Clostridia & Food Allergies: Excellent News, Silly Conclusions

For those of you who are vigilant microbiome news junkies, you may have already come across this one last week: researchers found that inserting a major class of human gut bacteria — Clostridia — into mice with peanut allergies eliminated the allergy. And they found that inserting the other major class of human gut bacteria — Bacteroides — did nothing to alleviate the allergy.

Clostridia!

If you’ve been following this blog for a while, you know that this is the class of bacteria, more than any other, that we like to obsess over around here.

Clostridia are the bacteria that make up the majority of people’s “Firmicutes” in gut reports. That’s why I’ve tended to use them a bit interchangeably in the past (though I should probably stop that). They are usually broken into two clusters: Ruminococcaceae and Lachnospiraceae (also often called Cluster XIVa and IV). And those are the exact clusters that were found to ameliorate the allergies. And Bacteroides are the other side of the coin — they tend to make up majority of the other major gut phylum, Bacteroidetes.

The most important, and longest running argument on this blog, has been about Clostridia/Firmicutes: they grow on fermentable fiber from plants and are the main beneficiaries of resistant starch intake, they are the ones that produce the majority of short-chain fatty acids like butyrate, and they seem to be universally correlated with health promotion. Lower Clostridia? Almost never good. And the other dominant, and related argument on this blog has been this: that these effects are due to their interaction with the immune system. Remember, it is said that 70% of our immune system is in our gastrointestinal system. All these people experiencing sleeping/dreaming effects with resistant starch? Probably the Clostridia, and their SCFAs, modulating the immune system.

And the general theory I put forward in this post, about what exactly makes Clostridia so special, was this: that from the little research I could dig up, Clostridia seem to be the adherent bacteria in the human gut. That they are the ones residing in the mucosal layer, acting as a defensive barrier, providing SCFAs to the epithelium, and thus directly communicating with our immune system. The other bacteria, like Bacteroides, seem to inhabit the luminal space — the hollow cavity of the intestine.

Gut-Bacteria

So…was that right? The researchers who conducted this recent peanut allergy study sure seem to be saying exactly that:

“These bacteria are very abundant and they reside very close to the epithelial lining, so they’re in intimate contact with the immune system,” Nagler says.

In one quote, we get significant support for two major lines of argument from this blog: that Clostridia are a special and important class of gut bacteria in the human gut because they are the mucosal-adherent bacteria, and because they modulate the immune system.

In case you were interested in the nitty gritty of this particular study, it looks like the Clostridia eliminated the allergies through regulation of an immune modulating cytokine, just like we talked about in the sleeping & dreaming post:

To identify this protective mechanism, the researchers studied immune responses to bacteria in the gut. Genetic analysis revealed that Clostridia caused innate immune cells to produce high levels of interleukin-22 (IL-22), a signaling molecule known to decrease the permeability of the intestinal lining. Children with food allergies are know to have greater permeability in their guts when they eat problem foods.

In a second part of the experiment, the antibiotic-treated mice were either given IL-22 or were colonized with Clostridia. When exposed to peanut allergens, mice in both groups showed reduced allergen levels in their blood compared to controls. Allergen levels significantly increased, however, after the mice were given antibodies that neutralized IL-22, indicating that Clostridia-induced IL-22 prevents food allergens from entering the bloodstream.

As for how, exactly, Clostridia modulates this immune signal, the researchers stayed pretty general. As you know, we’ve focused on short chain fatty acids as the likely mechanism (but have certainly kept the door open to other possibilities):

“They are always signaling to our bodies, but we’re not usually making a response to them. We found they generate particular signals that promote the production of mucous and natural antibiotics the body makes to reinforce the barrier [of the intestinal lining] and prevent those food allergens from getting past the epithelial barrier and into our blood,” said Nagler.

Alright, enough of this victory lap stuff. Time to vent some frustration.

While this study is a really great one to see, the ultimate conclusions drawn by the researchers, both in the study and the media reports, is disappointing, to say the least. Why? Because both in the study itself and in the many news reports about it, what the researchers say essentially amounts to this: “We need to put Clostridia in a pill.” 

Exhibit A:

Nagler and her university have filed for a patent application on the new findings. The ultimate goal is to “interrupt [the allergy] process by manipulating the microbiota,” she says—a probiotic consisting of Clostridia could be a new allergy therapy, for example. Nagler knows of none on the market yet, and they would need testing in people before becoming a treatment of choice.

Exhibit B:

“The exciting implication for consumers is this gives us a way to intervene and see if we can now use modulation of the bacteria in our gut as a way to prevent or treat food allergies,” Nagler said. “We could use the Clostridia to develop a novel, new treatment we can give to people with food allergies, or to protect people before they get food allergies, to elicit this barrier protective response. This is a totally new probiotic.

Nagler said that several companies are already working to develop this new probiotic. “In fact,” she added, “we are working with one company. Clostridia are very difficult to work with because they can’t be exposed to oxygen. The good thing about them is they form very stable spores that can live under very extreme conditions. We can potentially collect spores of Clostridia and create them as a pill.”

Exhibit C:

Clostridia bacteria are common in humans and represent a clear target for potential therapeutics that prevent or treat food allergies. Nagler and her team are working to develop and test compositions that could be used for probiotic therapy and have filed a provisional patent.

Sigh. Big, big sigh.

