Eating Plants & Quitting Smoking: Was I right about Firmicutes?

Some new evidence brings us closer to the possibility that I was.


That’s from a 10-day experiment conducted by American Gut/Human Food project founder Jeff Leach, which he posted on the project’s Facebook page. In addition to consuming a high protein/fat paleo-ish diet, Jeff professes to normally consume a very high plant fiber diet. For 10 days, Jeff dropped fiber consumption entirely but kept the rest of his diet the same. And those are the results — a complete reversal of Firmicutes and Bacteroidetes. Less noticeable, but no less interesting, is the reversal of Actinobacteria and Proteobacteria.

This is relevant on many levels.

First, this helps lay to rest, once again, the unsubstantiated hypothesis that high firmicutes are connected to obesity. Here, we see it’s a direct result of fiber fermentation in the gut.

Second, this reversal is EXACTLY the same reversal we saw in the cigarette smoking study I posted recently: cessation of smoking results in a rise in Firmicutes and Actinobacteria. And I posited that a reasonable assumption is that picking up the smoking habit does the reverse.

So now we have two completely different actions that are generally regarded as healthful — eating plants and quitting smoking — leading to precisely the same shift in microbiota.

Lastly, this experiment supports (but doesn’t yet prove) the case I made in my posts exploring the Resistant Starch experiment — that for Resistant Starch to be the holy grail in restoring a healthful gut microbiome, we should be seeing some changes in Firmicutes, and specifically the Clostridia clusters IV and XIVa (“Ruminococcaceae” & “Lachnospiraceae” on these gut reports). “Tatertot” Tim’s results, after extended supplementation with Resistant Starch in the form of raw, unmodified potato starch, did not show this — he had higher than average Bacteroidetes & lower than average Firmicutes. Michael Pollan and Jeff Leach — plant-lovers both — had the reverse. (But Tim’s reports DID show much higher than average Actinobacteria, specifically Bifidobacteria, which may explain why Resistant Starch is leading to many beneficial effects. I touched on that here and at the end of the smoking study post.)

But again, that assumes that a high Firmicutes/low Bacteroidetes ratio is necessarily healthful and should be sought out. Right now we can only confidently say that it is not detrimental and is a result of plant consumption. If anything, the Resistant Starch experiment shows (with the extremely limited data we have so far) that beneficial effects can be realized without this ratio.

But the fact that both smoking cessation AND plant consumption lead to this ratio certainly tips us further toward that conclusion. And there is plenty of more evidence that paints a very convincing picture, in my opinion:

What else do we know about Firmicutes and Bacteroidetes?

  • Besides the obesity link, I have yet to see anything correlating high firmicutes to disease.
  • Quite a few disease-specific studies correlate high bacteroidetes to more disease (Type 1 Diabetes, IBD, Obesity, Metabolic Disease)
  • Firmicutes are almost exclusively gram positive. They do not produce endotoxins, and so they cannot contribute to endotoxin-induced inflammatory disease.
  • Bacteroidetes are ALL gram negative. All endotoxin producers.
  • Firmicutes — specifically the butyrate-producing Clostridia clusters — live in the mucosal lining of the intestine. It’s where all the butyrate production is, the preferred energy source for colonocytes. They seem to be the guardians and nourishers of the gut barrier.
  • Bacteroidetes, conversely, are predominant in the luminal space — the hollow space within the large intestine.

Those last four points seem especially illustrative to me. Here is the (speculative) picture they paint: it seems to me that if Firmicutes/Clostridia — the intestinal barrier’s front line of defense — aren’t guarding the mucosal barrier, endotoxin-producing Bacteroidetes have free reign to opportunistically bloom and invade. Not outright bad guys (after all, they are at least the second largest group in most people), but hey, if their natural antagonistic counterparts decide to go on vacation, they have no choice. Ecosystems 101.

Again, highly speculative. Just a hypothesis. Hypotheses aren’t meant to be believed, they’re meant to be tested. And until someone lends me an RV and a gallon of methylamine, that will have to wait.


— Heisenbug


20 thoughts on “Eating Plants & Quitting Smoking: Was I right about Firmicutes?

  1. Is there a link to the list of high fiber veggies that Jeff used? Or are they the same that are typically listed (onion, garlic, leeks, artichokes…)?

  2. It would be interesting to know total amount of bacteria… maybe high fat + no veggies can lead to a majority of bacteroidetes, but a very lower number overall. Would that be less inflamatory? So much unknowns…

    • Ive read all this here….. I my self did the american gut… I had crohns disease –I say had.. I changed my diet to FATS, lots of veggies onions etc eggs omega 3 and I have very little Firmicutes and alot of the following Genus Bacteroides 37.3% Genus Serratia 3.8% 0.19% 20x
      Genus Parabacteroides 20.1% Family 0319-6G20 0.1% 0.00% 43x
      Genus Akkermansia 13.2% Genus Bilophila 0.6% 0.17% 4x
      Genus Serratia 3.8% Family Alteromonadaceae 0.0% 0.00% 10x

