More Confirmation from American Gut + A Unifying Theory of Gut Health

In case you haven’t seen it yet, Jeff Leach of the American Gut Project finally got around to writing up his 10 day no-fiber experiment.

As you may remember, this experiment, which he initially posted on the American Gut Facebook page, was the topic of a previous post on this blog and a major piece of evidence for the case we’ve been building. Jeff’s experiment showed two things: 1) that the abundance of Firmicutes — specifically butyrate-producing clostridia — was driven by the consumption and fermentation of plant fiber; and 2) that the consumption of plant fiber led to the exact same microbiota shift as does the cessation of smoking. This combination is significant proof toward the microbial origin of heart disease hypothesis.

Now, Jeff has posted an extended explanation, and I’m happy to see that it is a confirmation of our own interpretation of the results. Specifically, Jeff notes:

Consequently, the relative abundance of the Family Ruminococcaceae took a hit along with the Family Lachnospiraceae and the Genus Ruminococcus. These three are known plant fermenters – that is, they metabolize dietary plant polysaccharides – that didn’t seem to compete very well as the fermentable substrates (fiber, resistant starch) dried up.

Those two families — Ruminococcaceae and Lachnospiraceae — are the butyrate-producing Clostridia clusters IV and XIVa we’ve been talking about, and the ones we assumed were to blame for the drop in Firmicutes.

Another useful bit of info from Jeff that we did not previously know: the diversity of his microbiota was halved during the no-fiber experiment. This lends a powerful piece of support to the notion that plant fiber consumption contributes to microbial diversity — something we also see in the cessation of smoking. (As I explained in the last post, microbial diversity also seemed to make mice smarter, but we’ll get back to that.)

Lastly, Jeff offers that the most likely explanation for the rise in Proteobacteria and Bacteroidetes was the rise in pH of his gut — it became less acidic. This also confirms the speculation we made about the nature of the Bacteroidetes-Firmicute relationship — that when Firmicutes dried up and stopped producing acidifying short-chain fatty acids, Bacteroidetes would opportunistically bloom as a result of a more favorable environment.

Of course, it still remains to be proven that this shift leads to adverse health consequences — that is a case we’ve been building here through the linking of different correlations. But I’m also happy to report that, in an exchange with Jeff, he informed me that he was also planning to measure health markers from blood serum and stool — including SCFAs and lipopolysaccharides (which are a byproduct of endotoxin-producing bacteria). So that may tell us a lot.

Lastly, reading Jeff’s post, I realized that there may be something that I haven’t touched on enough here and which may go a long way toward helping people understand the broader picture. And that’s the role of acidity and alkalinity in the gut. I think this concept can go a long way toward establishing a unifying theory of gut health.

In case you haven’t figured it out by now, acidity is a good thing. Acidity is a byproduct of fermentation in the gut — when plant fiber is consumed, it feeds specific groups of bacteria — Firmicutes, Actinobacteria (ie, Bifidobacteria) — that in turn produce short-chain fatty acids and other metabolites that make the colon more acidic. A very self-serving thing to do, as these bacteria thrive in a more acidic environment, and their competitors — Proteobacteria and Bacteroidetes — do not. Those groups prefer alkalinity. What’s the best way to boost their numbers? As Jeff showed: stop consuming plant fiber. No more SCFA production, less acidity.

But that’s not the only reason I consider this a useful concept. Take a look a probiotics and fermented foods — an aspect of gut health promotion that many people are much more familiar with. What bacteria predominate? The lactic acid producing bacteria (LABs) — Lactobacilli and Bifidobacteria. These are acid-loving bacteria. How else do you think these bacteria can survive the harsh conditions of your stomach and make it into your gut? And again, a real self-serving bunch, as lactic acid lowers pH like no one’s business. Good for you, good for them. It’s almost as if we co-evolved with these bacteria by consuming them for ages and ages.

But it goes even further than our friendly LABs. What about other traditional, fermented foods, like Kombucha? Kombucha is primarily made up of beneficial yeasts, and some bacteria. This can differ among types, but let’s take one of the more popular brands — GT Kombucha. The primary organisms: Saccharomyces boulardii and Bacillus coagulans. S. boulardii is a strain of yeast that is known to be highly resistant to acidic pH. And guess what makes Bacillus coagulans — perhaps the most common soil-based organism in probiotic products — extremely unique for a Bacillus genus bacteria? It produces lactic acid! In fact, it was called Lactobacillus sporogenes until the smart people in lab coats got their act together and realized they were dealing with something else.

And finally — guess what all that acid in your stomach does, besides break down all that food? It keeps the bad guys out — bad guys who can’t handle the heat. A major function of stomach acid is to protect your exposed gut from all of the pathogens with which you are in constant contact. (Something to consider the next time you pop that acid suppressing pill, maybe?) And if you were a bad gut bug hell bent on invading a human, what would you do? Develop acid resistance. Even pathogenic yeasts rely on a drop in acidity to overgrow.

It’s almost as if acidity tolerance + inducement is a defining requirement for commensalism.