First things first: I find it pretty disturbing that the first thing health research labs do, once they make an important discovery about human health, is to immediately file a patent. Furthermore, it’s one thing to patent some kind of novel, synthetic, chemical drug, and another to patent something that’s essentially a part of and produced by the human body. These are native human gut bacteria. You’re patenting the idea of putting them in a pill? What’s next, a patent on Vitamin C chewables?

Which brings us to the real reason I find this so frustrating: everything about this study, and everything we know about Clostridia in the human gut, points to the fact that probiotics are not the answer.

As I just said, these are native human gut bacteria. They live and grow inside of you. They can’t survive outside of a human. They exist because you exist. They need you, you need them. Heck, the researchers said it themselves!

“Then we tried to find out which bacterial population it was, and in a whole series of experiments, we settled on Clostridia, which are oxygen-sensitive bacteria,” Nagler said. “They can’t live outside of an environment that is oxygen free. Deep inside your body, deep inside your intestines, there’s no oxygen, and that’s where this kind of bacteria live.

In other words: you don’t need to “seed” or “infect” yourself with these bacteria, as if they are some exotic, hard to acquire bug. Don’t believe me? Here’s the proof: EVERY SINGLE INDIVIDUAL GUT REPORT I HAVE EVER SEEN CONTAINS THESE BACTERIA. I have never seen a report showing no Clostridia. Not one. If you are a human, then you almost assuredly have Clostridia in you.

What DOES differ, from person to person, is the amount. In some, they are the predominant bacteria. In others, a tiny fraction. And what do you think accounts for that? Do some people have access to a magical Clostridia tree? Is there a secret, members-only Clostridia CSA you need to join?

No.

From everything we’ve gathered here on this blog, it’s quite clear that the quantity of these bacteria aren’t related to some type of external exposure. Rather, they respond to the intestinal environment and the inputs into that environment. Clostridia grow when you feed them plant fibers, and they thrive in an acidic intestinal environment — one where a lot of fiber fermentation is taking place, which itself drives down the intestinal pH. Which means that not only a lot of fermentable plant fiber, but also a diversity of fermentable plant fiber, is a pretty good bet.

In other words: if a rainforest is dying because it isn’t raining enough, you don’t plant more trees. You make it rain more. Get it?

As for the question of why this fact isn’t abundantly clear to, or promoted by, the researchers who conducted this study, I think that’s patently obvious. Don’t you?

— Heisenbug

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66 thoughts on “Clostridia & Food Allergies: Excellent News, Silly Conclusions

  1. You, Sir, are my favourite microbiome blogger on the planet.

    Why? Well, because you just ‘get’ it. This relentless quest to buy a fix drives me nuts. Sure, reintroduce with a FMT pill because of abx overuse but, really, just eat good food ie sources of fibre and not some processed crap. Ditto the paleo stuff. Eat meat etc if that’s your thing but please, please, please … do yourself a favour and load up on the fruit and veg otherwise your intestinal pH will be so high that pathogens are going to love their new little habitat.

    Okay, so where was I … oh, yeah, praise for Mr H. … Brilliant, informative etc etc.

    I’d join your cult in a flash, dude … but I’m riding so many of those bandwagons these days! 🙂

    • Chris,

      I have visited your website and I am sorry to hear of your troubles.

      Could you clarify a bit?

      – was there also high fungal overgrowth in you gut test, except high Klebsiella? Do you have the full report?
      – you have done FT via eating poop capsules, and do you feel absolutely fine since then? (I expect it was a healthy donor)
      – but you state at “About me” that you are now on a survival diet of raw fruits and some veggies mainly, no animal products…

      Does it mean that you still cannot tolerate any other foods and cannot gain any weight, or is your “About me” page not updated?

      • Hi Gemma,

        Yeah, I had some Candida Albicans in there. Plus the typical symptoms associated with that kind of thing; white tongue, thrush, mucous in the stool etc. But I had that under control long before the FMT treatment. That was largely because of the diet alteration. One thing I know is that fruit/fructose does not promote fungal/yeast/candida growth. If that were the case I’d be a walking mushroom farm and so would my wife. In fact, the fruit/veg dominant diet we have made the white tongue and thrush disappear. But, het, each to their own.

        As for the stool donor … I used my wife. I have a friends that are naturopaths so we kinda had a barrage of CDSA , IgG tests done along with the usual serology stuff through our local doc. My wife is an awesome donor.

        As for my survival diet… yeah, not updated. That was pre-FMT. I kinda just eat whatever now. But I’m not a dick about it. I’m still extremely high-raw fruit and veg. I have introduced resistant starches into my diet but I am slowly phasing that back out again. I’m jumping off that bandwagon due to a few concerns based on my own little n=1 experiments!

        My lifestyle is all pretty simple really: no meds, no alcohol, no dairy, no high ppm glutinous grains, no soy, very little animal protein, very little sugar (those fluffy marshmallows are my undoing!), lots and lots of soluble fibre. Plus exercise. Not hardcore shit though. Just stretching, bit of a run, some low weights.

        I’m not good on the sleep front though.

        I’m also in the garden a bit these days. Want me some soil-based organisms!

      • Hi Tim,

        I used to track your comments on another blog a long time ago. But I can’t remember whose. I always found your comments extremely insightful.

        So, yeah, I’m not really sure exactly what my daily fibre intake is now. It’s all from vastly different sources, mostly fruit though. I think it used to be close to 100 servings (cups) a week.