      I eat a shit load of veggies so I dont buy it… Today these results are a year after I now have no disease and all docs are lost.. i factor in my health Akkermansia as the avg person has 3 to 5 percent me alot more… when your low you get type 2 and auto immune dieases.. ( crohns and type 2 run in my family ) i genetic tested and carry 5 genes for gluten and 2 for type 2 HLA DQ I great NO sickness , no allergies , no sinus issues etc – stuff I had my whole life.. All gone.. Ive taking a big interest in this… Ive done many advanced tests… and where I found my problem was YEAST…. all these studies focus on bacteria you dont hear shit on yeast… which can be from bakers or brewers yeast ASCA antibody or AMCA candida . Every person with crohns seems to be high in one if these and some others ,. For me it was AMCA– candida yeasy and ALCA — sugars.– sugars digest as starch grains milk . I removed all the starch you guy talk about… the sugars MIlk and grains… over time I got better.. all my docs are lost…as they focus on bacteria.. and all the bullshit meds to turn off stuff ,anti inflammation drug etc — for me I dont see it.. I can prove in many tests MY yeast was to high….killed /lowered it… diease is gone… what does it eat… starch , grains and milk… again I eat high fats good fats LOW starch veggies and chicken meat s etc all three meals as well eggs and nuts.. the opposite of what they tell you with crohns… yet im healed I plan on doing the american gut sample again… to see whats happen in a year . Maybe once you get yeast under control… and your bacteria come back— they eat the starch… thats not the case for me thou… dont see in my testing and results.. seek out doing this advanced test… So what bacteria and YEast toxins are being released in your body —OAT test
      as well there advanced comp stool test read the sample reports etc Id be happy to share every thing ive done and seen I documented my life day one with crohns in testing, advanced testing and tests docs have no clue about… it pointed to HIGH yeast and low gut bacteria… when I started great plains results showed half of the gut bacteria i have now and tons of yeast…. now everything is good… no yeast higher bacteria..I also factor my Akkermansia bacteria… I did advanced NMR lipo profile several times my LDL particles are low like 135 smalll dense total is 1300 LDL particles My size is good.. theres a fight here is it total number and small particles or best size and least amount of small particles… there two experts who both say different.. I dont know I feel great now.. im 41 , did a cardiac calcium score i was a 1 , when I was sick my cholestrol was 147 total…. today im 227 and could careless I feel great.. I point it all back to YEAST…..

      • I’m sorry, but the lack of sentence structure in that comment leaves me lost. It sounds like the commentator has some good ideas about candida, but the ideas are buried a bit.

  3. I suppose you could speculate as to why the Japanese who eat Natto AND smoke cigarettes have a surprisingly low incidence of cancer. I thought it was the vitamin K2 but maybe there’s more to it.

    • Hi Gabriella,

      I too have been wondering whether certain habits/diets are protective from the microbial impact of smoking. People have been smoking tobacco for a long time. But the high levels of the diseases it’s associated with are new, relatively speaking.

  4. New reader. Couldn’t find a generic place to say thanks…so here. Thanks. Wonderful stuff. Here via Seth Roberts.

    Do you have a current positions summary page of any sort. I hear your analysis, and scientific approach. I don’t have the bandwidth to follow your method…and am chasing the engineering questions. What/how.

  5. I am addicted to this blog, devouring all the articles since I discovered it via Twitter. I also gave up smoking 1 year ago this week (yay!) but I have since gained 20lb. Since I gave up by switching to an electronic cigarette, I am still getting my intake of nicotine, albeit in a safer delivery method. So the lack of the appetite suppressing effects of nicotine can’t explain the vast uptick in appetite that I have experienced.

    Are you really sure that the increase in firmicutes is not to blame in this instance? They seem to be very good at procuring more energy out of food.

    Also, and I can’t find any evidence of this elsewhere, anecdotal or otherwise, my switch to e-cigarettes prompted a complete remission of my IBS. I went from having to be super careful with FODMAPS to having somewhat of an iron stomach. Firmicutes to the rescue?

    • That is really interesting. I don’t think it’s been shown that firmicutes DON’T have the capacity for enhanced energy harvest, only that it’s not necessarily connected to obesity. So who knows.

      The IBS remission is very interesting, too. If there is a microbiota connection, I wouldn’t count out the actinobacteria/proteobacteria ratio. That’s about as solid of a microbiome health marker as there is. Firmicutes/Bacteroidetes is much shakier — still lots to figure out there.

      • “If there is a microbiota connection, I wouldn’t count out the actinobacteria/proteobacteria ratio. That’s about as solid of a microbiome health marker as there is.”

        Whoa. Do you have some studies in mind? I’m pretty sure I’ve read most of your blog posts, but I don’t remember seeing anything about that… but I easily could have missed it.

        Or, at least, about what ratio should one be looking for?

        (Sorry, I’d google it, but that seems like one of those searches without enough terms to make quick progress.)


  6. People who quit smoking usually start eating a lot more carbs to give them the feel good mood support they need to get through their first year of not smoking. Some of the carbs they suddenly eat more of are fruit, french fries, bread, that cause the very changes in gut bacteria that someone is attributing simply to “quitting smoking”. Not convinced that simply removing smoking causes the gut bacteria change mentioned. And taking that “study” results and leaping forward in logic with it would thus be a mistake.

  7. When people quit smoking they almost always gain weight. This seems to counter your conclusion.

    I have Crohn’s disease and would like to follow your work as it likely is important concerning this disease.

    How can I do that?

    Thank you.

    Dan Bergman

  8. My American Gut sample showed higher-than-average firmicutes, lower-than-average bacteroidetes, and much-higher-than-average bifidobacteria. I’m normal weight (BMI 23.5, but who knows how much visceral fat I’m stashing). From everything I’ve read I should be obese with those ratios, but your post helps shed light on our very limited current understanding of the microbiome.

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