling?

      Everything else I see says that pectin is about 1% of the weight of most fruits we eat.

      But there are lots of papers on the prebiotic effects of pectin. I always thought it was one of those factors that contribute to the overall harmony of the gut biome, you know, that whole keystone/co-feeder thing.

      Kind of like from here:

      "The analysis revealed a different pH protein distribution that was mostly acidic in the presence of pectin and neutral-alkaline in the presence of inulin. Both prebiotics stimulated the production of butyrate, a relevant healthy bio-molecule not detectable in the presence of glucose, that was measured by HPLC analysis to be 14.5 fold higher after growth in the presence of inulin, as compared to pectin. Three specific proteins were detected at pH 6 after growth in the presence of pectin or inulin. They could be correlated to the stress resistance and/or to the production of butyrate, the common phenotypic characteristics induced in the bacterial strain by the two prebiotics."

    13. In

      I found the following passage interesting:

      . Baobab seeds are a good source of protein and, due largely to their high fat content, their energy content is equivalent to that from honey. Although the seeds are inadequate in three essential amino acids, minimal amounts of meat would complete these requirements. In addition, the baobab seeds are a more dependable energy source than honey. Women consistently returned with dozens of baobab fruits or with signi"cant quantities of seeds over the majority of months of the year either through direct fruit collection or through collection of seeds in baboon dung piles. Honey is available in quantity only for a few months each year, as is true for non-baobab fruits. Overall, this suggests that baobab is an important, probably preferred, plant food for the Hadza even though other plants are eaten in signi"cant quantities. Maintaining areas with healthy baobab groves is important for the future of Hadza and of other people living in agriculturally marginal regions.

    14. Tim,

      I don't understand your request. Here is the GRAS approval for baobab. It has a lot of info.

    15. Oh, sorry. I was just trying to figure out the pectin content of the baobab fruit or powder. I have a feeling that baobab fruit/seeds are truly deserving of the label 'superfood'. If it really does contain 30% pectin, that would change my feelings on how much pectin is a good amount. I always try to think in terms of how much is found in foods we eat.

    16. It is not clear whether you've read the GRAS application, but on page 21 it says that baobab is just over 30% pectin. The 1/3 I mentioned before came from the baobab nutritional label on the one I am using. The difference can reflect rounding.

    17. For some reason the pdf won't load. I'll keep trying!

    18. I don't know why. I can't get it to load by cut and pasting from this page, but it seems correct. Try Google using "baobab fda application" and it shows up as the first result for me. I just checked, and the fda website seems fine. You'll be amazed at how much info is there.

    19. OK! I'm in.

      Hard to say how accurate this is:

      "Previous publications by Sanghi et al. (1978) and Nour et al. (1980) have reported that Baobab fruit pulp contains a high amount of pectin (soluble dietary fiber). According to these researchers, the amount of pectin can be high as 56% by weight of Baobab fruit pulp. However, the nutritional profile in Table 1 (page 9) shows that the total dietary fiber content of the Baobab dried fruit pulp is 5 1.4 - 52.28 per 1 OOg of fruit pulp. On further analysis, the pectin (soluble dietary fiber) content of Baobab dried fruit pulp was found to be 30.9g per lOOg of fruit pulp with the remainder being insoluble dietary fiber (Appendix 2). According to the data in Tables 2 and 3 (pages 17 and 18 respectively), males aged 14 - 16 years old are expected to be the heaviest consumers of smoothies and fruit bars containing Baobab dried fruit pulp. At the anticipated level of intake of log of Baobab dried fruit pulp in smoothies and 15g of Baobab dried fruit pulp in fruit bars, the highest amount of dietary fiber consumed would be 5.228 and 7.838 respectively (see Table 6)"

      At any rate, Baobab powder is undoubtedly a good addition to smoothies, etc... Would be cool to get hold of some baobab fruit and seeds.

    20. The Novel Foods application for the EU seems to suggest that they retested samples of baobab and arrived at similar conclusions

      See page 20. The percentage varied by region. Another study suggest varies by season. But all seem to agree on approximate level (25 to 50%).

      I've read stuff that baobab makes an excellent source of pectin for jellies. Apparently a gin maker won an award using baobab as a botanical. Maybe I should add gin to my fart drinks?

    21. I see you can make your own pectin easily, too:

      Pectin does seem cool, so a natural source like baobab sounds great! I was looking, pectin supplements are like $10 for 50 grams. Then there is Sure-Jell pectin sold for jelly making, but has other ingredients (Dextrose, citric acid). And not sure how that stuff is to mix, does it get super thick, really fast?

    22. Baobab seems to be high just in anything (oxalates, calcium too), kind of a very unique food source in that respect... and nice to look at as well.

    23. The Hadza must consume an incredible amount of fermentable fiber. Australian Aborigines use Baobab as a staple too. And as soon as they can walk, the women spend most of their day digging up various tubers, which they roast quickly to remove the skins. So I imagine they consume a lot of raw starch.
      Does anyone know how much pectin is in citrus peel? Maybe I could just put the white pith from grapefruit skins in the smoothies.
      The citrus pectin powder I add now does thicken them a bit, but not nearly as much as guar gum. Must get some PHGG.

    24. Stuart, can you buy Baobab over here in Australia? Be great if you could. I was looking into various Baobab powders, but they all seem to come from overseas. Seems crazy when we have some here.
      I wish we could more easily access what Aboriginals ate. They would have a diet full of things that are far more nutritious than what we can find at the supermarket, which mostly seems full of such standardized vegetables. Every week it is pretty much the same thing, only the fruits seem to change.