        I guess, on a good day, I’m consuming about 2000 calories of fruit (papaya, bananas, melon, apples, pears, strawberries… plus seasonal changes ie figs, mango, lychees). Add to that a steering-wheel sized bowl of leafy greens.

        However, on a bad (read: many days post-FMT), my intake of fruit and veg is lower and my intake of rice goes through the roof. Rice consumption on these days (cooled rice) is about 5 cups. Plus about 1000 calories of fruit in the morning.

        From my personal experience (bearing in mind that I had klebsiella overgrowth) the increase in rice consumption doesn’t result in greater health. In fact, the best I’ve ever felt was zero RS (apart from bananas which is probably only a minimal source due to ripeness) but a total caloric intake of about 3000 calories of fruit consumed between 6am and 2-3pm. Then a switch to leafy greens in the afternoon.

        That said, it is very time consuming eating this way. Plus the fruit management is a bloody nightmare.

        I do occasionally eat animal protein but, for me, nothing compares to the raw diet for general health and brain clarity.

        Also: zero supplements and zero meds (OTC or otherwise). Dodgy disclaimer: I bought some miyari (clostridium butyricum) the other month. Took it for a few days then kinda just forgot about it. Couldn’t be assed really.

        I also don’t do potato starch or plantain flour. I’m just more interested in whole food sources for fibre. Tastes better. I guess I’m just basically replicating a chimp diet, albeit on a lower level since I can’t consume 6kg of fruit and veg a day without going broke!

        My sister put herself and her son on the same diet (no animal proteins etc) and his iron levels jumped from 1 to 17…!!

        In my (uneducated and moronic) opinion – fibre is where it’s at.

      • @Tim:

        One more thing on my RS issue.

        I expressed my concern to Dr David Topping (the Chief Scientist behind that Hungry Microbiome/RS video – https://www.youtube.com/watch?v=NI3KtR3LoqM) about RS and klebsiella and he replied thus:

        “…it is possible that the overgrowth is metabolising not starch but the products of amylolysis in the small intestine.”

        Therefore some of us consuming RS could be feeding these bad bastard bacteria (think c.diff, klebsiella et al) their yummy sugar meals. Not ideal, really.

        All depends on what bacteria are present (or not) in the GI tract, I guess. But who knows, I’m just a rank amateur with this stuff?!

      • Chris,

        thanks a lot for the clarification, here some more questions from me 🙂

        I am not sure that fructose could not feed candida, I rather tend to think that it was the high inulin and pectin content, plus all the other associated compounds and various other sugars from your vegetables and fruits which contributed to your lower inflammatory status.

        So it is not really about fructose only, though we know that inulin is in fact a polyfructose.

        Inulin is anti-inflammatory, see:

        Inulin stimulates phagocytosis of PMA-treated THP-1 macrophages by involvement of PI3-kinases and MAP kinases.
        http://www.ncbi.nlm.nih.gov/pubmed/22038771

        But phagocytosed candida does not mean dead candida, it can wait in the macrophages, so you had better watch out.

        Do you eat also garlic, onions, leeks (inulin!) and other such vegetables, or only leafy greens?

        Have you tried some other herbals against Klebsiella? (in case it is still there?) And can you see the garlic and onion in the paper below?

        In-vitro antibacterial activity of herbal aqueous extract against multi-drug resistant Klebsiella sp. isolated from human clinical samples.
        http://www.banglajol.info/index.php/ICPJ/article/viewFile/10534/7784

        “Among the 35 samples tested in the present study, 19 crude herb extracts were found to exibit their antibacterial properties against Klebsiella sp. isolates. viz. Spondias mombin L., Allium sativum,
        Terminalia arjuna (leaf), Citrus limon L. (fruit), Tamarindus indica L, Phyllanthus emblica L., Syzygium aromaticum, Olea europaea L., Terminalia arjuna (bark), Eucaplytus globules, Nigella sativa L., Cinnamomus zeylanicum, Allium cepa, Cinnamomum tamala, Camellia sinensis, Citrus limon L. (fruit), Polygonum tomentosum, Ficus carica and Lagerstroemia speciosa. The maximum antibacterial activity were found up to 90% in Citrus limon L. (fruit) and Syzygium aromaticum (leaf) followed by 85% activity were found in Spondias pinnata (leaf).”

        Next, you mention animal protein, not sure what you mean by that. I hope you can slowly shift your diet towards eating whole animals (animal fiber), not only some animal protein. Surely you know that raw fruit and vegetable diet is not sustainable in long term.

        Also, nobody would expect you to profit so much from RS supplementation, if at all, given your health condition.

        It has been stated many times since the “RS discovery”, by Tatertot too, that RS and inulin should be the base of fiber rich diet, but all the other compounds that naturally come with these two basic polysaccharides in real foods are needed too.

        Speaking about starch: have you ever tried to eat a raw potato? Instead of all that rice? It would be a great source of some starch, but most of all a good source of many other anti-inflammatory compounds.

        Good luck!

      • Gemma,

        I’m sure the candida is still there. I get signs of it when I include too much sugar in the diet, especially now that I’ve deviated from raw.

        Prior to going raw I consumed the juice of two whole lemons a day to keep certain symptoms at bay. This happened for years. I also took Grapefruit Seed Extract at high doses to knock the klebsiella. All that was well and good but it was completely over-shadowed by the benefits of a raw food diet.

