Friday, September 5, 2014

RS2 vs RS3 Put to the (Gut) Test! Part 2

I love all of the gut tests available to us now!  The two that have gotten the most attention are American Gut and uBiome.  Neither require a doctor's orders and are relatively cheap ($99 and $89 respectively).  uBiome gets you a report in about 6 weeks, while AmGut takes 6 months.

I think both tests are far from perfect, as Mr. Heisenbug recently discussed:






Later,
Tim
 
Edit to add my full AmGut Taxa Report from 2013:

Kingdom Phylum Class Order Family Genus Relative Abundance (%)
Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides
46.52
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae ---
13.06
Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium
11.32
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae ---
5.27
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium
4.81
Bacteria Firmicutes Clostridia Clostridiales --- ---
2.21
Bacteria Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae ---
2.10
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae ---
1.69
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Paraprevotellaceae] Paraprevotella
1.25
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Sutterella
0.96
Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Parabacteroides
0.91
Bacteria Tenericutes Mollicutes RF39 --- ---
0.90
Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Phascolarctobacterium
0.79
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnobacterium
0.78
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus
0.76
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia
0.76
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Barnesiellaceae] ---
0.64
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira
0.53
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus
0.50
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospira
0.48
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Roseburia
0.41
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Paraprevotellaceae] ---
0.38
Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio
0.37
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus]
0.27
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Odoribacteraceae] Butyricimonas
0.24
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Dorea
0.23
Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella
0.21
Bacteria Bacteroidetes Bacteroidia Bacteroidales --- ---
0.13
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Odoribacteraceae] Odoribacter
0.12
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus
0.12
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae [Eubacterium]
0.10
Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae ---
0.10
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella
0.09
Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Akkermansia
0.07
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae ---
0.07
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Anaerostipes
0.07
Bacteria Lentisphaerae [Lentisphaeria] Victivallales Victivallaceae ---
0.06
Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
0.05
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium
0.05
Archaea Euryarchaeota Methanobacteria Methanobacteriales Methanobacteriaceae Methanobrevibacter
0.05
Bacteria Firmicutes Clostridia Clostridiales [Mogibacteriaceae] ---
0.04
Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Dialister
0.04
Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus
0.03
Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Bilophila
0.03
Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae ---
0.02
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae SMB53
0.02
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae Oxalobacter
0.02
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Finegoldia
0.02
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae ---
0.02
Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae Neisseria
0.02
Bacteria Actinobacteria Actinobacteria Actinomycetales Corynebacteriaceae Corynebacterium
0.02
Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae ---
0.02
Bacteria Cyanobacteria Chloroplast Streptophyta --- ---
0.02
Bacteria Firmicutes Clostridia Clostridiales Dehalobacteriaceae Dehalobacterium
0.01
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Slackia
0.01
Bacteria Actinobacteria Actinobacteria Actinomycetales Micrococcaceae Rothia
0.01
Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae ---
0.01
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae Holdemania
0.01
Bacteria Firmicutes Bacilli Turicibacterales Turicibacteraceae Turicibacter
0.01
Bacteria Firmicutes Bacilli Lactobacillales Leuconostocaceae Leuconostoc
0.01
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae ---
0.01
Bacteria Firmicutes Clostridia SHA-98 --- ---
0.01
Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae Granulicatella
0.01
Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas
0.01
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Limnobacter
0.00
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Anaerotruncus
0.00
Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae ---
0.00
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus
0.00
Bacteria Firmicutes Bacilli Lactobacillales --- ---
0.00
Bacteria Bacteroidetes Flavobacteriia Flavobacteriales [Weeksellaceae] Chryseobacterium
0.00
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Adlercreutzia
0.00
Bacteria Actinobacteria Actinobacteria Actinomycetales Propionibacteriaceae Propionibacterium
0.00
Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
0.00
Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Haemophilus
0.00
Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Morganella
0.00
Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Enterobacter
0.00
Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae ---
0.00
Bacteria Proteobacteria Betaproteobacteria Rhodocyclales Rhodocyclaceae Thauera
0.00
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae Janthinobacterium
0.00
Bacteria Proteobacteria Betaproteobacteria Burkholderiales --- ---
0.00
Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium
0.00
Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Brucellaceae Ochrobactrum
0.00
Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas
0.00
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae cc_115
0.00
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae Coprobacillus
0.00
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Peptoniphilus
0.00
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Parvimonas
0.00
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Anaerococcus
0.00
Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Veillonella
0.00
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Caloramator
0.00
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae 02d06
0.00
Bacteria Firmicutes Clostridia --- --- ---
0.00
Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
0.00
Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae ---
0.00
Bacteria Firmicutes Bacilli Lactobacillales Aerococcaceae Aerococcus
0.00
Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
0.00
Bacteria Bacteroidetes Bacteroidia Bacteroidales [Paraprevotellaceae] [Prevotella]
0.00
Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae ---
0.00
Bacteria Actinobacteria Actinobacteria Actinomycetales Actinomycetaceae Actinomyces
0.00


113 comments:

  1. Tim - yes please update on Nancy. It was reading Chris Kresser's article and your comment about Nancy and morganella morganii that prompted me to look at my Australian stool test and realised I too have this bacteria, however I don't know if its pathogenic strain or not. I had fecal transplants in December and I'm fairly certain that's where it came from as I never had this show up on previous stool tests. It seems the clinic I went to does not do thorough testing of donor stool, they check for things like HIV and Hep B but not for other things. Very disappointing.

    I'm trying to avoid antibiotics so am instead doing a biofilm protocol (as the streptococcus overgrowth in my gut has returned) along with targetted antimicrobials including the herb Sage (salvia officinalis) as this seems to be the most effective in the literature I could fine. I am also tossing up using PEG to do a washout.

    I was using potato starch and banana flour (and seemed to have looser pants!) but stopped when I saw your comment about morganella morganii.

    cheerio
    AJ

    ReplyDelete
    Replies
    1. I think almost everyone has Morganella, it showed up as .001% in my AmGut but not at all in the uBiome. I think it's one of those 'lurkers' just waiting for an opportunity to grow out of control and take over.

      I just heard from Nancy! She is doing well and getting ready to do another gut test. She's been doing potato starch, RS foods (tiger nuts!), and probiotics.

      Good luck with what all you are doing, too. Let us know how it turns out.

      Delete
    2. Correction: Nancy does NO potato starch yet! She said that when she tried, she could not tolerate it at all, but is looking forward to adding it soon.

      Delete
    3. Thanks Tim :)


      No idea why the morganella would suddenly show up in such large amounts after fecal transplants which are supposed to be curative for dysbiosis! I have putrefaction so maybe something is going wrong there with animal protein digestion allowing it to overgrow (but this was present before fecal transplants too).

      I noticed on an MDA thread you mentioned Factor S and gut bacteria for sleep - do you have any good links I can read up about it further? Specifically about the gut bacteria link (as I've found general Factor S info).

      thanks

      Delete
    4. Oh, I seem to tolerate RS fine. I only stopped it when I ready about Nancy and how it could possibly feed pathogens. I did benefit from taking it with psyllium (rotated with green banana flour) - clothes were looser.

      Delete
  2. Fascinating results, thanks for sharing. Btw, low Akkermansia has been linked to obesity/metabolic syndrome.

    http://www.pnas.org/content/110/22/9066.full

    ReplyDelete
    Replies
    1. Akkermansia is a funny one! My wife (always skinny) had 4.5% Akkermansia while I had less than 1%...you'd think some of that would rub off on me!

      Delete
  3. What a long post, could you make it shorter next time, as I almost missed the question directed to me :-)

    Well, Oxalobacter formigenes is the one that feeds on oxalate and it is advisable to have it. Unfortunately, this poor bacteria is one of those always affected by antibiotics.

    If not metabolised by bacteria, the oxalate levels in the colon go up and some troubles start developing (think kidney stones, but not only that), and people feel they have to go on low oxalate diet, which is also not good, as they miss a lot of beneficial foods.

    Fortunately there are other bacteria that CAN metabolise oxalate but the question is if they do.

    A good news is that Oxalobacter can be reintroduced.

    But we do not see if Tim has Oxalobacter formigenes or the other one...