    25. Some fifty pages about "Pectins: Structure, Functionality and Uses", p. 353
      (and yes, found in potato or sugar beet pulp too)

      Food Polysaccharides and Their Applications

    26. Thanks Gemma.
      You are amazing. 30- 35 % pectin in citrus peel. It didn't seem to mention what percentage was in potato pulp.
      Interesting stuff about inulin in the previous chapter too.
      I wondered about the solanine possibility with the potato aftertaste too. This is a variety of pink skinned potatoes that NEVER seem to go green in ultraviolet. I often put them around the bases of my roses as an evaporative barrier, and after about two months in full sun they go black, but prior to that, no green whatsoever. Weird. It could be solanine even with no green could it? In any case, I'll try with some different types.

      So you're a chocaholic are you? ".. one piece, maybe two, maybe three.." Ah, theobromine - SUCH a good drug.

      . Well I got some in a Brisbane metro health food shop the other day ( baobab powder) You can buy the same brand on ebay from an Australian supplier. But it's made in China. I think I'll find a Baobab tree in a park and when it fruits, stock up. I've no idea how easy the fruit would be to dehydrate. The bigger trees must have several tons of fruit. I've always wondered whether my livestock would eat them. I had no idea they were such nutritional powerhouses for humans. But then, a month ago, I was only dimly aware that I even had a microbiome, let alone how to care for it.
      There's probably hundreds of baobab trees in parks across Brisbane.There's an idea for small business. I once stood in an ancient hollowed out baobab trunk in the Kimberley - about 5 metres across internally- that the local tribe had used as a sacred site for hundreds of years, And when the white settlers arrived, it was co-opted as a jail for difficult aborigines.The irony.
      Guns germs and Steel Have you read the book?

    27. Stuart

      I'd love to have baobab trees here. I've seen TV shows where roadside stands sell baobab in the Caribbean.

      I've never seen a baobab fruit in person. But I've read many times that the baobab is also a "producer's dream fruit" because it does not need dehydration. As I understand it, the powder you get in the bag comes from several small marshmallow-looking bits from the fruit. Those marshmallow-looking bits are simply milled into the powder, bagged, and shipped. You might not need the milling step. I think the milling might reflect the use of baobab as primarily a food additive here rather than a fruit. I'd love to get some of the bits, but I haven't seen them here.

    28. Amazing Wilbur. What a find. Isn't it interesting that they grow wild all over the tropical /subtropical world. Maybe humans spread the seed as they spread globally from Africa. Maybe the same goes for cattails (bullrushes). But you would think then that there'd be tigernuts growing wild here.
      Btw.I loved commenter Kate's description of her 'Wilburesque' smoothies.

    29. @Stuart

      Chocoholic, me? Never!

      Here a nice book about baobab: The African Baobab

      and here an article and a short video and how Hadza process it.

    30. Stuart,

      No wonder that my gut buddies seem to like baobab a lot. I mentioned before that I started baobab because Leach was so excited by it. That was earlyon, before I understood what I do now. It gives me new appreciation for an old friend.

      I also read that the baobab tree can upwards of 30,000 gallons of water in its branches and trunk, providing a source of water during droughts. It truly is amazing.

    31. Cool, thanks everybody! Now I want some baobab!

    32. Thanks Stuart! I'm the anon from Australia. Melbourne actually, and there are no local baobab trees here. Darn!
      Yes I saw the powders from overseas on ebay. I was hoping for something local. Seems crazy to be importing it. But that seems to be the way of the world at the moment. I saw lemons from the States the other day.

    33. Gemma.
      Interesting video.Seeing the Hadza cracking the nuts reminded me of my trip to the Australian Kimberly ( in far north Western Australia - quite honestly the most spectacular scenery I have seen anywhere in the world) where the local Aborigines intricately decorate the pods in traditional designs with a hot wire, and sell them to tourists Because, as Wilbur mentioned, the 'fruit' pulp inside is so dry, they don't even bother removing the pulp. Baobabs are so adapted to dry climates aren't they? Water storage in the trunks , no wasteful water use in the fruit pods.They're probably slow growing though so my baobab grove probably isn't going to happen. Sigh!
      Rebecca Sompson mentioned so many interesting facts about the Hadza (why did she use the term Hadzabe?) like the no leader egalitarian social structure, no starvation record in their oral histories - while neighboring farming/ livestock herding tribes are plagued by hunger, even the kids eat up to 150 g of fiber / day, and that desert rose hunting toxin they use on their arrow tips - which can fell a giraffe. Wasn't that Jeff Leach in frame towards the end of the video:? Are they colleagues? Actually I think I could listen entranced to Rebecca Sompson reciting bus timetables. She has the most intoxicating voice I've ever heard.
      I've always felt sorry for dogs that they can't eat chocolate.

      @Australian Anon,
      Yes isn't the food miles thing a worry?

      They are indeed remarkable trees. I've always thought they looked a bit prehistoric.

    34. Did you see the article linked to in Rebecca Sompson's report?

      Really worth reading. Baboon brains, anyone?

      Australian anon

    35. @Stuart

      Read her article too (it was in the other link in my comment).

      Hadzabe may be the native form of their name, I guess.

      I think it was Paleophil once saying that the shape of baobab tree is engraved deep in every human, "remembering" Africa" sort of, that is why we like it. It means shelter, food, water, life...

    36. Thanks Gemma and Au anon, those articles were unforgettable.
      And yes, you're right about the baobab Gemma - primordial is probably a much better word than prehistoric.