        As for potato, yep, tried it. Not good. Potatoes were a huge allergen on my IgG tests. Great way to ensure a multi-day migraine! I’m very careful of any potato flour and starch as well.

        Animal proteins… well, I consume some meat. But basically I just listen to what my body says. I’ve been doing mostly raw for 18 months now. But I’m not 30 Bananas a Day or low carb or whatever the hell people are doing. I’m just ‘Eat lots and lots of stuff’. Basically just high-calorie and diverse. Nothing complicated. I just eat things I like to eat. And I eat lots of it. I know a few people who are struggling with the 30BAD thing and I certainly can’t understand the low-carb, low-calorie stuff. But if it works for others…

        Same with me.

        The thing is, I came from a very low baseline of health and tried all the diets. A dominant raw diet worked for me. When I eat animal proteins ie a steak, chicken breast, fish etc, I feel like shit. As do my family. I’m not adverse, emotionally, to eating food from animal sources, I just feel better eating whole plant foods.

        I do eat occasionally eat onion, garlic etc. But I basically stick to foods that I could or would find palatable on their own. Also, I minimise my intake of proline-rich foods, so spinach instead of kale etc. Sweet potato instead of potato.

        But the reality is that I’m doing fine on mostly raw at the moment. Like I said, it has been 18months. If I get any adverse effect in the coming years then I will most likely alter the diet. But as it stands it’s working more than fine. I’m not trying to change anyone’s dietary regime with my dietary dogma. It’s just the way I live. I’ve got no vested financial, ethical or ideological interest in whether people eat the way I do. It made me better but hey, I have different genes, microbiome, environment, lifestyle to others.

        I’m healthy because of my diet and lifestyle. Tim’s healthy because of his. I do occasionally eat some of what Tim eats but by and large I do my own thing. The only reason I’m trawling these types of blogs is too keep abreast of the microbiome in relation to FMT. That’s the stuff I’m passionate and dogmatic about. Simply because the treatment is a game changer. And in many cases can be the difference between life and death.

      • Chris,

        thank you very much for you long reply.

        Do you feel fit and healthy in that case, can you do what you want in your life or not?

        It is not very clear to me. Neither it is clear what you really eat…

        And no, I am in no way implying you should eat the same way as somebody else.

        Good luck!

      • Gemma,

        The problem with raw potato is that it tastes like shit!! 🙂

        I’d prefer to et a shoe-box full of figs.

        Which I do, when in season!

      • I guess tastes differ Chris, and I must be pretty far gone if I find potato starch has no taste at all. In a glass of water. I prefer it in a little bowl of yoghurt though. With a little bit of honey if I take it at night. Which I usually do.

      • Thanks, Gemma.

        It’s all a learning curve, isn’t it? I guess we all just keep experimenting to see what works.

        A year or two ago Paleo was really kicking into gear… and now I know countless people on that diet that are telling me they feel like crap. And, yet, others are doing fine on it.

        In my enquiries, I have noticed that the one common link to illness and poor diet responce appears to be abx overuse and/or dybiosis.

      • James,

        I’d be keen to try the potato starch in a few different ways but I’m conscious of the high allergy readings I have for potato. This may change once the gut fully heals itself. I expect this to take some time. We have some data that even post-FMT bacterial CFU takes some time to rise. We’re talking maybe a third of expected harvestable bacteria from stool.

        The take away from that is the seed, weed and feed track takes years to fully work. Which is why I try to feed the good bacteria as much fibre as I can to fast track the recolonisation process.

      • Yeah, I am aware of aware of that paper, Gemma. It was the one I sent through to Dr David Topping at CSIRO.

        Apologies for not addressing my current health. I’ve been largely symptom free for 18 months and have been able to eat other foods for the last 100 days (post FMT). My health is fine. In fact, i havent even had a flu (or any illness) since going on a raw dominant diet. That’s 18 months. So my immune system must be operating well.

    • Chris I completely and utterly concur, except for the bandwagons. Don’t have too much use for them. I have and will be spreading the word. It’s our own natives we have to look after

      • Yep, totally agree, James. Bandwagons not so good. Inevitably the wheels will fall off.

        I just kinda do my own thing. I know exactly what to expect when I eat certain foods. I track the diet and lifestyle routine of 5 adults and 3 kids (one of whom is on the autism spectrum) very closely. We’ve learned quite a lot about what does and doesn’t work over the last 2 years.

        Plus we’ve done 7 separate FMT treatments with 3 different donors so it’s been interesting watching and learning stuff on that front.

    • Chris,

      I am wondering — any chance of you getting some baobab into your diet? If I remember well — the commenter Wilbur includes baobab in his diet too. Full of oxalate, full of calcium, full of everything…

      I am reading it grows in Australia as well.

      Baobab, the tree of life.

      The essential part of Hadza nutrition.

      And please, do not tell me you might be allergic to baobab…

      I hope you do not mind me commenting on you again, your story is most touching.

      • I’ll check it out, Gemma. God knows where I’d source it from. The only baobabs I know of are the ones in the remote north west and I’m located on the sub-tropical beaches on the east coast.

        I’m only really allergic to work, Gemma. Everything else I can tolerate up to a point. Work is a no-go zone though!