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    Replies
    1. That is really interesting. Is this found in soil?

      Can anyone point me in the right direction to find out if different SBO's inhabit different soil types and soil strata?

      I'm looking at things like the deep tap rooted medicinal plants, things like burdock. My hunch is that part of the benefit of root medicines come from the microbes they carry.

      Delete
    2. Thanks, Gemma! Interesting. I wish these reports went down to the species level.

      Wildcucumber - Sure, the SBOs are found all throughout the soil, but they are concentrated, as you guessed, on plant roots. The people who discovered antibiotics found them while studying soil bacteria.

      SBO is kind of a misleading term, because nearly all of the microbes we call 'probiotics' can be found in the soil, and especially around plant roots.

      Delete
    3. Thanks Tim - I'm trying to figure out if there are specific plant/microbe relationships ie roots of yarrow having different microbial partners, than say, mullein. Sorry, going off topic here...

      Delete
    4. No, I love the topic! If I was rich, I'd be testing my garden soil as much as my poop.

      Different plants definitely have different sets of microbes. Legumes are known for attracting nitrogen-fixing bacteria, and my uBiome showed several different types of nitrogen-fixers in my gut.

      Here's something to read: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394661/

      Root Biology is a science all its own, people spend their whole life studying it!

      Delete
  4. Why do conclude that some might 'have done irreparable damage' when your tests show that you have increased almost all of the microbes with eating real food? I realise that you're still below average in some but if you can improve from any level then I can't see the damage is 'rreparable'.

    In any case, very interesting to see. I just saw shipping to Denmark is only $20 - there is no excuse now :)

    ReplyDelete
    Replies
    1. I really don't think the averages mean much because most people eat crappy food. It's just good to see where you stand with other test participants.

      I also don't thinking being above or below average can tell you a whole lot, either. Who knows why I have so much Bifido and almost no Prevotella? Does that mean I'm right and others are wrong? Probably not.

      I like to think that we can get the microbes we need if they are lost from antibiotics (or for whatever reason). It's a shame that modern medicine isn't more advanced in this area.

      Delete
    2. I agree that it might not mean much to compare with the entire population.

      My point is that you have increased almost all of the microbes, which is good. So someone coming from a crappy diet 'should' be able to improve their microbes too - not necessarily perfect them though.

      Delete
    3. Yes, unless the gut has been overtaken by pathogens (such as Nancy's 25% Morganella) or yeast. In which case eating a diet like I recommend can make things immeasurably worse.

      If someone has terrible digestion, best to find out why and work on clearing them out, either naturally or with antibiotics (sad to say).

      Two years ago, I was a firm believer that everyone could just eat right and get good guts--that idea has changed after seeing so many sob stories of broken guts and the problems caused by RS, etc...

      For instance, Nancy would get instant diarrhea with just a small spoonful of potato starch.

      Delete
  5. I forgot to ask. How much inulin did you take before the experiment? Did you ever do any tests to see how inulin impacted your blood sugar? From what I can read it should have minimal impact and the caloric value is only 1.5/1g because most of it isn't digested.

    ReplyDelete
    Replies
    1. None, really, other than what was in my food. Dandelion greens a couple times a week, onions, garlic, too. I haven't played with inulin much at all and haven't tested BG with it, but I assume it wouldn't spike blood sugar at all.

      Delete
    2. Thanks. You just mentioned it in the previous post and I wasn't sure if you actually used it.

      Delete
    3. Inulin is hard, hard, hard to get in a real diet. I couldn't find Jerusalem artichokes anywhere, so dandelions were the only real source. There is lots of inulin in nature, and in paleo food sources (the real paleo foods!), but not in our current food supply.

      Delete
    4. Tim, can you grow Jerusalem artichokes where you live? We did a big planting of them this spring. They should be ready soon. We had some in our garden years ago and had some good recipes for them, but we couldn't stand the farting. We only ate them occasionally back then because of that, and then finally just got rid of them. So it will be interesting to see if eating them regularly along with all our other fermentable foods will decrease the gas over time.

      Delete
    5. No, they don't grow here. Leeks and some onions do well. Garlic is iffy.

      Delete
  6. Tim, do you know anything about this guy? http://wid.wisc.edu/featured-events/c4-public-lecture-meet-your-inner-microbial-zoo/ I'm wondering about going, but the lecture description sounds a little over my head.

    ReplyDelete
    Replies
    1. No, never heard of him. Looks like an interesting lecture, but probably above my head, too! Let us know if you go--take notes!

      Delete
  7. So interesting. The only time I had anything "loose" was while taking a certain antibiotic. It was very like the way a C-Diff infection sounds - that bad. But, the second I stopped the antibiotic - early, obviously - I was back to constipation. I'm amazed I could go from one extreme to the other so quickly.

    ReplyDelete
    Replies
    1. Fun Fact of the Day:

      The contents of your large intestine are liquid until the last 12" or so. A big job of the large intestine is to control hydration of feces.

      Delete
  8. What do you all think of the fact that the hadza tribe showed no bifido?

    ReplyDelete
    Replies
    1. I think it just 'is what it is.' I would love to see a Hadza baby's gut sample, surely they must have bifido. When do they lose it? Why do we keep it? This is why there can be no one perfect gut biome. I'm sure it depends on local conditions, diet, genetics, etc...

      The only thing I think that my gut test shows conclusively is that eating RS3 instead of RS2 did not cause a big crash in any important microbes nor allow a pathogen to take over. Diets low in fermentable fiber have very little of the Clostria Clusters that produce butyrate and other SCFAs, that's the 'big deal,' really.

      Delete
    2. Sure. Apparently they have none at all, but I think they haven't tested infants.
      http://www.nature.com/ncomms/2014/140415/ncomms4654/full/ncomms4654.html

      "Complete absence of bifidobacteria, as observed in the Hadza, has never to our knowledge been reported for any other human group."

      "Future work must focus on the GM of breast-fed Hadza infants to determine the role of bifidobacteria in the kinetics of assembly and development of the Hadza GM, and to learn whether this bacterial group is completely absent in all Hadza, including infants, or whether it is definitively lost from the gut ecosystem post weaning. It is important to note that while bifidobacteria are considered a beneficial bacterial group in western GM profiles, their absence in the Hadza GM, combined with the alternative enrichment in ‘opportunistic’ bacteria from Proteobacteria and Spirochaetes, cannot be considered aberrant."
      "these findings illustrate a need to reevaluate the standards by which we consider GM ‘healthy’ or ‘unhealthy’, as they are clearly context dependent."

      I'm with you, it is what is. But it certainly shows that we needn't think of high bifido or even complete absence of bifido as markers of health.

      Delete
    3. You are very astute.

      Have you heard of the re-POOP-ulate project? A team of Canadian scientists have developed a blend of microbes to use as a fecal implant to fight C-diff infections.

      Their recipe is: http://www.microbiomejournal.com/content/1/1/3/table/T1

      It's almost the entire Clostridium Cluster chart plus a few more.

      Another strange thing in my report: No E.coli.

      E. coli is considered a universal microbe in humans...where is mine? It's even in the rePOOPulate recipe.

      Delete
    4. Me?... Astute...? Nah! Feel totally stupid most of the time. My gut was a total mess. I'm just trying to figure some things out. All I really know is that most doctors have absolutely no idea, and could even be said to be giving us stuff that is to our detriment! I could rant about that but will refrain.
      YOU are the one that figured this stuff out!

      Hmm... maybe it is the ph of the gut, plus all that it entails (tighter junctures, better overall environment, simply getting fermentable fiber in the first place), that is more important than the various strains... ???

      Off to look up what a Clostridum Cluster is... !

      Delete
    5. "What do you all think of the fact that the hadza tribe showed no bifido?"

      If I remember well, it was mentioned in the study (or elsewhere) that bifido were acquired by humans via interacting with domestic cattle, where the bifido comes from.

      The whole human population originated in Africa a very long time ago and migrated to the other parts of the world, carrying both their own genes and their gut microbiome, both changing on the way as people were meeting and mating with other populations, meeting new pathogens and eating new food sources.