    37. Yes, thank you very much. Those were fantastic articles.

  9. Tim - you are the bomb!
    This is super cool.
    Thanks for everything you do.

  10. Tim, I too did an American Gut sample in June 2013. I recently happened to look at those results again online, and I was surprised to see that they were a little different from the results that were available to me a year ago. I don't think that I would have even noticed, except that the "enriched taxa" and "rare taxa" were completely different, which made me do a double-take. Looking through the full list of taxa, I didn't see any big changes, mostly just the addition of some very low-abundance taxa, and a few tweaks to other numbers. Did you notice something similar?

    1. That's normal. They re-run the samples and make updates. Not sure what prompts these re-runs, maybe new technology or updated databases to compare against. Mine hasn't changed much since the initial report 1 year ago, maybe 1-2% on some of the higher numbers, and about 50 new microbes in the .01-00% range.

  11. Yeah, me too; implanting anything in fat people (or thin people, for that matter) at this stage is likely a bad idea (perhaps with the exception of c.diff). Although it is a bit TMI, I had a lot of mucus before when I had high Akk but after getting UC I have now very little and much less Akk too. So you could be right, that it stimulates what is needed or something.

  12. I have an interesting (to me) thread of thought I have been researching lately. Over at Animal Pharm, the Dr. has been going on about Akkermansia muciniphila, which is correlated with decreased fat and increased muscle along with a lot of other health markers. There are some studies on rat which show Akkermansia muciniphila to cause these health benefits directly. The interesting thing is that Akkermansia muciniphila is a mucus degrader, not starch or fiber degrader, and the population is directly affected by the thickness of the mucus layer, and only indirectly by what is eaten. The mucus layer is increase by increase butyrate, but only to a certain point, at which further increases in butyrate result in a DECREASE of the mucus layer. In rats, enough butyrate (unlikely to be produced by PS consumption) results in a mucus layer the same thickness as the controls. Acetate, on the other hand, increases the mucus layer in direct proportion to the amount of acetate in the large intestine. PS increases butyrate, but does not seem to increase acetate. On the other hand, FOS digestion is largely degraded into acetate.
    Interestingly, the study Dr. BG cites for Akkermansia muciniphila was on observational study done on elite rugby players in which all players had high levels of Akkermansia muciniphila. The conclusion was the increased food requirements and exercise resulted in increased Akkermansia muciniphila, but if the rodent studies are to be believed, the researchers got the causation backwards; the reason the subjects were elite athletes was because they had elevated levels of Akkermansia muciniphila.

  13. After rereading the post and all the comments, a couple of other thoughts occurred to me:

    1. If the tests are a percentage of the gut population, of course Akkermansia muciniphila is going to go up, if there is a major die off, as it is protected in the mucus layer. This would also be true for periods of low food in which the rest of the population was starved, while Akkermansia muciniphila happily ate food provided by YOU.

    2. If you have a lot of mucus (which could indicate damage to the large intestine), you are going to have a lot of Akkermansia muciniphila, but that would only be correlation with the gut damage, not causation.

    3. One of the defining characteristics of UC is a thin or compromised mucus layer, so it would make sense that the number of Akkermansia muciniphila would go down with UC.

    4. When rodents were fed live Akkermansia muciniphila, they gained muscle and lost weight and fat. The same thing happened when they were fed 0.3 grams a day (70 or so grams for a human) of FOS which indirectly increased Akkermansia muciniphila.

  14. Tate - Great synthesis of Akkermansia! It is a very convoluted concept and hard to simply say that anytime Akkermansia numbers go down it's 'bad' and when they go up it's 'good.'

    This is probably the study you are referring to: Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

    Some snippets from this paper:

    "A. muciniphila may represent 3–5% of the microbial community in healthy subjects, and its abundance inversely correlates with body weight and type 1 diabetes in mice and humans, although a recent metagenomic study found that some of the genes belonging to A. muciniphila were enriched in type 2 diabetic subjects."

    "We recently discovered that the administration of prebiotics (oligofructose) to genetically obese mice increased the abundance of A. muciniphila by ∼100-fold. However, the direct implications of A. muciniphila for obesity and type 2 diabetes have not been determined, and the precise physiological roles it plays during these processes are not known."

    While I think that Akkermansia is a very, very interesting microbe, I just don't see how we can use it as a marker for health.

    In my gut tests, while eating the potato starch enriched diet, my Akkermansia was .07%, while eating a real-food, high fiber diet it was .19% (or .12% according to uBiome). I was neither obese, diabetic, or overtly cancerous.

    My wife, while on a SAD diet had Akkermansia of 4.6%, and another we know with decidedly dysfunctional gut problems had .26% Akkermansia (Neither eating PS or much RS of any type).

    Another person, very healthy by her assessment, and eating a healthy diet supplemented w/4TBS/day of potato starch, had an Akkermansia count of .03%.

    The highest count of all these people was the 4% in a person with lifelong gut problems, a history of massive antibiotic usage, and a rail-thin phenotype.

    According to uBiome, the thousands of samples they have analyzed had a normal range of 0% to 4.1% with an average of 1.2%.

    Soon, I will be showing you all a before and after AmGut test where potato starch (for 6 weeks) seems to have lowered Akkermansia from 17% to 1.4% while raising Bifido from .95 to 5%.

    And while I'd love to jump up and down and shout about how this is absolute proof of the effectiveness of PS on gut health, I also have an AmGut test from a person taking 4TBS/day of PS for months who showed .13% bifido.

    So, clearly, I think we just have to keep an open mind on all of this.

  15. Tim, you wrote above that 1 tablespoon of pectin or psyillum husk is a lot, and you would never get that in real food, which is very interesting.
    Would half a teaspoon (or even less) of each be more appropriate?