    • Chris

      Ive chatted with tator and Gemma , maybe I may be some assistance… from my long journey 2.5 years in now.. I wont REPEAT my story (HAHA) I tend to rant. But Chris I ended up with a screwed up gut.. Started with gluten, then milk…and starch F-ed me up if I ate it.. We are all different and what works for one dosent always work for others…I see you 86 of the menu – grains milk and soy… I did the same. I started out first making SCD yogurt and followed that diet… Your friends are naturopaths If you did just IgG testing dont count on it…Ive done them all , IgG , great plans , enterolab, Elisa act so on etc. If you are high in yeast…your sugar diet is never going to fix the problem.. to LC it will eat the ketones to HIgh carb and or sugar your in the same boat. What tests did you do??. As well many foods are similar in sugars and proteins. if your high in yeast – yeast make arabnoise— if you eat your share of apples there high in arabinose. until your normalized again–they will cause problems… Fungi…. can make vit C — so if your diet is Super high in vitamin C(fruits) your going to have the shits…to much vit C is converted to oxalate acid. A tip for you would be…to compare foods on a OXALATE list…eat low oxalate(pick your fruits and veggies from there) , low arabionse as well….. dont over do your calcium. Have you gene tested your self for HLA DQ 2 /8 this can be done at lab corp. The more genes you have the more problems you may have with mannose Food type, arabnose and oxalate acid. I cant explain my whole 2.5 years but if you would like more info on what I did… I can tell you. Too each is own thou… For me at my worst starch made my hands hurt , back and nose bleed. There was no way in hell for me to do RS….Today I am randomly eating some. If you didnt get a good amount of lacto or bifido strains in when you started to clear up your problem in the past — your not going to get any where fast. If your vit D is low..KIss yourself …. and if your not getting in some bacteria…probiotics and sometimes we need them as food based ones may not make it further in the GI tract… due to acid. Im a big, kraut eater now, kimchi and high does of many lacto and bifido strains…

      For me my whole gut crash —traced back to amoxicillin — ive found Its a NO NO for me and my genes ( gluten genes HLA DQ

      • Eddie, I had a lot of what you are talking about. I avoided all major sources of proline pre-FMT due to my concerns with HLA DQ2 & 8. I didn’t bother testing for it since my symptoms seemed indicative to those of someone with this allele.

        I do eat rice and potato now. I just try to lay off it. I’ve not been ill for at least 18months by just sticking to my high-fibre low inflammatory diet. The last three months (post-FMT) have just been the icing on the cake, since I can tolerate all foods again. That said, I still stick with a high-fibre diet most days. I live on the coast in Australia so my Vitamin D is gained by at least thirty minutes exposure of full sun (shirtless) a day, virtually year round.

        As far as testing goes, I did a CDSA, IgE, IgG, and various other serology tests.

        I totally agree on the amoxicillin front.

        Side note on FMT: We’ve (me treating myself, my family and my friends) have now done 7 FMT capsule treatments using three different donors (all tested – stool and serology) and it seems the best donor is my wife who has the same high fibre, low inflammatory diet as I do.

        My diet took all my IBS/allergy symptoms away but the FMT allowed me to absorb nutrients and diversify my food groups.

        I don’t have IBS or allergy symptoms to date. Again the diet and FMT is the reason for this.

      • chris ,

        Interesting– myself – the cure was LOTS of fibers inulin, chicken meats fish— lots of veggies thu.. the opposite of what your GI says…At first it was bad…but it all changed Have you done ubiome or AMgut ..be neat to compare..

        my allergies all went away as well….37 years of random nose bleeds stuffy nose and hemorrhoids .. my diet is high oxalate foods… and high lacto and bifido strains and the occasional yeast killers… I watch the foods high in arabionse —get my calcium from nuts and plant sources… most of all the problems are solved 2.5 years… people laugh at my breakfast of 2eggs with chia seeds — whole pepper red green or yellow, celery , almonds and walnuts , kraut and two cooked onions….and coffee latte with almond milk…. veggies get rotated…broccoli cauliflower bok choy . not big on fruit… some berries

      • I haven’t done uBiome or Am Gut yet, Eddie, but it would be interesting to compare our respective bacteria make-up since we both achieved cures. Maybe you have more microbes that ‘digest’ animal protein and I have more that like to dine on fruit!!

      • Chris,

        Have you looked at greatplains lab — I also used this lab several times while tracking my change
        I did the OAT test — heres a sample from there site http://www.healthlinkpartners.com/testkits/images/test-pdf/Organic%20Acid%20Test.pdf as well I did there comp stool another sample from there site http://www.healthlinkpartners.com/testkits/images/test-pdf/Comprehensive%20Stool%20Analysis.pdf

        To me its Im thinking depending on how many HLA DQ genes you have— I can say amoxicillin is a trigger for me yeast/mold antibiotic — cant count out it also killing– off good lacto / bifido as well …. Ive worked hard on raising my lacto/bifido probiotic wise… worked on lowering yeast — and foods simular sugar/proteins (arabionse , mannose , casien(milk) gluten and soy…. over time its all seem to fix itself and re balance

        I say from , removel of those foods to give my immune system a break and the lowering of ryeast and high input of probiotics.. I now can enjoy much of what I missed before…

        Im going to due my ubiome soon and Amgut again… I will compare them and post in the future … I m sure they will be different– as I feel great and many life long minor things are gone

    • Hi Antonio. Clostridium butyricum has nothing to do with these two Clostridia groups. The “Clostridium” in the name is irrelevant. Most of the bacteria in the Clostridia groups do not belong to Clostridium. “Clostridium” tells you nothing, really — after all, Clostridium difficile isn’t exactly a friendly bacteria you should be ingesting!