      Hadza, one of the few human groups that never left Africa, and never kept any domestic cattle. MAYBE that is why they show no bifido. But that does mean that the function bifido perform in our babies (when normally born and breastfed) is missing in Hadza. It is simply performed by other bacteria with who knows what names. And there were many surprises in Hadza guts!

      That is why the researches study also the functional gene diversity of the gut microbiome, not only the taxonomy (a big part of Hadza microbiome had no names anyway). That means they study not only what bacteria you have, but what they can do, what enzymes they are able to express etc.

      Delete
    6. Errata: should be:
      But that does NOT mean that the function bifido perform in our babies (when normally born and breastfed) is missing in Hadza.

      Delete
    7. Good memory!

      "We hypothesize that the lack of bifidobacteria in adult Hadza is a consequence of the post-weaning GM composition in the absence of agro-pastoral-derived foods. Support for this hypothesis comes from the observation that other populations in which meat and/or dairy consumption is low to absent, such as vegans and Koreans, also have very low representation of Actinobacteria and Bifidobacterium. The continued consumption of dairy into adulthood could be one reason most western populations maintain a relatively large bifidobacterial presence. Aside from bifidobacterial species of human origin, the majority of Bifidobacterium have been isolated from livestock animals such as swine, cattle and rabbit. The Hadza neither domesticate nor have direct contact with livestock animals. Thus, as they lack exposure to livestock bifidobacteria, this raises the question of whether the necessary conditions for interspecies transfer and colonization of bifidobacteria do not occur for the Hadza."


      Delete
    8. Also
      "In our study, more than 33% of the total Hadza GM genera remain unidentified."

      Delete
    9. Agreed, Gemma. That's what I was thinking too. I guess people who consume zero dairy products also have no bifidos. A lot of people are dairy averse these days even if they have no problem with lactose or casein. And they don't eat fermented dairy either. Tim does. Maybe that's why the 'average' bifido in the Ubiome studies is so low.

      Tim, would be interesting to not consume any fermented dairy for a couple of months and see what effect that has. Or have you tried that already?

      Delete
    10. Gab - I know, I would love to have 6 of these kits and do a sample for a different style of eating every two months.

      But, I think watching the ebb and flow of microbes is nothing more than a way to pass the time, it doesn't really mean a whole lot other than the fact that you harbor a colony of individual microbes that change with the food you eat.

      What I think is more important is to find people with severe gut dysbiosis and test them, see what pathogens lurk and what is missing, then try to get rid of the pathogens and build up the good microbes using just food interventions.

      On my milk consumption. I don't drink milk, haven't had a glass since I was about 10. When I was doing the first test, I tried some kefir, but didn't much care for it, and was not eating yogurt at all, and still had 12% bifido or so. On the second test, I was eating yogurt almost daily because I wanted to see if it would boost my nearly non-existent lactos. It didn't.

      Delete
  9. About onions, most days I eat a whole onion, half in the morning, sauteed with eggs and peppers, and the other half at night, sauteed and added to some kind of cooked protein. I saute the onions for about 7-9 minutes on medium heat. Am I doing any good, or does it (the onion or garlic) need to be consumed raw to get the benefits?

    ReplyDelete
    Replies
    1. I think cooked is fine, better on some regards.

      Here is a paper that looked at certain markers of onions when cooked:
      http://www.ncbi.nlm.nih.gov/pubmed/11349895

      "We examined the following cooking methods: boiling, frying with oil and butter, and microwave cooking. Various cooking methods do not consider the degradation of quercetin conjugates when cooking onion. Microwave cooking without water better retains flavonoids and ascorbic acid. Frying does not affect flavonoid intake. The boiling of onion leads to about 30% loss of quercetin glycosides, which transfers to the boiling water."

      So unless you are boiling the onions, I'd say cooking is fine.

      Delete
    2. If you're making a stew or the like you would drink/eat the cooking water too getting the good stuff anyway.

      Delete
    3. "does it (the onion or garlic) need to be consumed raw to get the benefits?"

      I think rotating both methods would be better, as heat can destroys some enzymes.

      There are many traditional ways that help provoking the create and release of the protective compounds we are after.

      If you eat the plant part very fresh, as it is, you may miss some, as they are simply not there. Only a stressed plant starts creating the protective compound as it thinks it was attacked by en enemy.

      So for instance garlic releases its enzymes after is has been crushed and mixed with some salt, and left sitting for some 15 minutes. The cell walls are damaged, enzymes released. It tastes even better like this than completely fresh.

      A nice, traditional recipe to include garlic: Aioli (raw garlic, egg yolk, olive oil, lemon juice, salt). http://en.wikipedia.org/wiki/Aioli


      Delete
    4. Gemma, since enzymes are protein and made of amino acids, wouldn't stomach acid and enzymes degrade ingested enzymes anyway? Isn't this why pancreatic type enzyme supps are encased in (brain fart time....) stuff that doesn't dissolve in the stomach but does dissolve in the duodenum?

      Delete
    5. something about Paleo diet must be working because about 6 months ago if i tried to eat raw onion i would get terrible pain within 10 minutes or so. Yesterday i tried about a half onion just to test and had no pain whatsoever. :)

      Delete
  10. Gabriella, you asked :-)

    Garlic clove DOES NOT WANT to be eaten, therefore up-regulates its defense when attacked by such a brute force. It tries to cause harm even after it is eaten.

    The list of beneficial compounds is very long, many still unexplored and the effects not explained. Garlic was proven IN VIVO to be anti-bacterial, antiviral, anti-fungal, anti-cancer, anti-parasitic, anti-inflammatory, even anti-wrinkle :-)

    Therapeutic Uses and Pharmacological Properties of Garlic, Shallot, and Their Biologically Active Compounds
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874089/


    and here we have the anti-wrinkle effect:
    Anti-wrinkle and anti-inflammatory effects of active garlic components and the inhibition of MMPs via NF-κB signaling.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774756/

    ReplyDelete
  11. while i was looking at Amazon reviews i saw this excellent 14 pg protocol for SIBO and Candida. they say it would also work for leaky gut.

    Hope its ok to post, i think many folks would find it useful and they seem to have covered all the bases from l-glutamine to chlorinated water to fermented foods and on and on. Kind of depressing to think that it may take all the things that they recommend to cure the gut because i dont think i can afford them all.

    i was hoping prescript assist and the 2 other probiotics along with some RS and sauerkraut would do the trick but i kind of doubt it now. :(


    http://bit.ly/antisibo

    by John Herron and Laura Christenson Barker

    hope thats ok

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  12. was wondering what is the cost to get one of those stool tests like metametrix? i thought it was like $400 or so but the site doesn't quote any prices.

    What have other people been doing and do you need a doctor to request one?

    thx.

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    1. Metametrix requires a doctor and can be expensive without insurance! It is a totally different kind of test than AmGut or uBiome. It won't show the diversity or individual populations, just a broad overview of how you fit in with others who have had the test.

      It will show much more than uBiome and AmGut in the way of overall gut health...SCFA levels, pH, and other markers. It's a diagnostic tool for health. AmGut and uBiome are just a look at what microbes you have and not used by medical professionals.

      Delete
    2. @wondering

      and Hello TIM and GEMMA been reading some of your stuff here!!!

      Wondering another option is great plans lab ---645.00 will get you there OAT (urine) and COMP STOOL tests very good at PH, yeast markers break out of SCFAs etc vitamins ...bacteria and yeast markers etc

      the stool readings like TIM says are very basic broken out as 1x 2x 3x 4x or NONE not really telling you strain or type just levels. Where the AMgut and ubiome are so C@@L..... a great tool you GP can sign for the great plans or Metametrix test they will be clue less reading it thou..all up to you ( or you can chat with the lab and they can explain more of your results)

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    3. thanks Tim and Edward for the info.

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    4. @wondering - Check out directlabs.com. They have quite a number of the Metametrix and Genova Diagnostics tests at a discount. And they don't require a doctor's Rx. Go to the Order Tests section and look at Gastrointestinal in the Category dropdown. I've been told that there are some tests that they aren't allowed to show on the website, but are actually available if you call and ask about them. To compliment the results from the tests, both Metametrix and Genova have guides for each of their tests, which have detailed interpretations of the results. HTH

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  13. Fine post, very informative, Tim.