    Also, out of interest, how much would a 'natural' dose of Green banana flour be?
    And same question for Inulin powder. What is a sensible amount?

    I think I'm going to try out some raw potato next. My next experiment!
    Seeing as approx 4 tbsps of starch are in a small one it does seem like some of the criticisms of PS are a little overstated, and it's all getting a bit overly complex and alarmist. I like your in the middle approach. And this is from someone whose gut doesn't function so well.

    1. I think a heaping spoonful of psyllium husk is about right to use. I think that this type of fiber is pretty plentiful in nature, as from the skins of whole grains, seeds, and nuts. I was just making a comment on the 'ancestral arguments' that no one probably ever spent much time removing psyllium husks and eating them on a daily basis.

      I laugh that people always say 'potato starch is unnatural' but have no problem recommending psyllium husk or purified inulin etc...

      I think psyllium husk is probably comparable to oat bran, wheat bran, and that type of fiber. It contributes to bulking the stool and also has other fermentable components like Beta-Glucan. The studies are compelling that adding a fiber like psyllium husk helps spread the effects of RS out over the whole intestine.

      As far as pectin, from Wikipedia, a list of pectin contents:
      Typical levels of pectin in plants are (fresh weight):

      apples, 1–1.5%

      apricots, 1%

      cherries, 0.4%

      oranges, 0.5–3.5%

      carrots approx. 1.4%

      citrus peels, 30%

      So, you can see, that most foods we eat are 1% or less in pectin. To get a TBS (approx 8g) you'd need to eat almost 2 pounds of most fruits that are high in pectin.

      So, I guess by that logic, 1TBS of pectin would not be totally out of the question. But 4TBS would be the equivalent of eating 8 pounds of fruit. Contrast that with 4TBS of potato starch which could come from 1 plantain or 1 (1/3pound) small potato, or a small yam as grew all over Africa.

      Green banana flour -- 1 green banana will produce about 6-8TBS of flour.

      Inulin -- Also found in high levels in the wild. Some plants like chicory root and Jerusalem artichoke are like 50% by weigh inulin. But I think that inulin is found in just about the same concentrations in nature as RS, so 1-4TBS a day is a very good target.

      Funny thing with is not a very popular fiber supplement and the recommended doses are always very low. You can probably guess makes you fart! Metamucil had a product that contained inulin, but pulled it off the market when everyone complained of gassiness.

      My only problem with inulin supplements are the cost. Maybe better to find Jerusalem artichokes and eat a big slice of that every day.

    2. Thanks so much Tim!
      Just tried a little bit of raw potato. Not too bad. I wonder if you could add a little bit of sea salt to the slices 5mins before eating. I remember that Gemma once suggested doing that to crushed garlic.

    3. Salt would just be for taste. Adding it to garlic actually serves a purpose of stressing the bulb to generate some Allicin activity, I believe.

  16. Some more questions than answers on Akkermansia :-)

    (and I like the thought that it comes to help in case it is needed or appears to be high in case when the nutrients are scarce).

    Actually it is a funny one, as it is a Gram-negative bacteria producing LPS, which are normally inflammatory, but in case of Akkermansia they are inflammatory in a good way, so its presence keeps the mucus in shape. It can produce propionate and acetate and helps keeping the endothelium healthy.

    Microbes inside—from diversity to function: the case of Akkermansia

    But why would it so increased in some unhealthy people? And what does it eat when fed to obese rats?

    So what about this: Akkermansia also produces chitinolitic enzymes that may break yeast cell walls. See:

    Comparative Analysis of Glycoside Hydrolases Activities from Phylogenetically Diverse Marine Bacteria of the Genus Arenibacter

    Yeasts are often overgrown in some cases... And cancerous tissues display aberrant glycan structures too, and maybe Akkermansia finds a lot to eat there...

    1. Always lots of questions! I think it seems pretty clear that Akkermansia is an active little bugger, and needs to just be given some room to do what it needs to do.

      I didn't realize it was gram-negative! That's kind of ironic since most first-line antibiotics target only gram negative.

      I really think that every single gut report I've ever seen has some Akkermansia in it. I wonder if it is extremely resistant to effects of antibiotics or if it's just easy to pick up from the environment?

  17. THx Happy Viking and Tate for your questions!

    Your F praus was only half of the normal healthy avg (ubiome) with you were on 100g starches + 20-40 g RS2. Not sure that was great since the RS2 was such a high dosage.
    The Akkermansia at that time was 0.07% (normal healthy avg = 1.2%). Your gut Akk at the time was 17-times BELOW average.

    Low Akkermansia is a hallmark of NASH/fatty liver which you had a bout of early this year, June 2014. I applaud the 100 lb wt loss you've done such a great job sustaining! However I think when high dosage RS2 lowers or suppresses the flourishment of a good phylogenetic core symbiont like Akkermansia, there is metabolic problems, perhaps similar to what you experienced, no?

    It might have been the perfect storm (like my GERD induced by potato starch):
    --summer fruit trigger
    -- high dosage RS2 that lowers mucosa-biota like Akkermansia
    -- higher insulin resistance and body fat (loss of lean core gut flora by high dosage RS2: no Bifidobacteria longum, low Roseburia/XIVa/Lachno, low Akkermansia combination)

    When scientists give live Akkermansia as a probiotic to NASH/fatty liver models of animals, it improves NASH and all the metabolic parameters associated with the condition: SIBO, permeability, high LPS, endotoxemia, elevated blood sugars, etc.

    What you probably experienced when you had the NASH episodes earlier this year.

