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.