    I'm also doing some experimentation w/ those critters. Wrote a post about uBiome and will be following up with my results.

    Yep.

    -Joe

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    1. Nice! I just put you on my blog list so I can catch the results. Nice blog, by the way.
      Tim

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    2. Appreciate the compliment Tim, esp. from you.

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  14. Hey Tim, awesome, thought-provoking post and great to see the new blog. Your mystery of no E. coli might be a matter of fiber lowering pH where E. coli are pH sensitive. With all that dietary fiber, you must have a high acid gut, but it's also the quality of acid and if pepsin is inhibited based on soluble vs. insoluble fiber. Apparently, it's pepsin that counts in lowering E. coli.
    http://jmm.sgmjournals.org/content/55/9/1265.full
    http://www.ncbi.nlm.nih.gov/pubmed/24394334

    You probably have E. coli, but it just didn't register and would be raised if you reduced fiber intake based on pH and quality of gastric acid. E.coli, as you point out, is a keystone species. I was surprised to learn recently how it's one of the very first microbes to appear in the infant microbiome along with Bifidobacteria. They both stimulate the infant immune system in Peyer's patches of the small intestine (B-cell maturation). So, maybe it's Proteobacteria like E.coli doing the job of Bifidobacteria in populations like the Hazda (and Koreans, etc.) where Bifido is found reduced or absent. E. coli gets a bad rap.
    http://www.jimmunol.org/content/188/9/4315.long

    I've been wondering about crossfeeding between E. coli and Bifidobacteria where E.coli produce ammonia from nitrogen and Bifido lower ammonia.

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    1. Hey, Keith! Thanks for stopping by.
      Interesting what you say. I would love to see a before and after with someone who has loads of e. coli or well-known pathogens. I was surprised, too, by lack of e. coli. I just added my full AmGut taxa report at the end of the article above, you'll see very little of any proteobacteria, and the only possible place e. coli could be lurking is the line that lists .02% of an unknown genus in the family Enterobacteriaceae. So, it's possible I have some e. coli.

      I had my pH tested a while back, it was 5.7, I think, on the low edge of normal.

      Domain: Bacteria
      Kingdom: Eubacteria
      Phylum: Proteobacteria
      Class: Gammaproteobacteria
      Order: Enterobacteriales
      Family: Enterobacteriaceae
      Genus: Escherichia
      Species: coli

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  15. Take a look at the pie charts in this blog (you've probably seen this before).
    http://humanfoodproject.com/going-feral-one-year-journey-acquire-healthiest-gut-microbiome-world-heard/
    When Jeff stopped eating fiber, proteobacteria appeared out of nowhere. He explains the overall shift to Bacteroides as raising pH which makes sense, however, I think it's also about meat mowing down Firmicutes via nitroso compounds produced in meat fermentation. The shift seems too radical to be explained by pH alone.

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  16. Wow,
    Hadza microbiome: Oxalobacter formigenes, Bifidos present up to age 5 and much more discussed in a new blog by Jeff Leach. And yes, some news on FT from Hadza donor.
    (Re)Becoming Human: what happened the day I replaced 99% of the genes in my body with that of a hunter-gatherer
    http://humanfoodproject.com/rebecoming-human-happened-day-replaced-99-genes-body-hunter-gatherer/

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    1. I just read it. Great article on our Ancestral Gut Microbes! I love this bit that Jeff wrote, and it's just as we have been saying around here. I think soon Jeff will be on the RS Bandwagon, maybe even drinking super-fiber smoothies!

      " I think the dominance of Bacteroides in the western gut has to do with pH levels, which is “mainly” driven by fermentation of dietary fiber (fermentation of fiber equals more SCFAs and thus a more acidic colonic environment which strains of Bacteroides don't like). So with the average American eating less than 20g of fiber a day – pitiful – we are likely lugging around the most alkaline guts in human history which in turn is allowing certain species of Bacteroides (and some opportunistic pathogens) to flourish. Again, if we squint for a moment and lean on the gut of the Hadza, then maybe we shouldn’t let Bacteroides dominant our gut – and by doing so, who else is getting nudged out or down and potentially dragging us closer to ill health? I suspect the Hadza keeo Bacteroides levels low with their high, daily levels of dietary fiber which keeps their colonic environment very acidic. In addition the high protein-fat and sugary argument doesn't hold with the Hadza either as they will often gorge on meat-fat and eat piles of sugary honey for weeks on end during the wet season - and we see no blooms in Bacteroides when we sample during these periods. It's the Fiber Stupid!"

      Delete
  17. Dr. B G said...
    Even warm has substantial RS3 (except rice -- Tim Steele read all of the rice charts wrong; hat tip Gemma).

    Is this true?

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    1. As to the 'warm' part - I don't remember what she was talking about, but probably saying that you can reheat cooked RS sources and still get RS. Yes, that's true.

      On the rice...if you look at the big RS chart I made a couple years ago,

      http://freetheanimal.com/wp-content/uploads/2013/08/Resistant-Starch-in-Foods.pdf

      The values for rice are right, in the 2-5% range (not much). It was just that later on, we were finding tons of studies that showed rice was more like 10-15% or even higher.

      Ever-vigilant Gemma figured out the disparity, these papers were looking at dried weights and not cooked, as-eaten, weights making the RS content seem much higher than it really is.

      So, as the original list showed, rice is not the greatest of RS sources.

      Delete
  18. Great report and writing Tim,so very interesting,,keep up the good work

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  19. Hey, fascinating writeup! Apparently there are also significant variations in the human microbiome over quite short periods of time (see this article http://www.ncbi.nlm.nih.gov/pubmed/21624126), so that could be involved.

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  20. Couple of questions please !

    I am looking for most convenient ways to get enough inulin and RS3 in my diet and so far 2 choices seem practical:

    1. Red lentils - in the resistant starch pdf you created it is stated it contains 13.8 grams of RS and in the chart on "Dietary fiber" article it is stated it contains 4g of inulin which seems solid, so 300g of red lentils per day pretty much covers all my RS/fiber needs?
    Btw are those numbers for cooked and cooled red lentils?

    2.Roasted and cooled potatoes also seem convenient for RS3 but I am still unsure what roasting actually means, is that simply baking in a oven at 200 C or so?

    Any other ideas how to easily get the needed RS3 and inulin from food?

    Thank you very much for all your help !

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    1. All you really need to do is to start incorporating foods that contain RS and inulin on a regular basis and let the numbers fall where they may.

      For instance, I started today with a slice of dried green plantain (10g RS2), then ate a small handful of cashews (1g RS1). My lunch was a previously baked potato, reheated, with a spoonful of chili on top and some fresh mushrooms (10g RS3). For dinner, I will thaw out some rice and make a stir-fry with asparagus, onions, garlic, other veggies and chicken (5g RS3 + 5g inulin).

      So that's like 30g+ of RS and inulin combined. I doubt my counts are exact, but you can see it's easy to incorporate these foods into your diet. Well, not a low-carb diet, but a real-food diet.

      There are days I get stuck eating in a restaurant or don't get to eat how I like...these days I'll make a nice smoothie in the evening with inulin powder, potato starch, a green banana, or a raw potato...the powerhouses of fiber.

      But some other ideas for you: Add cooked or raw onions and garlic to every meal. Try slicing and drying green plantains. Try the smoothies with a small, raw potato. Pre-cook and store all your starches in the fridge or freezer. For inulin: Asparagus, onions, garlic, Jerusalem artichokes.

      Snack on nuts if you must snack.

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    2. Tim, can Green Plantains be used RAW? I think the ripe ones can, but when it comes to green ones, the recipes always call for cooking?

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    3. Yes, but they are pretty much inedible. I've heard of people putting them in smoothies. I like to take plantains that are completely green and slice into slabs and dry them out and eat like crackers. I think green plantains are probably one of the world's healthiest foods.

      When completely green, regular bananas are almost the same exact thing as green plantains. I usually buy a bunch of very green bananas every Friday. Saturday and Sunday I will slice one and eat it while drinking my coffee. You need something to wash it down with.

      To peel green bananas or plantains, cut in half long-ways, then work the meat out of the skin with your fingers and fingernails...takes some practice, but it's the easiest way I have found.