    On this Amgut that you posted -- what was the gut's Akkermansia abundance? What is the dose of inulin -- sorry -- not clear to me -- 50 grams? (or total prebiotics/RS = 50 grams)?

    THx -- for mention in the post.

    I discuss some cons to RPS/RS2 on my latest Bulletproof podcast and the testing to quantify one's Bifidobacteria longum and Akkermansia -- core microbiota for leanness and longevity!! lol:

    The latest study (HT Gerstmar ND): authors say "For instance, a decrease in Akkermansia muciniphila causes a thinner intestinal mucus layer and promotes gut permeability, which allows the leakage of bacterial components. Interventions to increase Akkermansia muciniphila improve the metabolic parameters in obesity and NAFLD. "

    (NAFLD = fatty liver = NASH)

    1. I love Amgut, but uBIOME provides the raw taxonomy to 'visualize' the Bifidobacteria spectrum:
      --B longum [++this is the ancestral phylogenetic core (Tim's 0.0021%; healthy averages are ~ 0.4-0.5%. RS2 fails to feed this strain. Eats specific food (inulin/yacon/GOS-beans) except no RS2]
      --B animalis [++RS2 overfeeds this strain IMHO, not ancestral and not as protective against NASH, obesity, autoimmunity or SIBO; Tim's = 98% animalis on ubiome]
      --B lactis
      --B pseudocatelenum
      --B breve
      --B bifidum

      World J Gastroenterol. 2014 Jun 21;20(23):7381-91.
      doi: 10.3748/wjg.v20.i23.7381.

      Role of gut microbiota and Toll-like receptors in nonalcoholic fatty liver disease.
      Miura K, Ohnishi H.

      Emerging data have shown a close association between compositional changes in gut microbiota and the development of nonalcoholic fatty liver disease (NAFLD). The change in gut microbiota may alter nutritional absorption and storage. In addition, gut microbiota are a source of Toll-like receptor (TLR) ligands, and their compositional change can also increase the amount of TLR ligands delivered to the liver. TLR ligands can stimulate liver cells to produce proinflammatory cytokines. Therefore, the gut-liver axis has attracted much interest, particularly regarding the pathogenesis of NAFLD. The abundance of the major gut microbiota, including Firmicutes and Bacteroidetes, has been considered a potential underlying mechanism of obesity and NAFLD, but the role of these microbiota in NAFLD remains unknown. Several reports have demonstrated that certain gut microbiota are associated with the development of obesity and NAFLD. For instance, a decrease in Akkermansia muciniphila causes a thinner intestinal mucus layer and promotes gut permeability, which allows the leakage of bacterial components. Interventions to increase Akkermansia muciniphila improve the metabolic parameters in obesity and NAFLD. In children, the levels of Escherichia were significantly increased in nonalcoholic steatohepatitis (NASH) compared with those in obese control. Escherichia can produce ethanol, which promotes gut permeability. Thus, normalization of gut microbiota using probiotics or prebiotics is a promising treatment option for NAFLD. In addition, TLR signaling in the liver is activated, and its downstream molecules, such as proinflammatory cytokines, are increased in NAFLD. To data, TLR2, TLR4, TLR5, and TLR9 have been shown to be associated with the pathogenesis of NAFLD. Therefore, gut microbiota and TLRs are targets for NAFLD treatment.

    2. "Your F praus was only half of the normal healthy avg (ubiome) with you were on 100g starches + 20-40 g RS2. Not sure that was great since the RS2 was such a high dosage.
      The Akkermansia at that time was 0.07% (normal healthy avg = 1.2%). Your gut Akk at the time was 17-times BELOW average."

      Is uBiome really a collection of 'normal, healthy guts' or a collection of SAD guts? I should think the latter!

    3. It is as best to compare ;) Yes imperfect, I concur. But what is clear is obesity, T2 diabetes and NASH are related to low, suboptimal levels of Akkermansia, Roseburia XIVa and dysbiosis. Thx DJ!

    4. DJ ~ Hadza, Malawi, and ameriindians have these similar or better abundances on 16S rRNA studies of the gut microbiota (ubiome is not 'off' too much imho):

    5. Dr. BG you wrote you got GERD induced by potato. Did I read correctly or am I missing something? Thanks

    6. The great "doktor" mis-diagnosed me, lol. Turns out I was fighting a set of gallstones for several years that seemed to be GERD. Got rid of the gallbladder in 2016 and the "GERD" disappeared. Never trust a doctor who has never seen you in person!

  18. Hi, Grace! Thanks for stopping by to clear things up.

    I think my liver is just fine now. You know, I had a real case of NAFLD back from 2005-2010, confirmed by ultrasounds, liver labs, and it frikking HURT! This summer when I was doing the all real-food high-fiber experiment, I noted some of that tenderness in my liver, but I am 100% positive it was from some of the crazy things I was eating at the time to boost my fiber content, like handfuls of cocoa nibs. I also experienced a bout of what appeared to be gout at the same time.

    I think I was a casualty of over-exhuberance in trying to get 50g of fiber from real foods...I am of the conclusion it's nearly impossible.

    On the inulin with real food diet. I would say it was maybe 10g/day. Mostly from the dandelions.

    the 50g was total fiber, as best I could estimate, from all the foods I was eating. The only RS2 I was getting at that time was from some dried plantains and green bananas.

    Oh! And we found the AmGut raw data files. We are running them through MG-RAST as we speak. Hopefully I will have a better assessment of the Bifido species soon.


    DJ - I'm with you! I'd love to see an AmGut or uBiome category for high-fiber, paleo people,

  19. AmGut gives the Akkermansia -- is yours still 17-fold below normal? What is it?

    I notice Kate's -- you just posted -- her Akkermansia (and B longum??!) dropped significantly as well. Hers dropped below healthy norms like yours and others on high dosage RPS.