      • Actually, I didn’t meant they were the same but they can both work forma autoinmunity problems. what I don’t understand is the problem you’re talking about with this new product. Once it reach the counters you can buy it or not, like the other. And I can’t figure a way they could preventiva other people making another one.
        Obviously I am missing something, that’s what I am asking for.
        Salud.

      • What I do find interesting though is the species belonging to Clostridia Cluster XIVa, these are the big-time butyrate producers.

        When I see gut tests that have loads of pathogens, there seems to be a marked reduction in CC 14a.

  2. The incentives are the same as in the rest of the drug industry, and a pill is easier to sell, and more profitable, then an admonition to change one’s diet, and add more inexpensive vegetables.

    • problem is aside carrots and white potatoes, vegetables aren’t inexpensive anymore. Maybe they would be though if more folks ate them and we had quantities of scale as a factor. For example sweet potatoes are mostly $1.49/lb where i shop, 4 small turnips in a bag for $1.50/lb, a bunch 3 small beets with greens attached for $2, winter squash 98c/lb and often things that you think would be inexpensive like zucchini are high priced as well. Its to the point that you almost have to grow these things yourself and then you gain the added benefits of higher quality and greater freshness than the stores can provide. Farmers markets i dont always trust and the prices are often absurdly high anyway.

  3. Mr. Heisenbug,
    I believe I have candida overgrowth and I do have h.pylori antibodies in blood, but stool test was twice negative. Does that mean I need much more fermentable fibers or less? I read women with excessive candida should limit fermentable fibers? Can you tell me your opinion since I really want to feel good about eating them!
    Thanks! Your blog is great!

  4. Thanks for this very informative post! So glad you are back blogging. We need this information. OK, I’m going to go eat some salad now.

  5. a researcher at Great Plains Laboratories
    reports a number of cases where a course
    of anti-clostridia drugs Metronidazole and
    Vancomycin reduced autistic symptoms
    and improved digestion with autistic
    children
    ?????

    • Kat—

      You ll find all these kids have high arabinose markers.(out the roof)….. yeast markers and Clostridia ( high(HPHPA markers)
      These kids have problems with milk, grains and oxalate foods… You see the the diets swing from SCD , LOW oxalate , gaps etc

      Yeast make arbinose — foods high in grains etc are high in arbinose , milk casien resemebles YEAST , soy can swing oxalate or close to yeast, Gluten HWp1 protein is similar to yeast. Foods high in oxalates can bug them….. you see the messy gut ( opening up and all the oxalates poring in

      you need calcium, and oxalates for your gut…

      what do Bad strains of clostrida eat???

      • Hi Eddie. I stumbled onto this blog when researching clostrida after learning about the recent study being discussed. It’s obvious that I have a lot to learn about gut bacteria. We have a 6 year old daughter that has a severe peanut allergy. She had antibiotics only once, for an ear infection, when she was around a year old. We eat a lot of organic vegetables (from local farms when possible). We grow some ourselves. We ferment our own cabbage and carrots. We eat very little sugar. We eat a little grain, mostly rice and quinoa and corn. We eat a little meat, usually grass-fed and/or organic. We eat organic yogurt, sometimes homemade. I’ve always felt that by giving our daughter the strongest immune system possible, we might fight against the allergy. Most people think that’s nuts, but you (and others on this page) know it’s not. The peanut allergy is terrifying and the research is exciting. My question is: what else can I do to make sure her system has enough of the good clostrida? Thank you for your time.

  6. Hi shant
    so to get clostridia i shouldnt be looking for a probiotic capsule for it?
    instead just eat RS and plant ferment able fibers?
    can you do or point me to a post listing the foods?
    thanks

    • Lots of articles about the gut/brain connection and autism. We’ve had some positive results if you count personal anecdotes. We did and FMT capsule treatment on my 6 year old nephew a couple of months ago. He’s on the autism spectrum. There has been slow and steady improvement in his disposition with each passing week.

      • Forgot to thank you for these links, Gemma.

        Was surprised to see that my ‘survival diet’ was inadvertently low in oxalates. No wonder it worked.

      • Hey Chris,

        yes no wonder that low oxalate diet worked, though it is more complex than it seems.

        We NEED high oxalate foods to keep us healthy and fight pathogens, but we do not want the pathogens MISUSE the excess oxalates to fight against us. The excess oxalate in the gut should be degraded by bacteria, there was Oxalobacter formigenes mentioned, that is a obligatory oxalate degrader. If this one is decimated by abx and missing in your gut, there is a problem. Was it one of those you were lucky enough to get reintroduced via FT?

        Other bacteria can degrade excess oxalates as well, the question is if they do.

      • I’m going to get my wife tested through uBiome to see if the O. formigenes is present. I certainly felt like I was operating better on the diet post-FMT. The fact that I had some high oxalate foods in there (figs etc) might also suggest that the bacteria was missing. My body weight went up 10% in three months so something was missing in there!

        I should probably order a DNA test for myself while I’m at it, I guess.

  7. Hi Gemma , tatertot , Dr H

    I’ve heard onions and garlic are a double edged sword. I know you promote it’s use but I think its feeding my sulphur reducing bacteria. Do you have any suggestions how I can weed these??

    • @Saphna

      In short: I would worry much more about not getting the well known health benefits from eating onions and garlic etc., than about some bacteria in you. You specify nothing more… So in that case I may perhaps conclude: just give it some time, and see?