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    4. Thnx Tim, I was wondering if eating plantains green is BAD for you, or just not tasty... Since you think they are OK to consume raw, I will start putting some in smoothes...with all the other goodies and Stevia - not a problem.

      Delete
    5. I too have eaten several raw bananas and plantains with no obvious bad effects. Except that I just can't get past the taste, and the calories seem too high relative to the fiber. (Beans are similar in the calorie to fiber ratio, but I love them and eat them a lot. You'll never hear me say that I love a green banana.)

      Regarding Tim's earlier suggestion to add garlic and onions whenever possible, I've been looking into that quite a bit. It's something I do. The research is overwhelming - it's a popular research area. As I read it, there is quite a variation among types of onoons, as well as parts of an individual onion. Red onions are different from yellow in the flavonoids they provide. Green is very good and are suggested to be closest to wild (uncultivated) onions. The skins, tops, and bottoms of onions provide varying fiber types, and the bottoms have more minerals. From experience, I know that the roots of green onions are significantly sharper in taste than the rest of the onion. I believe I read once, but have been unable find since, that the onion skins normally tossed have nearly 75% of the quercetin in an onion, something that might be important to hypertensives. Garlic skins seem similar. It is my belief at this time that adding onion and garlic skins to an already "complete" diet can provide many benefits.

      Delete
    6. When cooking soups and stews, I have always tossed in the whole onion or garlic, peel and all, and separated the skins and bits out after it's cooked, but usually find most is fine just left in.

      I think leeks are underrated, too.

      Have you caught on to the "crush and rest" advice?

      Delete
    7. I caught on to that advice after reading Jo Robinson's book, "eating on the Wild Side". My wife and I have a very choreographed routine in the mornings where I chop half a bulb of garlic for my omelette and let it sit while she gets my kid ready for school. She then cooks me the best garlic and onion garlic one could imagine. Farm eggs and cheese from 100% grass fed cows, of course. Topped with Carolina Reaper-habanero hot sauce fermented, along with more garlic, in my basement. Hot barely describes it. The heat just as much reflects the garlic and onion as the hot sauce, I think.

      As much as possible, I try to keep everything as raw as possible. So the skins I chew on while chopping the onions and garlic. I once swore they were inedible, but they actually break down mostly after a few minutes. Oddly, I find them milder than the "meat" of the onions and garlic. Except for the roots of green onions which definitely burn.

      Every study I've run across says that whatever compound is degraded by heating, but from very little to a lot. None says heating helps. For example,

      http://www.ncbi.nlm.nih.gov/m/pubmed/22881190/?i=6&from=/16388813/related

      This is just one of very many.

      I keep buying leeks and never using them. I don't understand why. Part of the problem I think is that I have often read that the green part is the best, but the ones I see in the stores are almost all white. Cultivation at work, I guess.

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    8. Seems we had a paper around here that showed allicin from crushed and rested 10 minutes garlic could be cooked and still retain allicin, but can't seem to find...I'll put it here if I can find it.

      But, those skins. I think the skins are part of the magic in nuts as well.

      Almond skins antibacterial, fight H. pylori

      Almond skins grow Bifidobacteria

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    9. The allicin paper with crush/rest advice here, anti-cancer effects tested on rats:

      The Influence of Heating on the Anticancer Properties of Garlic

      Basically Wilbur is right, thermal treatment destroys some of the allicin, even when crush/rest method is used, but some is still there, the anti-cancer effects are only reduced.

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    10. Tim, speaking of soups/stews... Last night as an experiment I threw in a handful of dried tigernuts into a chicken/veggie stew. After a low simmer of around 40 minutes, wow, very nice. They rehydrated and plumped up. Added some nice extra crunchy tidbits to the stew. Kinda reminded me of the effect (not taste) of water chestnuts in chinese food. Good way to add some extra fiber to a soup/stew. So many uses these little crunchy tubers have.

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    11. Thanks, Gemma.

      Brad - I had not considered using tiger nuts in soup/stew! Great idea. I'll try this weekend. Along with garlic skins. My wife will not like, I can guarantee!

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  21. Tim, would adding the raw potato and/or raw potato starch to any smoothie containing fruits, blunt the glycemic response from the fruits? (I think this is similar to the FTA mashed potatoes concept?)

    Also, with respect to the potato jacket or skin - any issues with eating that part raw or cooked? also thinking that for a bit of dirt, to not wash them lol - but heck, I get mine from the grocers, who knows what they have been in a long the way.

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    1. No idea...you'd have to check with a BG monitor. Do you have one? If not, pick up a cheap one at Wal-Mart and 50 test strips, it will set you back about $50 put it's fun to track your FBG and post-prandial spikes. Take a reading every 10-20 minutes after eating to get a good feel for your insulin response.

      I always peel store bought potatoes or scrub well if baking. Grow your own or find a good organic source nearby, some places do 'dig-your-own' potatoes and right now is the season in many places.

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  22. Tim,
    Is it true that RS2, although butyragenic, doesn't feed the core microbiota very well, but RS3 does? So does RS2 do anything special that RS3 can't do in your colon? Apart from being more convenient of course.
    Also does RS generally do something that other fermentable fiber can't do? I mean eating starches as leftovers maximises the RS3. So assuming that you've maximised your RS3 intake by retrograding the starch in your cooking. Do you think RS2 has a place in making up the shortfall, or just use a combination of other fermentable fibers (eg one of the gums,inulin,glucomannan etc)? This is assuming that you can tolerate them all of course. That way you're getting some RS and some of all sorts of other fermentable fibers. Not forgetting lots of cellulose to spread the fermentation out of course.
    Where does RS2 figure in getting the best combination of fermentable fiber in sufficient quantity?
    After all, hominids consumed RS2 for millions of years before RS3 came along. Did this 'new version' do everything good ole RS2 did , and then some? . Or does RS2 do something for microbiome health that RS3 can never hope to achieve?
    If it doesn't have some special unique trick that any other fermentable fiber can only dream about, why use it at all? Why not just use a broad range of the other fermentable fibers, particularly the ones that do actually feed a wide range of the 'core' strains? Why is it a mistake to bank on RS3 being 'better' than RS2 ? I do realize that you personally have done human gut health an incalculable service in 'waking the folk up' about the microbiome, but does RS2 now have an important role in gut health, or is it just the jar your reach for when you are running low on other fermentable fibers that feed more of the good guys and/or you're all out of leftover cooked starch?

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    1. Sorry about the trouble you had posting! Glad it worked.

      "Is it true that RS2, although butyrogenic, doesn't feed the core microbiota very well, but RS3 does? So does RS2 do anything special that RS3 can't do in your colon? Apart from being more convenient of course."

      This whole line about RS2 'not feeding the core' is just baloney. However, if you were to eat nothing but RS2 and meat and fat, then yes, I would agree you are not going to get a very good gut flora. I really can't understand the RS2 bashing I see at 'certain blogs' lately.

      I do feel that RS2 does something special that RS3 and other fibers don't. One thing is it's very resilient nature that requires many different species to break it down. It doesn't feed certain 'core' strains directly, but I think that is a good thing. It recruits several types of microbes to break it down, and a long chain of butyrate production and byproducts that feed others, including bifdo and others.

      Another thing that RS2 does, that other fibers do not, is the adhesion of pathogens to the RS granule in the small intestine, as seen in the Oral Hydration Therapy solutions for cholera victims that uses RS, and also the persorption of RS2 raw starch granules into the actual blood stream. This is a natural phenomenon, seen with similar sugars in human breast milk, that are thought to travel the bloodstream of the baby mopping up pathogens for disposal.

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    2. haha - needed two posts!

      "If it doesn't have some special unique trick that any other fermentable fiber can only dream about, why use it at all?"

      OK, as much as I love RS2. I think with the proper attention to diet and supplements, RS2 supplementation is NOT needed by anyone. I've maintained this position since about Day 2 of learning of the prebiotic effect of RS.

      A diet filled with cooked, cooked and cooled, and raw starches (ie. carrots, green bananas, and whole grains) as well as inulin-rich foods and other fruits and veggies, will provide all of the prebiotic fiber one could ever need.