Be good to the acid lovers, and they’ll be good to you. Keep it acidic, my friends.


— Heisenbug


16 thoughts on “More Confirmation from American Gut + A Unifying Theory of Gut Health

  1. Thanks for keeping us not only informed but up on our toes as well. I must admit it sometimes scares me that we get too excited too quickly about something we just discovered or some dots we appear to be able to connect. As Jeff commented : “As with any ecosystem, it’s the community as a whole that’s likely more important, not single members per se. Connecting the dots when there are lots of them – and they are shape shifting all the time – is proving to be tough (a similar reality has slowed our understanding of the role of human genes in disease). This will take some time – but the writing is on the wall..” My feeling is, we are at the beginning of something that could take quite a few twists and turns before we dare to state unequivocally all fiber is okay, some is better, and some is not so good.

  2. Does mean that the teaspoon or two of Bragg apple cider vinegar in a glass of water that I have been drinking in the belief that it will help improve the health of my gut is actually makes things worse by making the pH more akaline?

  3. Thanks, I feel much better. 🙂 You mentioned kombucha and increased consumption of plant fiber. What other ways are there to help the acid lovers?

    • Plant fiber is the only one mother nature really requires of you. But any other fermented/probiotic food probably helps. And staying away from any unnatural, processed food is probably a good bet too. There is some evidence that suggests wheat/whole grain consumption leads to a growth in certain types of bacteria (prevotella) that might not be so great for you, but jury’s still out on that.

  4. Hello, thanks for sharing insightful reading. Regarding Kombucha, Paul Stamets has a great article on the topic. He’s a mycologist, he stated in the article that the Moscow Central Bacteriological Institute identified the gelatinous mass as Bacterium xylinum and within this matrix lived, in symbiosis, Saccharomyces ludwigii, S. pombe, Bacterium gluconicum, B. xylinoides, B. katogenum,Pichia fermentans, Torula species and “other yeasts. You might read the full article on his a adventure with the concoction, quite amusing.

  5. So are you saying that the only healthy gut is an acidic gut? If that is the case, we should be able to see this across all mammals right?

    I wonder what the pH of a tiger gut is, and how it’s maintained. Perhaps they directly excrete more stomach acid but we can’t do that because our bowels are too long.

    • Not necessarily. Acidity promotion, within a certain range, is (presumably) a good thing because it supports a healthy human microbiome. Trying to draw comparisons to other animals would be quite difficult, especially in the case of a tiger — carnivores have a very different GI.

  6. Hello there, i am hoping to get some clarification after stumbling upon the many correlations between the gut microbiome and overall health and how we interpret signs of health.

    After stumbling upon the apparent correlation between the gut microbiome between obese people, people who quit smoking and that study where people are put on a carnivorous diet vs a vegan diet which resulted in a shift from more firmicutes to more bacteroidetes (and starting to lose weight on the carnivorous diet vs the vegan diet), i have become a bit confused.

    This site seems to have shown conclusively that it is not the addition of meat, fat and protein but the lack of plant fibers which causing this shift and that the potential weight differences (less) which seems associated with more bacteroidetes vs. firmicutes is not a good indication of overall health.

    This would make sense from an evolutionary standpoint, seeing that it would logically aid survival if available nutrients would be digested as efficiently as possible, yet with the advent of easy and processed calories this beneficial trait has become an apparent disadvantage.

    It would appear to me that the widespread incorporation of refined sugars in most things people tend to eat if they do not consciously look at what they take in is a main cause of the weight gains we can observe in people who’s gut microbiome could actually be deemed healthy and beneficial.

    I am a smoker with a quite physically demanding job and i also do a lot of strength training and due to my exercising i started to contemplate quitting smoking to aid in generating a slight caloric surplus. However, as a quite lean male, i have inhibitions which are quite similar to those more seen in females in that i would not like to end up with skinny fat / belly fat if i would quit smoking. I see so many skinny fat people around me that have jobs which burn between 1000 / 1500 calories a day on average only on their jobs and who even do cardio exercises on top of that but who still have the belly while not eating that much at all.

    Furthermore, there also appears to be a relation between skinny fat and obese people their hormone levels, in which testosterone is lower then in people with a lean BMI where the added fat in people with a higher BMI is also a cause for higher estrogen/ lower testosterone, which appears to aid in a higher BMI.

    This also seems logically explainable through an evolutionary framework in that people with a lean body mass and high in testosterone could potentially function better as a carnivore / hunter (with a gut microbiome suited for that purposes opposed to a gatherer which would be more suited to expand less energy and digest more efficiently the diverse nutrients it gathers.

    Although i am mainly considering the male part here, could it be somewhat accurate to state that aesthetically, society admires lean alpha male carnivores running on testosterone / bacteroidetes opposed to potentially more healthy herbivore / omnivore like males who have to be quite careful in monitoring their caloric intake and macro’s to keep their BMI’s in check?

    Thx and sorry if i have been longwinded and posted something on a part of this site where it is not appropriate/relevant anymore, i am just eager to learn a bit more.

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