This Is Your Brain On Fiber

Alright, the brain post. As promised. Please note, this is not a deviation from our central line of inquiry — we’re dot connecting, always. So hang tight! We’re going somewhere with all this…


One topic we haven’t covered here yet is the microbiome and the brain. But not for lack of interest. Quite the opposite — it’s too big, too important. I just haven’t been ready for it. Excitement overload, you might say. And the other reason is that the research in this area is more limited. But fear not, there is plenty enough to make for another episode of You Can’t Be Serious? Theater. I’ll start with a flurry of the more commonly cited studies involving experiments with isolated bacterial species, and then end with what I would consider to be the most compelling and authoritative study yet done on the gut-brain link — and what it all means for the case we’ve built so far.

Infection with C. jejuni & C. rodentium

Over the past decade, researchers have shown that introducing non-invasive strains of gram-negative bacteria into mice can alone stimulate anxiety, apart from any inflammatory or infectious effect of the pathogens. A series of three studies introduced the bacteria Campylobacter jejuni into mice to induce “sub-clinical” infections, which did not stimulate any immune response. The experiments showed that the pathogen induced an anxiety response in mice directly through neural pathways.

Similar studies were done with gram-negative bacteria Citrobacter rodentium. One study showed that mice infected with C. rodentium elicited anxious behavior without any signs of immune stimulation, showing the effect being transmitted directly from the gut to the brain. In another experiment, mice exposed to C. rodentium showed impaired learning and memory. Pre-treatment with probiotics prevented these effects. The study concluded: “The intestinal microbiota influences the ability to form memory.” The study also looked at germ-free mice (mice without a microbiota) and found that they lacked non-spatial and working memory altogether, regardless of infection, “indicating the requirement for a commensal gut microbiota in memory.

C. jejuni and C. rodentium belong to the Proteobacteria phylum. Proteobacteria go down when you eat plant fiber and stop smoking.

Probiotics: Lactobacilli and Bifidobacteria

There is a decent amount of research on specific strains of probiotic bacteria — specifically the lactic-acid producing bacterial groups Lactobacillus and Bifidobacterium. The vast majority of bacteria found in fermented foods and probiotic supplements belong to these groups. They are also normal commensal residents of the human gut.

In one study, supplementation with the probiotic bacteria Lactobacillus rhamnosus in mice was found to significantly reduce anxiety and depression. The effect was not found in mice whose vagus nerve was removed, proving a direct gut-to-brain mechanism. Another study found L. rhamnosus effective at attenuating Obsessive-Compulsive behavior in mice. The probiotic was found to be as effective as Fluoxetine (better known as Prozac, which is often used to treat OCD).

In a study using maternal separation as a standard inducement of depresson in mice, the administration of Bifidobacterium infantis was found to reverse depression and normalize motivation.

The combination of Lactobacillus helveticum and Bifidobacterium longum has shown anti-anxiety and anti-depression effects in mice, rats and humans. That same combination was shown to reduce post-myocardial infarction depression in rats.

And finally, a human study — perhaps the definitive one in this class of studies. 36 women with no gastrointestinal or psychiatric symptoms were split into three groups: one fed a fermented milk product (ie, yogurt with lots of lactobacilli and bifidobacteria), one fed a non-fermented milk product (no probiotic bacteria), and one with no product at all. Brain scans showed that in the women consuming the fermented yogurt, wide-ranging alterations in brain connectivity and regional stimulation were observed. They showed decreased reactivity in an emotional reactivity task (angry and frightened faces) and increased connections in cognition-associated areas of the prefrontal cortex.

Lactobacilli belong to the Firmicutes phylum. Bifidobacteria belong to the Actinobacteria phylum. Firmicutes and Actinobacteria go up when you eat plant fiber and stop smoking.

Diet, Microbial Diversity, Cognition

An interesting study. As opposed to the previous studies we just looked at, which tested the effect of introducing isolated species of bacteria into the microbiome, this study looked at the existing microbiome of mice as a whole — a lot more like the studies this blog has covered so far. Specifically, the researchers wanted to see if a diet-induced change in mice’s microbiota could have an effect on learning & memory. 

The researchers designed two diets with nearly identical nutrient ratios — calories, amino acids, fatty acids. One diet, however, included lean beef, which was known to have the ability to modulate mouse microbiota. Results: the study found that in lean beef fed mice, microbial diversity rose significantly. And so did learning & memory ability. A decrease in anxiety was also observed. It should be noted that while they went to great lengths to equalize the diets, they were not perfectly identical (specifically, the lean beef diet contained more taurine and double the fat). As such, microbial causation was not proven, but a correlation between microbial diversity and better learning & memory ability was firmly established.

Microbial diversity goes up when you eat plant fiber and stop smoking.

The Big One

Finally: the mouse study to rule them all. One reason I like this study is that, as in the previous study, it looks at the mouse microbiome as a whole. But the other is the methodology — germ-free controls and microbiota transplants galore. Solid isolation of microbial causation. As such, I’ve found it to be the most oft-cited study in gut-brain research.