      I tried a diet like this for a couple months, and I found it was lacking most days in overall fiber. I ended up eating crazy amounts of things like cocoa nibs, raw oats, and dried plantains.

      I am of the firm belief that most people require 30-50g of high qiality, mixed fibers daily. I would never in a million years discount the value of RS2 in this mix. But I would also never in a million years tell you that RS2 was imperative. It's the mix that's the magic.

      For me. I find the easiest way to implement all this is to just eat my normal, daily diet which is as high-fiber as I can make it (ending up usually at 10-15g fiber) and then take a 'couple spoonfuls' of some supplementary fiber.

      At work, in my desk drawer, is a mixture I made up. It has semi-equal parts glucomannan, inulin, and a smaller amount of apple pectin. I mix a big spoonful of this with a carton of yogurt or with some cold sour cream to put on a cooled potato. Usually at home, after dinner, I will add a spoonful of potato starch to some type of 'dessert' concoction like a mushed up banana mixed with blueberries and coconut milk. On days when I totally blow my fiber count, I will just take 3TBS of potato starch mixed in a glass of water with dinner or soon after...that's usually reserved for days that I get stuck eating at a restaurant or friends house.

      I hope that all makes sense.

      Here is a great paper, just released this week. It talks all about the importance of gut microbes in metabolic syndrome. Please note that not once does the paper mention RS. But also please note as you read through, the vital role that butyrate plays in the prevention of disease.

      Then if you feel adventurous, look at any study on RS (1,2, 3 or 4) and see how they all increase butyrate. The butyrate production is what I'm after in trying to keep up with 30-50g of fibers per day, and without either supplements, raw potatoes, dried plantains, or handfuls of cocoa nibs, I have not found any way to keep the level this high with just plain old foods.

      Gut Microbes and MetSyn

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    3. Let's make it a hat trick!

      "After all, hominids consumed RS2 for millions of years before RS3 came along. Did this 'new version' do everything good ole RS2 did , and then some? . Or does RS2 do something for microbiome health that RS3 can never hope to achieve?"

      Here's what I think. I think that it's too easy to get lost in all this. I don;t think that we are at a point yet where we can say: Eat X amount of X fiber and you will develop X bacteria.

      I do think we are at the point where we can say: Eat X amount of X fibers and hope to achieve a gut flora that consists of beneficial strains of bacteria that will crowd out pathogens by creating SCFAs and lowering the pH of the gut as well as creating many other compounds that beneficial bacteria create and also to help chelate toxins.

      Genetics can also play a big role. As can past antibiotics use. If I had a preference, I would be eating a diet that provided 50g+/day of fermentable fibers consisting of about 20g inulin, 20g RS3, 10g RS2, and whatever sub-fibers come along with that diet...and you can bet it would be substantial!

      But this diet would be nearly impossible to do eating regular foods as normally prepared. You'd need several pounds of cooked and cooled starches, several pounds of inulin rich foods, unless you ate a big Jerusalem artichoke or chicory root every day. And you need quite a few raw grains or raw starches for the RS2.

      This diet would have been no problem for hunter-gatherers, but it just does not fit my eating habits.

      Here is another paper that shows the importance of varied fiber types on microbe survival:

      http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096097

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  23. Thank's Tim. That's clarified the RS2/RS3 superiority issue enormously. And I had that pathogen adhesion RS2 trick in the back of my mind, from reading one of the studies you mentioned in an earlier post It did strike me as a bit odd that we had eaten raw starches for such a prodigious span of evolution before the mastery of fire, yet RS2 was being touted as vastly inferior to RS3.
    Also I've read people commenting that livestock are never fed a lot of raw potatoes. But that's simply not true. We've fed our goats horses and cattle raw potatoes (not green of course - in fact the goats even love browsing on nightshade leaves) most days for over thirty years, and they've always thrived on them.
    One of the things that feeding my microbiome properly with fermentable fiber has resulted in for me personally is that I just don't feel like eating nearly as much food as I used to, yet I've actually put on lean weight. So the prospect of trying to get that 50g of fermentable fiber from real food would be exhausting. Perhaps if food and eating was the most important thing in my world. But it's not, So I'm just glad I've got a blender and a vast selection of fiber powders are readily available inexpensively.
    But now I'll feel confident that RS2 can figure in my increasingly varied bionic smoothie mix.
    We call cattails 'bullrushes' in Australia, being ex Brits. I grew up half a kilometre from a marsh full of them. Never knew of their starchy subterranean prowess.
    And I remember reading that 1923 raw starch digestibility study you mentioned. Aint the internet grand?

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    1. I think that the holy grail of gut health we be to first determine approximately how much butyrate we need to feed and fuel the entire colon, then to determine what mixture of fibers will provide this.

      Just from what I've seen, I think a fiber-filled, real-food diet plus about 20-40g/day in supplementary potato starch, inulin powder, green banana flour or Hi-Maize corn starch will do the trick.

      Just too many studies that use this approximate amount and show the lowered pH and increased butyrate we desire.

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    2. I also think that once you are tolerating that 50 g it may not hurt to GRADUALLY ramp up the amount so that the population of healthy gut microbiota reaches some physical limit imposed by the size of your colon. Do you know what the lowest recorded gut pH is? What happens if it's too low? And can you have too much butyrate?
      Also, and TMi alert. I've cycled from constipation to diarrhea for about forty years.Never too alarming - I just got used to it - but clearly indicative of some kind of intestinal dysbiosis. I really had zilch idea about the importance to health of the microbiome till that fateful day about a month ago when I was reading about the choline factor on Hyperlipid and Googling some comment Chris Masterjohn made that I couldn't get my head around took me to FTA (which I'd previously never heard of) . After being mesmerized by some comment shitfight Richard's outspokenness had generated, I took a breather with an R.S FTA post. From then, for me personally things moved remarkably quickly. I just wish someone had done what you lot have done forty years ago. My life would have been very different.
      In any case, one of the tell tale signs for me that I was finally on the right track was that my bowel movements changed to perfect, day after day after day. I'd never experienced regularity like that. Never. You know how they advise you to always go at the merest hint that you need to- to prevent constipation. Well now things have settled down in that department so much that i don't even feel the need to go any more. I just pay my respects because it's that time of day again, Quite bizarre really after so many troubled years.
      Sorry for the distal detail. And I loved that fun viscosity fact you mentioned about the last few GI tract inches.

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    3. A good, daily dump is hard to beat! I have a friend that goes once a week, "like clockwork." And others that go 3-4 times a day. Back in my old life, eating a SAD diet and drinking heavily, a trip to the bathroom meant a long occupation of the premises and howls of horror from anyone re-entering the area too soon.

      Now, it's once a day, usually right after a cup of coffee, and no odoriferous evidence left behind.

      As to pH. I think it seems that a fecal pH of about 5.6 - 6.5 which is considered 'slightly acidic' is perfect. Above 7 is too acidic. The only way to effect change is by eating fibers. Eating acidic food doesn't work. The pH should normalize when butyrate and lactic acid are being produced in the correct amounts. I spent quite a bit of time and money trying to figure ways to easily check this at home, but have not come up with anything yet. I hope one day there will be some DIY sample kits for some quick and easy markers like butyrate, pH, and maybe a few microbes.

      pH can be too low, but that condition is usually caused by dysbiosis of the flora. Too many of the wrong kinds, possibly fungal, and they will produce a very acidic gut that only a few pathogens can thrive in.

      Too much butyrate? I doubt it. But measuring butyrate is a funny thing. Some people who eat almost no fiber show high butyrate levels in feces. Colonic uptake of butyrate can be impaired when the microbiota are all wrong. The butyrate is supposed to get absorbed by colonocytes, but colonocytes can also receive fuel from blood glucose when there is not enough butyrate. This alternate fuel leads to changes in the ways the cells behave and regenerate and was the subject of a study I talked about frequently, a very good read if you haven't seen!

      Colorectal Carcinogenesis: A Cellular Response to Sustained Risk Environment


      Sure, building up is fine. And probably wise. But I think the body is incredibly adaptive and your guts will know exactly what to do.

      I think the whole 'Fiber' movement was derailed in the 70's and never progressed. By labeling fiber as only soluble and insoluble and setting an arbitrary standard of 25-35g/day, the science of fiber simply died.