  8. You need sulfur reducing bacteria to perform vital housekeeping duties in your large intestine: https://microbewiki.kenyon.edu/index.php/Large_Intestine#Methanogens_and_Sulfur_reducing_bacteria

    And if you have any explosives laying around, you can make them less dangerous!
    http://www.ncbi.nlm.nih.gov/pubmed/9662613

    But, as Gemma said, onions and garlic have many more positives than negatives. They are natural antifungals, for one. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC203719/

    And antibacterial, for two! http://www.ncbi.nlm.nih.gov/pubmed/6669596

  9. I think you are making quite an assumption when you conclude there will be no value in directly supplementing with clostridia. We have an epidemic of antibiotic overuse that is decimating bacterial diversity in American guts.

    Yes, everyone who is alive is harboring SOME clostridia, but are they the RIGHT clostridia, and are they the entire compliment of clostridia strains that should be present, or a mere fraction that survived antibiotic onslaught? To the extent that new probiotic supplements in development are able to restore key ancestral strains, they could be immensely valuable.

    • Thank you so much!

      I’d love to know your opinion on calcium bentonite clay with regards to our gut flora.. I was under the assumption that it kills the pathogenic bacteria while allowing the good gut flora to thrive UNTIL I came across this article

      http://www.ncbi.nlm.nih.gov/pubmed/22970735

      Influence of bentonite particles on representative gram negative and gram positive bacterial deposition in porous media

      I would love for any of you to tell me what gram negative and gram positive bacteria are and if soil based organisms are affected by bentonite clay?

    • I’m quite sure these bacteria weren’t selected because they were the “right” strains or “ancestral.” They’re just what they found in humans, so they put them in a pill. And there isn’t much evidence that probiotic supplementation leads to significant colonization. I don’t discount the idea that it may aid in that process, but it’s very speculative. Hyping up Clostridia probiotics right now is akin to a doctor recommending lap band surgery to someone who is complaining about weight issues before having a conversation about diet.

  10. Sapna – You have stumbled across something completely unrelated to taking bentonite clay as a health supplement. The paper you linked is from the Environmental Science Technology Journal and is discussing the use of bentonite particles in a water filtration system (aka porous media). The full text would have made that clear, but no worries!

    Here’s a good full text paper on the traditional uses of clay: www . ncbi.nlm.nih.gov/pmc/articles/PMC2904249/

    And here’s another, addressing exactly what you ask: www . ncbi.nlm.nih.gov/pmc/articles/PMC2413170/

    “To our knowledge, these experiments represent precedential investigations of a novel geological nanomaterial that displays broad-spectrum antibacterial effects against human pathogens, including antibiotic-resistant strains.”

    Somehow, and don’t ask me how, bentonite clay has the ability to selectively kill pathogens and leaves beneficial microbes alone.

    • Except those studies didn’t look at whether the clay “leaves beneficial microbes alone”. So, we have no idea whether the ingredients in those clays kills beneficial probiotics as well as killing bad bugs. Unfortunately.

      Nature isn’t always what we want it to be.

  11. Hello Mr. H,

    Great blog. You have some great info. I know that it is good to just eat plenty of different kinds of fiber, and whatever bacteria that are supported by doing so is good, and I suppose I don’t need to know what specific bacteria that is to get these benefits. But I am still confused about some things.

    I understand clostridia is good, but otherwise for other fermicutes, why is there so much data that shows an increase in fermicutes and decrease in bacteroidetes causes obesity and weight gain and other health problems. In fact I have seen a decent amount of data (and first hand accounts) suggesting smoking cessation causes weight gain regardless if diet and food intake does not change. I think I have seen some other people bring this up, but I don’t think I saw an answer from you. I was hoping you could give some insight.

    Not that weight is that important, but everything I have read not on your blog seems to suggest weight gain is a symptom of other underlying problems.

    I have also seen data showing that decreasing weight, seemingly independent of the method, increases bacteriodetes and increases fermicutes.

    Also you said this property about these bacteria seems to be true with non-human animals as well. So does that mean mice as well? If so this study also seems to suggest the opposite of what you have been saying.
    http://mbio.asm.org/content/5/3/e01011-14.full
    (Of course the Saccharomyces boulardii could be doing something special in this case, that changes how the whole thing works)

    Is it that a healthier gut with more fermentation allows the fermicutes to stay lodged in your mucosa and hence doesn’t come out in stool and so don’t show up in a stool tests, while bacteroidetes do ( or are being expelled more)? I find this unlikely.

    Could the difference be in people who have a diet high in (good) fats with mostly vegetables, versus a standard high protein and carb diet with similarly mostly vegetables? I could see that being an issue. All the cases I have seen showing an increase in fermicutes with an increase in plant based foods seemed to be in diets that were higher in healthy fats and lower in protien and carbs. As far as I can tell, the cases that had an increase in bacteroidetes ( as well as benefits and weight loss) with more plant based foods, were likely cases where the previous diet was more protein and carb based, with less fat.

    I eat mostly a plant based diet with very low carbs (non vegatable and resistant starches that is) and lots (and lots) of healthy fats, so if what I said was true your assertions would apply to me. I have a healthy digestive and immune system, no known allergies, and am lean, so I don’t need much help in this area, but I am trying to help my mom and rest of my family.

    Thanks!