    These are vital for the lean core phylogenetic microbiota

    If you have Roseburia growing in your uppergut (contributing to endotoxemia, NASH, the latestin bout -- in June few months ago) then you may want to consider clearing up your uppergut and not 'push' the Roseburia with inulin until you do.

    Justin a budyy just lowered his LFTs from high levels from 50 to 20's with yacon syrup for 2 months (STOPPED ALL RAW POTATO STARCH). Yacon boosts both bifido longum and AKKERMANSIA.

    You mentioned to me your last LFT was 35, upper range of normal, but not optimal IMHO. Youthful LFTs (ALT, AST) are more like 15 and below for males (< 12 hawwt grrls).

    Hope they get better over time for you. I think they are a good proxy for endotoxemia and LPS from vipers in the uppergut (the alcohol producing ones, yeasts, E coli, etc).

    Thank you for pushing the diverse spectrum of plant polysaccharides and fiber for optimal gut health. I know you helped me advocate 7 steps and encouraging the whole fiber spectrum/RS3, and again I appreciate you mentioning diversity here. Gut flora diversity is the key to health and longevity.

    You are a fantastic and intrepid experimenter!! thx

    1. My Akkermansia was .07 while supplementing with RPS, .19 on high fiber RS3/Inulin.

      Latest ALT and AST from Oct 2014: 17 and 16, respectively. The ref ranges given were 10-34 and 10-40. HbA1c was 5. HDL 45. I'm happy! My HDL used to run in the 20's on LC, low fiber.

  20. How do you get the raw AmGut? What is MG RAST? Thx!

  21. As we know insulin is modulated by many things -- for our gut flora, Akk is likely to be key. If you don't have the gut guardians in place -- B longum and Akk -- the barriers cannot be as strong and fortified. LPS and bacterial/yeast endotoxins leak into circulation. This ruins insulin sensitivity naturally and raises central inflammation.

    B longum makes up ~half of the bifido in healthy, disease-free subject stools and eats the same 'foods' as Akkermansia -- GOS-beans, inulin rich greens and roots, oligosaccharides (not RS2, raw starches) (Turroni et al, Fig 1B):

    Bradlow remarks 'Obese individuals show a decrease in the concentration of Akkermansia muciniphila in the mucus that lines the intestinal wall, resulting in thinner mucus and a weakened intestinal lining and permitting metabolic endotoxins formed by other bacterial flora like LPS to enter the blood steam and cause the chronic inflammation associated with obesity.'

    Horm Mol Biol Clin Investig. 2014 Jan;17(1):53-61. doi: 10.1515/hmbci-2013-0063.
    Obesity and the gut microbiome: pathophysiological aspects.
    Bradlow HL.

    Abstract While there is a large volume of literature describing a role for obesity as a risk factor for breast cancer and many other cancers, in the main a causal relationship has not been established. If the study is limited to breast cancer risk, it has been suggested that the increase in sex steroid formation that occurs in postmenopausal women plays a role. Obesity is known to be associated with chronic low grade inflammation, but no reason for this association has been offered in the past. The gut microbiome, while known to be enormous, has not in the past been considered as a metabolic role player in the body. This is now recognized to be the case. Recent studies have found the obesity is correlated with an alteration in the gut microbiome. In obese individual there is a change in the relative proportions of the two major classes of bacteria - bacteroides and firmacutes - with the latter dominant in obesity and resulting in the formation of increased amounts of metabolic endotoxins like deoxycholic acid and lipopolysaccharides (LPS). Obese individuals show a decrease in the concentration of Akkermansia muciniphila in the mucus that lines the intestinal wall, resulting in thinner mucus and a weakened intestinal lining and permitting metabolic endotoxins formed by other bacterial flora like LPS to enter the blood steam and cause the chronic inflammation associated with obesity. The change in the microbiome profile results in increases in bacterial strains that are more efficient at generating energy, leading to increased obesity. In mice, it has been shown that introducing gut bacterial flora from the cecum of obese mice into germ-free mice results in increased obesity with lesser food consumption while the reverse, introducing bacterial flora from lean mice results in a loss in weight. This raises the attractive possibility that manipulating the gut microbiome could facilitate weight loss or prevent obesity in humans.

  22. Christsenella -- Have you been tracking on your testing Tim? I have seen this go below detection limits after high dosage raw potato starch...

    (Unless VLC diet) High dosage RS2 is appearing also to be MOWING THIS SPECIES down by half or 2/3rds. WOW WTF.

    I have seen on several testing now. I bet Christsenella minuta is going extinct, just like Akkermansia and Bifidobacteria longum, no? What we feed, is that we select and get I think.

    The bacterium Christensenella minuta, a type of naturally-occurring bacteria in the stomach could fight off quick weight gain that usually leads to obesity.

    The study explored the fecal samples of 416 twin pairs in the United Kingdom and found that the said bacteria was more common in lean individuals. Also, the research team found that the abundance of Christensenellaceae bacteria was more similar in identical twins, compared to fraternal twins.

    The research team also experimented on mice, transplanting some of the microbes into mice. The procedure showed slower weight gain. The researchers were able to treat mice with the said bacterial family which made the animals gain less weight compared to mice that did not get the same treatment.

    Study leader Dr. Ruth Ley, associate professor in the department of microbiology at Cornell University, said that even though their initial findings had suggested the bacterium could be contributing to a lean phenotype, they had been fairly stunned to see its effect in mice and had repeated the experiment several times, according toreports from BBC.