      All that food manufacturers were concerned with was a 'high fiber' label, and that can still be had with just 5g of sawdust per serving. Non-fermentable fibers are important, but getting all your daily fiber in the form of a non-fermenting cellulose is absurd.

      I think it's funny that some people attack me for recommending potato starch when the food and supplement industry is still pushing non-fermentable fiber supplements and the average fiber intake is 5-10g/day for most people.

      1TBS of potato starch triples the fiber intake for most people, SAD, paleo, vegan, whatever. A LC Paleo diet is probably the lowest fiber diet of all, and the reason I spend most of my time on Paleo websites and forums. I love the Paleo diet, but hate the gut-starving aspects.

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    4. This is fun reading these posts. Stuart, I think I've found my Southern Hemisphere twin, although I am not ready to eat dirt yet.

      In terms of BMs, I love to walk. Before starting this, I either had to eat stuff that did not upset my digestion or skip my walks. Once I started the fiber, though, it was one a day like clockwork. Amazing, perfect, consistent stools just like described. For some reason, though, I've been a twice per day person for the last month. No idea why.

      It's funny: the first question people ask when they hear how much fiber I take is "Are you pooping all the time?" Nope. It's a dream compared to what it was before. Just another thing moved from the column of things I had to worry about to the column of things I don't.

      Regularity while traveling is also fantastic, although I've found that the bugs don't understamd time zones very well!

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    5. I forgot to mention that I have obtained dextrin and maltodextrin. I am also adding raw garlic and onion skins. I've always regarded them as inedible, but if you chew long enough they will break down. Several studies I've read say that the skins contain by far the most of the beneficial compounds in garlic and onions. I'd say that is true for the fiber. Gives the jaw and teeth a nice workout.

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    6. To add to what Tim and Stuart have already said, it is indeed difficult to consistently eat the level of fiber I do with modern veggies. This realization came to me about a year ago when I was watching a "critique" of Paleo that said we couldn't eat Paleo even if we want to. Because today's veggies look nothing like their Paleo counterparts. Today's veggies are sugary and sweet. Paleo ones were tough and fibrous, with defenses to beat their enemies. That's when I started taking fiber supplements. I try to increase the fiber content of my veggies by 3 to 4 times using supplements. Trying to do that eating just plants would be Impossible without adding a lot of daily calories.

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    7. @Wilbur

      Do you mean you eat the tough, outer garlic or onion skin? Wow.

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    8. OK, I ate the tough, outer garlic skin including the root zone, à la Wilbur. Not bad.

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  24. Wilbur AND Stu! What an honor. Thanks for visiting my little blog. So you guys are both from Oz?

    Have you guys ever read accounts of what the Paleo (American) Indians ate in the Hinds Cave area of the US? They have petrified poop remains for thousands of years worth of 'bathroom breaks.' My blog next week will talk about it in depth, with even some pictures. Those guys were some kind of hungry! They pretty much subsisted on things we'd consider inedible. Jeff Leach studied it all quite some time ago, and even published several papers, ie.
    Hinds Cave Coprolites and found they were eating about 135g or inulin-like fibers daily. In addition, lots of bones, scales, teeth, and hair from small animals and lots of plant pollen. The pollen was seasonally collected and eaten in large amounts.

    I was playing around last spring and got up to where I was getting about 100g of fiber/day, and can say it seemed a bit too much for me. Talk about leaving some impressive 'coprolites!' I find 30-50g seems to be just perfect, but as you said, hard to do with real food. Don't get me wrong, you could, but I just find it easier to eat normal things, maybe prepared a bit diffeently (ie. cooked/cooled, raw), but working and having a real life sometimes gets in the way of fiber acquisition and reaching for a jar is much easier.

    Hey, was it one of you guys talking about making potato starch in a blender?

    Cheers!
    Tim

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    1. You've probably seen it, but I like this article

      http://www.nytimes.com/2013/05/26/opinion/sunday/breeding-the-nutrition-out-of-our-food.html?pagewanted=all


      I know the 135 number well. It's my target. I can't say for sure that I hit it, but I do try. Most of the food I eat is raw. Even when I go to restaurants, I am known for asking them to make things differently so that they are more raw. Garlic and onion on my pizza (triple extras) are put on after. Chilies and raw garlic are mixed into my Indian dishes. (I learned that it it is traditional to eat a bit of raw chile followed by food.)

      This co proline talk is going on too long. But just this morning I looked in the toilet and remarked "what an impressive sh*t." Then I realized the other half was folded underneath!

      Not me on the blender.

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  25. Tim.
    I mentioned using a blender for making PS a while ago. I like it because it's not as much of a PITA to clean up as a juicer. But since I've been using a much broader range of fermentable fiber I just usually add a piece of raw potato. Dr B.G drew my attention to all the trypsin inhibitors in raw potato, and linked me to a rat study that connected long term raw potato consumption to bad things. She really doesn't like raw potato. But Gemma (and others) have mentioned its antimicrobial prowess, and I've been feeding them to several generations of various livestock forever, so I wonder. There's that Irish 'rock in the middle' potato eating custom too.
    In any case a small piece of raw potato won't do any harm I hope.
    One last copromention before we're done. Promise. My dogs have been getting oat bran, PS, psyllium husk, and inulin for a few weeks now and even THEIR business doesn't stink anymore. Whenever someone uses the expression 'As rank as a dog's do do' now, I chuckle. Of course I doubt whether any amount of fiber will make that particular item smell like roses, but whenever I leave the vicinity now, I feel enormously proud of my atmospheric footprint.
    ENOUGH!
    Wilbur, the sugary weak pap that passes for modern vegetables (as for fruit, it's ridiculous) is the reason that I started scavenging and eating outside cauliflower leaves. But it's the sugar that annoys me most. I am after all a recovering 'natural' fructose addict and long term candida captive. But I think Tim mentioned breaking a filling on a difficult tiger nut. I think we're really lucky that we can let machines do most of the work in breaking up cellulose, and just make an appointment with the dentist when accidents happen.. I'm not sure I even want to have do do the amount of chewing that Grok had to do. And although all the dirt must have done wonders for his microbiome, chewing on all the abrasive soil particles that refused to be brushed off must have taken its toll on his teeth. That's why I love my blender. I don't have to chew everything I eat. This is coming from a VERY slow eater. Onion skins you reckon?
    I remember you referring to 'your kid' 's birthday cake in an earlier comment. I would have thought that's an unusual turn of phrase for an Australian. Maybe you are just more Internationalized. Have you always lived in Australia?
    Tim, thanks for reminding me, I must get some bee pollen next time I'm out.

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    1. I must not have said what I meant above - I am not from Australia. I'm from the U.S. I meant that Stuart is my counterpart in the Southern Hemisphere.

      One thing we noticed about the dogs when we were all on the couch is that they have no dog breath. I've never had dogs that didn't have bad breath. Another thing I've noticed is that dogs just look happy and healthy. I've had several people comment on how I seem to blow healthiness or something, and maybe I am seeing it too in the dogs.

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    2. Stupid autocorrect : glow, not blow

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    3. Thank you for that correction. I was about to ban you.

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    4. I'm out of the starch I made with my juicer...going to give the blender a whirl soon.

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  26. @Stuart

    On raw potato issue: Dr. Grace seems to find just anything against anything coming from raw potaoes, starch granules included. Who am I to question her reasons for that?

    Anyway, haven't we been saying and reminding that the dose matters? And the synergy of all the compounds in raw potato must matter more than isolated factor of say trypsin or protease inhibitors that in the right does and form are used in cancer treatment, for instance. So you do not like to overdose on those, that is clear, because as with many other (not only cancer) medicaments, the overdose, or wrong use does the complete opposite. But there are many other compounds found in the potato, particularly kynurenic acid (KYNA) that is endogenous aryl hydrogen receptor agonist, which controls and influences many processes in the disease via IDO.

    Now, the highly speculative, and perhaps simplistic part of my thinking: what if adding extra portion of EXOGENOUS kynurenic acid disrupts the Ahr/IDO process if under control of a pathogen?