    Shoe

    • Hi Shoe. The simple answer is that the firmicute/bacteroidetes ratio theory is outdated and probably wrong. Other studies show the opposite, and most recent data show no real link.

  12. Hi, I just came across the article today and then this blog. Thanks for the 411. I, myself, have severe allergies to “LIFE” (Allergist’s joke). Besides being allergic topically and via respiratory, I am allergic internally to nearly everything they test for in scratch tests and blood tests. I have done the “avoid for two weeks and try a bite” thing also. So far I am allergic to foods…Tonya’s allergies:
    *Ginger, turmeric and cardamom (Zingiberaceae Family).
    *Olive, Olive Oil.
    *Sage (Artemisia family).
    *Artichoke, Sunflower, Safflower, Grindelia, Echinacea, Yarrow, Thistle, Sesame, Lettuce, (Asteraceae family).
    *Beef (Bovinae Family).
    *Crab, Salmon, Shell fish, Shrimp, most fish.
    *Wheat, Barley, Rye, Oats, Corn, Rice, (grains and grasses).
    *Banana, Strawberries, Kiwi, Orange (all citrus), Melon, peach, Pear, Apricot, Pineapple.
    *Carrot, Celery, Parsley, Parsnips, Fennel, Anise, Caraway, Cilantro, Cumin, Lovage, Chervil, Spinach, Onion.
    *Potato, Tomato (Night Shades)
    *Peanuts, Tree nuts, Soy, Lentils, String beans, peas, lupins, Carob, Alfalfa, Tamarind (Legumes).

    Things okay to eat:
    Garlic, cinnamon, pure maple syrup, agave, honey, cane sugar, salt, black pepper, chicken, pork, turkey, tuna (pure), eggs, milk, butter, cheese, plain yogurt, apples, blueberries, bilberries, cranberries, grapes, coconut, bell peppers, sweet peppers, broccoli, cabbage, cauliflower, Brussels sprouts, squash, cucumbers.
    I am lucky though, I have a friend who only ate chicken and rice until he was 19 and he went through many therapies.

    It is frustrating when eating with family, they ask, “Well, what if you just have a little, you know, everything in moderation.” They don’t get it. I bring my own food when we eat anywhere outside the house, even restaurants. My husband cooks for me. That is how I have survived this. I only by Organic. non GMO foods, and bottled water. Mostly, I eat blueberries with yogurt for breakfast and eggs and bacon for lunch and chicken and a cabbage or squash member for dinner. Apples, grapes and cheese for snacks. I switch it up and change the order sometimes or I eat raisins, coconut and Enjoy Life chocolate in yogurt. I have found two brands of store bought vanilla or chocolate Ice cream I can eat. Few other things that fit in my categories that I pig out on for comfort food when I am at my wits end.
    Since I stopped eating what I was allergic to, I haven’t had asthma (unless I am sick and when the wind is up) and I went from 212 lbs. to 140 lbs. I only found out about 3 years ago that I was even allergic to food. I have been to the allergist since I was in grammar school and I am now 46 years old. I just think about all the people out there suffering, that don’t have to suffer, if they would only test more people and if the FDA and EPA would actually do their jobs.
    Anyway. Thank you for letting me rant and for letting me read about your experiences. My doctors have not been helpful. I have gone through the Allergy Shot system twice and they “Don’t understand why it didn’t work. Maybe you (I) should just do it again.” AH, NO!

    • Have you had your histamine level tested? Do you have a disposition to low DAO enzyme activity? Half the stuff you listed is cross-reactive to birch pollen, the other are high histamine foods. I have a child with oral allergy syndrome with birch pollen cross-reaction; and histamine intolerance. Looks remarkably similar. Get your DAO level tested and get a genetic test for it. You can take the DAO enzyme orally. Try Seeking Health Brand on Amazon. 2 caps before EVERYTIME you put anything in your mouth.

    • Oh, and the allergy shots we are doing too. She can eat tree fruit again without the itchy mouth except cherries. It takes 5-6 years for that eradication to potentially maybe become permanent. If you quit before that time period allergy comes right back.

  13. does this supplement contain the same Clostridia used in the study?
    http://www.amazon.com/Advanced-Orthomolecular-Research-Probiotic-3-Probiotic/dp/B0082DDQH6

    i agree that going the western medicine route with this probiotic isn’t what’s best for people with allergies, but I could really use something like this to get my gut flora back on track. A few years ago i found out i’m allergic to many seeds, and over time it has gotten so bad that it seems i’m allergic to every plant in those seed families. my diet is soylent (1.3 or earlier), rice, potatoes and meats. and that’s it.

    anyways, great post, thanks

  14. Just found this article researching clostridia probiotics and I don’t understand this excerpt:

    “In other words: you don’t need to “seed” or “infect” yourself with these bacteria, as if they are some exotic, hard to acquire bug. Don’t believe me? Here’s the proof: EVERY SINGLE INDIVIDUAL GUT REPORT I HAVE EVER SEEN CONTAINS THESE BACTERIA. I have never seen a report showing no Clostridia. Not one. If you are a human, then you almost assuredly have Clostridia in you.”

    Are you saying that on stool tests everybody has clostridia species? Because I have a stool test which showed a few species that were low and clostridia were actually nonexistent, showing no laboratory growth whatsoever. So I’m looking for a probiotic to address that, and not having any luck. But I wanted to clarify, you claim to have seen several stool tests and everyone has clostridia?

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