    They group are also working to identify what genes influence the presence of Christensenellaceae bacteria and why it would have this effect on weight.
    "Once we have found out how it works in mice, if it seems like we can apply that to humans we can look into developing this as a probiotic to regulate weight," Ley said.
    "Our genes influence whether we are fat or thin by shaping which types of microbes thrive in our gut," according to the researchers.

  23. Dr, Grace - Since you are here, what do you consider a dangerous level of RS2? And I mean within the context of a normal, healthy diet for someone who is pretty healthy.

    1. I would like to know this, too. Your blog (Animal Pharm) is kind of all over the place. You make it seem as if one drop of RS2 hits out gut it is very bad. But it's still in your Version#3 Bionic thing. Please confirm!

  24. "I do believe that it was a huge mistake to tout ps as a panacea for all gut-related issues (not talking about you, but some people were really sure of themselves and insulted anyone who were skeptical about ps)."

    No good deed ever, ever goes unpunished. Ever.

    No matter how thinking evolves, everything must start someplace, and if it's to develop, it must have some fan base. And if it does, there will always, always be someone to deride the start of it, pretending that pointing out deficiencies is greater than the accomplishment. It always happens this way. It's very easy to fake a sense of self esteem and there are no end of people who love to see others taken down.

    But I understand the depravity of the world, embrace it even.

    Thankfully, Tim understands me better than me.

    1. ...And, neither Tim (who came up with the idea of PS) nor I, ever called it a "panacea" (whenever someone uses that word without a direct quote, they are operating dishonestly).

      We thought it would help and in case you haven't checked, the 100+ posts on FTA with 10,000+ comments clearly attest to that.

      Then, Grace convinced us to consider SBOs. I had my own great results with that (still do, my mom two...cured overnight 3 solid months of runny shit). So did others (as it stands, there are over 4,000 Amazon deliveries of SBO probiotics from the BIG 3, owing to those posts.

      It was probably Wilbur (I think) in comments, and Eddie too, who began to offer up clues as to many other beneficial fibers.

      But, I know, it wasn't 100% perfectly delivered at the outset for free.

      And naturally, I must face the consequences for even daring to promote it before it was, willing to take the risk that it would turn out to be useless or harmful (but it's's actually beneficial, but needed lots of voices to find out at what level).

      I'm just enough of an asshole to take that risk. No apology.

  25. Who's the comment moderator around here? What got deleted? Why?

  26. Dr B. G. , do you think RS2 (not just RPS -any source of RS2) should be included in a broad range fermentable fiber approach to gut health. Evolving hominids were eating raw starch for an awfully long time before the mastery of fire. You''d think our gut bugs would have developed a taste for it. And the emphasis on only getting fiber from real food seems strange to me. Mainly because modern fruits and vegetables have been so successfully bred for sweetness and tenderness they are nothing like those hominids evolved on. If it's fermentable fiber of a type that a particular gut bug thrives on, do you think they really care whether it's from real food or in a smoothie made with added fermentable fiber powders? Particularly, as Tim found out, it's actually quite difficult to get a high fermentable fiber intake from real food alone.
    Do you think eating raw starch in any regular amount, because it promotes the unwelcome strains. has no place in long term gut health? There's so many other types of fermentable fiber. Why bother with RS2 at all? For that matter do you even need RS3? All the important core strains are promoted by inulin too aren't they?
    That Scandinavian gut researcher you mentioned on Animal Pharm doesn't worry about RS at all does he? Inulin, pectin, and I forget the third type he takes.

  27. If you look at human breast milk and compare it to formula, the two main additives in recent years to make them more similar have been GOS/FOS . This has made the resulting gut population match fairly closely. (One interesting note is the LACK of diversity in breastfed infant's gut population when compared to formula fed infants. Perhaps diversity is overrated if the correct species are present.) If I understand it correctly, FOS is a type of Inulin. And PS has much the same results of GOS. So maybe a blend? In this blog post, it seems the prebiotics in breast milk tend to favor acetate production over butyrate.

    1. FOS is not a type of inulin, it is a polysaccharide (plant sugar) that generally is attached to the inulin found in plants. FOS is very sweet. Food manufacturers separate FOS from inulin and use the FOS as a low calories sweetener. It has decent prebiotic activities.

      GOS is also an interesting prebiotic and certainly has made infant formula more natural.

      My pet theory is that as ancient babies got weaned, RS was one of the first prebiotics they encountered and is very similar to GOS in prebiotic effect.

      I'm basing that on pre-chewed yams/tubers/tiger nuts that would have been easy for babies to digest.

    2. Sorry, I got that confused when I was is reading about FOS. Apparently FOS and inulin are generally found together as you say, and inulin can be degraded into FOS.

      I agree with you about ancient babies transitioning from mother's milk to foods which provide similar prebiotics as a very interesting theory. I think it was on Free the Animal where Tiger Nuts were compared to human milk as having a very close nutritional profile? My only hesitation on RS being the key is the acetate production being favored over butyrate production in breastfed babies.

      I have been experimenting with 1-4 tbs a day of PS for the last year or so. When I have stopped taking the PS, my allergies have clearly gotten worst. (I moved to HI, was living out of hotels for two months, and the stores here don't seem to carry PS.) Right now, I am around 90% better, but still have some lingering issues which I would still like to see resolved. One of which is weight loss. I have found weight loss to be difficult when taking PS. I am sure there are plenty of confounding factors, and I definitely see PS as a net positive.

    3. I would also be interested in seeing a breakdown of the different prebiotics in Tiger Nuts. All I can find is breakdown of macro nutrients and vitamin/minerals for Tiger Nuts.