    The fact that kynurenic acid was found in many foods known for their beneficial and medicinal effects (forest honey, broccoli, herbs,..) shows we are on the right track here, with a raw potato in certain diseases.

    Some reading about KYNA
    Kynurenic Acid in the Digestive System—New Facts, New Challenges
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772988/

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    1. Thanks for all of this! I have no problems with people eating raw potatoes. I ate one myself last night!

      I think you are definitely on the right track!

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  27. @Vegetable Pharm readers

    I feel like sharing and educating now :-)

    Distribution, synthesis, and absorption of kynurenic acid in plants.
    http://www.ncbi.nlm.nih.gov/pubmed/21157681
    Kynurenic acid (KYNA) is an endogenous antagonist of the ionotropic glutamate receptors and the α7 nicotinic acetylcholine receptor as well as an agonist of the G-protein-coupled receptor GPR35. In this study, KYNA distribution and synthesis in plants as well as its absorption was researched. KYNA level was determined by means of the high-performance liquid chromatography with fluorescence detection. KYNA was found in leaves, flowers, and roots of tested medicinal herbs: dandelion (Taraxacum officinale), common nettle (Urtica dioica), and greater celandine (Chelidoniummajus). The highest concentration of this compound was detected in leaves of dandelion--a mean value of 0.49 µg/g wet weight. It was shown that KYNA can be synthesized enzymatically in plants from its precursor, L-kynurenine, or absorbed by plants from the soil. Finally, the content of KYNA was investigated in 21 herbal tablets, herbal tea, herbs in sachets, and single herbs in bags. The highest content of KYNA in a maximum daily dose of herbal medicines appeared in St. John's wort--33.75 µg (tablets) or 32.60 µg (sachets). The pharmacological properties of KYNA and its presence in high concentrations in medicinal herbs may suggest that it possesses therapeutic potential, especially in the digestive system and should be considered a new valuable dietary supplement.

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  28. Presence of kynurenic acid in food and honeybee products.
    http://www.ncbi.nlm.nih.gov/pubmed/18231708

    Kynurenic acid (KYNA) is an endogenous antagonist of ionotropic glutamate receptors and the alpha 7 nicotinic acetylcholine receptor, showing anticonvulsant and neuroprotective activity. In this study, the presence of KYNA in food and honeybee products was investigated. KYNA was found in all 37 tested samples of food and honeybee products. The highest concentration of KYNA was obtained from honeybee products' samples, propolis (9.6 nmol/g), honey (1.0-4.8 nmol/g) and bee pollen (3.4 nmol/g). A high concentration was detected in fresh broccoli (2.2 nmol/g) and potato (0.7 nmol/g). Only traces of KYNA were found in some commercial baby products. KYNA administered intragastrically in rats was absorbed from the intestine into the blood stream and transported to the liver and to the kidney. In conclusion, we provide evidence that KYNA is a constituent of food and that it can be easily absorbed from the digestive system.

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  29. I should do a whole blog post on this some day, but have a read if you are interested. One of the better descriptions of maintaining a healthy gut biome I have read recently:

    Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    A snippet:

    "The diverse spectrum of glycans, which is present in the human colon, is derived from the diet (resistant starch, LC-AX, IN) 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 (Ze et al., 2012), LC-AX are specifically degraded by Bifidobacterium longum (Van den Abbeele et al., 2011) and Akkermansia muciniphila seems a crucial species for the initial breakdown of mucins (Belzer and de Vos, 2012). 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’)."

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    1. GOOD ARTICLE. Yes, this would be a great idea for a post. Seems like many of the FMT pills capitalize on the "microbial network" theory. Age and condition targeted treatments would be even better. Kind of ties everything together nicely. Going to reread that one a few times. What are the food sources of LC-AX?

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  30. Gemma and Tim,
    Those are great articles. Thanks.
    Wilbur,
    Maltodextrin and dextrin are normally highly digestible. But they can be made resistant and thus excellent food for gut biota. Make sure you got the resistant kind.
    It's a processed food - to make it resistant. So with your range of fermentable fiber, you may not even need it.

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    1. Thank you for the heads up. In the post that I first saw that you were using these, I saw that you seemed to be emphasizing the modifier "resistant." So the ones I bought both emphasize that they are fibers, prebiotic, and indigestible. Thanks to your careful wording, I believe I picked the right ones. I was less careful in my wording.

      I was unaware of these until you mentioned them. I did some research, and found some studies that certain beneficial bacteria prefer them (I should take notes, but I never do. I just let the idea become part of my thinking and run with it.). I've mentioned before that I start taking the fiber, and then it seems after about a week my body lets me know how much to include. Or to stop. Or to start again after stopping. It's weird. It's like deciding what to eat for dinner. I want Italian, or I want Indian, or I want pizza.

      I started acacia fiber some time ago. It was in the mix for a while, so I bought a couple of big jars. Then I couldn't do it anymore. Every once in a while, I see those big jars, and declare I am going to start it again. Every day that jar just sits there, and I cannot put any in the mix. I put them away.

      Yacon root is another one I don't understand. I started it, loved it. Then I noticed it gave me loose stools. I quit. Then over the summer I had an insatiable craving for it, and I was doing at least triple what I was doing before. No loose stools. Then it just stopped - I didn't want any more. And when I did eat just a little, the loose stools returned.

      The core for me is potato starch, inulin, larch, baobab, amla, and glucomannan. Every day with no variation. The others come and go depending on desire. Occasionally I have a day where I really load up on everything just because I feel like it.

      I tease a bit that your eating dirt is extreme. But really I do something similar. Our two 50+ lb (maybe 60+ now) 10-month old puppies play very actively in the dirt in the wooded area behind our house. Their coats seem to trap dirt, more so than any other dogs I've had. I play with them and pet them very frequently. And I very often purposely do not wash my hands very well afterward, even if I am about to eat. Just enough to get the obvious big stuff off. And the weird thing is that I want to do this, much like I want to use certain fibers. It feels good in a way.

      And I don't understand where to draw the line. Is it me? Is it them? Or are they me? Or am I them? It doesn't matter to me anymore. People with whom I discuss this are dubious. They are the ones still suffering, I am not. If this is one big placebo effect, well bring on more placebos!

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    2. @Stuart

      Here is a paper on those dreaded trypsin inhibitors from potato:

      Antimicrobial activity studies on a trypsin-chymotrypsin protease inhibitor obtained from potato.
      http://www.ncbi.nlm.nih.gov/pubmed/15809084

      "A 5.6 kDa trypsin-chymotrypsin protease inhibitor was isolated from the tubers of the potato (Solanum tuberosum L cv. Gogu) by extraction of the water-soluble fraction, dialysis, ultrafiltration, and C18 reversed-phase high performance liquid chromatography. This inhibitor, which we named potamin-1 (PT-1), was thermostable and possessed antimicrobial activity but lacked hemolytic activity. PT-1 strongly inhibited pathogenic microbial strains, including Candida albicans, Rhizoctonia solani, and Clavibacter michiganense subsp. michiganinse. Automated Edman degradation showed that the N-terminal sequence of PT-1 was NH2-DICTCCAGTKGCNTTSANGAFICEGQSDPKKPKACPLNCDPHIAYA-. The sequence had 62% homology with a serine protease inhibitor belonging to the Kunitz family, and the peptide inhibited chymotrypsin, trypsin, and papain. This protease inhibitor, PT-1, was composed of polypeptide chains joined by disulfide bridge(s). Reduced PT-1 almost completely lost its activity against fungi and proteases indicating that disulfide bridge is essential for its protease inhibitory and antifungal activity. These results suggest that PT-1 is an excellent candidate as a lead compound for the development of novel oral or other anti-infective agents."

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    3. You trying to kill us Gemma! Next thing you'll say is that we can feed raw potatoes to animals.

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    4. "You trying to kill us Gemma!"

      YESUGATHISCUGISUGATHECUGDEADLYUGASEQUENCETAG.

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    5. What? No heparin binding triplets or G-rich regions? You ARE trying to kill us!

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  31. Wilbur, I don't really understand the biochemical detail but when made resistant, they're both considered RS3 . It's cheating I know. Hopefully the gut bugs don't care.

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  32. 'The King and his Court'. My colonic royalty! Wonderful

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