    4. I found potato starch on the Big Island last year at Long's Drugs in the ethnic food aisle. It was called 'Aloha Brand' or something and appeared to have been made in Hawaii. Have a look!

    5. I am on Oahu and, now that I have a house, order it online.

  28. Got interested in gut flora based on Tim's and Dr. G's writings and so decided to do Ubiome test. Just got the results back.

    Can't find Akkermansia listed in my results anywhere (not a single mention in the Ubiome 'Compare' or 'Tree' view). Does that mean this bacteria does not exist in my gut, or is it listed with different nomenclature in the Ubiome results?

    Ubiome reports I have above average Firmicutes, below average Proteobacteria, below average Bacteroidetes, above average Faecalbacterium, above average Rosburia and really, really low Bifido and Lactobacillus

    Btw, I'm lean, in mid 60s with no digestion issues/complaints, nor other current major health issues/complaints. And no gluten or dairy sensitivities. I did quit consuming gluten products though, with the exception for beeeeeer.

    I am an APOE3/4 who had lousy blood lipid ratios, high trigs, low HDL and small dense LDL until I lowered carbs to 115-125g/day and jacked my fat consumption up to 60+% of calories per day. Also had fasting glucose and post-meal glucose levels that were probably too high - combo of lower carb and PS brought both those under nice control. All my current inflammation markers are very low.

    Hmmm...maybe I don't need Akkermansia due to my genetics? Could it be that focusing on a specific bacteria for someone's gut health will turn out to be as wrong headed as the medical community focusing on total cholesterol as the ultimate indicator for cardio health?

    I do buy-off on the gut diversity benefits and feeding the critters in a diverse fiber/RS manner. But being Akkermansia-challenged, without the obvious associated negatives, makes one wonder if the focus on individual species might be misplaced.

    1. Go to uBiome, Dashboard, Raw Taxonomy. You will see a text files full of weird names and numbers. Do a Ctrl-F search for Akkermnansia.

      You may find a line that looks like this:


      The count_norm 1183 means that my Akkermansia is at .1183%.

      Looking at my Compare, Genus, shows Akkermansia at .118%.

      If you don't see it in either place, it means they didn't detect it.

      I fully agree with you that worrying about this single species would be a big waste of your time.

      Any other surprises on your uBiome report? How much Bifido did it show?

    2. Hi Tim,

      Whoa...didn't really expect a reply. Thanks.

      I will do as you suggest for searching my Ubiome Akkermansia results.

      My Bifidobacteriales/Bifidobacteriaceae/Bifidobacterium = 0.0008%. And from what I can tell by my results, all the bad guys are well below the averages.

      I'm guessing the meager bifido %s might be related to higher than normal fat % in my diet; plus, consuming PS exclusively for several months. Before receiving my Ubiome results though, I had already decreased the PS consumption, while adding others to the mix, including inulin. I have not suffered any major gastric issues by doing so.

      I should add the context that a large percentage of my diet fat (and fiber) comes from avocados, nuts and dark chocolate on a daily basis.

      I do enjoy all vegetables but when the carb g's get above a certain point my glucose reacts poorly, and RS3 foods can cause blood sugar spikes if I'm not careful.

      With these Ubiome results, I plan to move slowly by tweaking probiotic input to better facilitate the bifido environment.

      As far as Akkermnansia, I'm not even going to worry about it since the evidence for its importance seems somewhat spotty at this juncture.

  29. To me...... personally.. From sick to health, inulin has been KEY.. as well fibers , my personal thought is one has to look at an OAT test as well to look at yeast /fungal markers. If your doing poorly with RS , odds are your natural internal yeast or pathogenic -- yeast/fungi or over grown strain from lab yeast put in beer or bread has taken control. Real foods /beer ferment with bacteria to break down yeast as well they work in a pair. Take real bread , it sits in a starter for hrs breaking down then rises and you bake.... take your trash USA bread , 30 min start to finish.. ad flour eggs baking soda , commercial packet yeast POOF bread and you bake. Everything starts in you stomach, lacto , and yeast. over growth or missing bacteria-- you are a mess. Then things can move up and down the GI track. Looking at many who complain --about RS , LOOK at your yeast levels- fungal markers (OAT testing) you have 2 things that eat in your GI track and bacteria isnt the only thing. Akkermnansia seems to be also an important bacteria... any diabetes person is missing it or has almost none. To much its not good as well. No one knows what the key exact amount is yet. Fasting shows increased levels. Healthy athletes seem to have more. What the key component is seems to work with something... Personally for my self I only have used plantain starch from chips.. I have had low bifido...I have many mutated genes.. FUT2 /card15 and NOD2 research shows people with these usually have high candida and low bifido. Seems bifido works and helps break down the wall. As time has gone on..I have very low to no yeast now. My bifido seems to be moving up now with the yeast low to gone. Time will tell -- health has been great for 3 years ( I havent had crohns or coltis in 3 years) my factor I say low yeast. (OAt testing is also a key in health testing) I ll send you my recent ubiome TIM , in email so you can see 2.5 years ago to todays. For me in research specific bifdio strains seem key and may be alot better then others ...We are born with certain bifido strains... many in probiotics dont seem to be the best

  30. Hello Tim

    Unfortunately Ubiome do not exist yet in Europe, but Genova does. So I have decided to take GDX 2200. Specially after reading this:

    What the article doesn't explain is if the gut flora goes back to pre-Pregnancy stage, after pregnancy or breastfeeding is over or before.

    Some of my third trimester symptoms are not completely gone and now I have problems with my throat. I don't know what is going on :(