The study had a familiar goal: to see if changes in the mouse microbiome had a direct, causal effect on mouse mood and behavior. To cause a shift in microbiota, researchers applied antimicrobials to one group of mice, but not to the control group. Also, just to be sure the antimicrobials weren’t having some other non-microbial effect, they also gave antimicrobials to germ-free mice — mice without a microbiota. Mice given the antimicrobials, but not the control or germ-free group, experienced a marked shift towards more exploratory behavior and less anxiety. The mice — which were a strain bred to be overly timid and shy — all of a sudden became “bold and adventurous,” in the words of one of the study’s authors. But that’s not all. Researchers then implanted the microbiota of the mice that were given antimicrobials into the germ-free mice. The germ-free mice, after the transplant, experienced the same shift toward more exploratory behavior and less anxiety. Thus, it was shown that the shift in microbiota was the cause for the change in mood and behavior.

Oh, and what exactly about this microbial shift caused this change? Let’s let the study speak for itself:

A 7-day course of ATM resulted in a significant increase in Firmicutes and Actinobacteria, and a decrease in γ-proteobacteria and Bacteroidetes. We believe that these changes in bacterial composition of the colon were responsible for the documented changes in brain BDNF levels and in behavior.

Ahem. Anxiety gone when Bacteroides and Proteobacteria go down, and Firmicutes and Actinobacteria go up. The same exact thing that happens when you eat plant fiber and stop smoking.

Once again, it’s our “golden ratio” of microbiota. But this time implicated in a completely different area of health — the brain. We now see that this exact same microbial shift can impact brain functioning. As I noted in my last post, the ability to show similar mechanisms in different factors of disease — or different areas of health, in this case — is a very good way to build a broader case. That we now see this microbial shift affecting both the brain and the heart further solidifies a link between it and general human health.

Neat, huh? Thanks for reading. See you next time…

Oh, wait. One more thing…


The fact that we’ve established a firm case for a causal link between microbiota and heart disease, as well as the possibility for microbiota to influence brain functioning, puts us in a position to do something interesting: it allows us to to test that second brain/microbiota link for specific cases. We’re now in the position to use these two findings to put other specific brain-related factors/attributes under suspicion of having a microbial link. How? By using the microbial-heart link as our anchor.



Assuming an established microbial origin for heart disease, and assuming an established ability for microbiota to influence the brain, it is possible that a brain-related factor with a strong correlation to heart disease is, itself, strongly and independently influenced by microbiota.


Here’s what I mean.

In the case of plants and smoking, we’ve essentially created two separate 3-pointed triangles of causality.

Smoking             Plant-Fiber

These two separate triangles have the same  direction of causality. We can be confident of this direction because both factors have been shown to directly cause this microbial shift. And these two factors are separately correlated to heart disease. The fact that they are so different, yet both cause the same shift in microbiota, reinforces the microbiota -> heart disease causation theory.

Since we’ve now established the possibility that this microbial shift can also affect the brain, we can do something interesting: we can test for other brain/microbiota links by replacing plant fiber and smoking with a brain-related factor — but only one that has been shown to have a correlation with heart disease:


You’ll notice that there’s one thing different about this triangle: the direction of causality. That’s because, in this case, our data shows that microbes cause the brain change, rather than the other way around. In the case of plants and smoking, we have proof of the opposite: plants and smoking cause the microbial shift. But it also makes intuitive sense — it’s hard to see how microbiota could force you to smoke or eat plants. But in the case of the brain, it’s a little less clear cut. Yes, our studies above show a microbial -> brain change direction, so we know that’s possible. But we also know that things like stress may affect our microbiome — the gut-brain is a two-way street. But since we’re specifically interested right now in a microbial -> brain change effect, we’re going to structure our theoretical triangle this way and let our reasoning ability decide if the brain factor we find makes sense or not. If it does, it’s correlation with heart disease will mean it is a side effect of the microbial mechanism, rather than a root factor like plant fiber and smoking.

Which brings us to the final, crucial task: finding a good brain-related factor correlated to heart disease.

To really make this worth our while, we’d have to find some kind of brain-related factor that has a really high correlation with heart disease. Something strong enough that would lower the probability of it being just a side effect of, or a precondition for, some other stronger correlation. And as I said, it would also have to make intuitive sense in terms of direction of causation . But most of all, it has to be a pretty strong link — something that comes at least close to smoking’s place as the NUMBER ONE predictor of heart disease. In other words, we’d have to get pretty lucky. And I just don’t see that happening any time soo…

Report: Low IQ second-highest predictor of heart disease (after smoking)

Uh oh.


— Heisenbug


16 thoughts on “This Is Your Brain On Fiber

  1. Great post. I only have to read it again, to make sure I got everything right!
    There was an Australian doctor who showed that stomach ulcers had a microbial base, and treated it accordingly. One more thing to show us how important good functioning gut flora is.
    I know you didn’t mention it but is there a connection to dementia? There is a connection between grains and dementia. I am assuming that grains have a negative effect on our gut bacteria, and “starve” our brains of the corrent nutrients and so dementia occurs.
    Once again, I have come to the conclusion how important good gut bacteria is for our overall health.

    • There isn’t a lot on gut bacteria and dementia. But there is quite a bit of research on dementia and metabolic syndrome. Some even classify dementia as a metabolic disorder of the brain. So if dysbiosis has something to do with metabolic disorder…

  2. Thank you for your blog post! I find the topic fascinating!

    You might be interested in this blog – It’s not mental – written by a mother of two daughters who recovered from serious mental health problems by solving underlying physical problems. Many of these can be linked to gut health (more connections!). Her thesis is that there isn’t necessarily something wrong with the brain, but that physical problems elsewhere are the root causes of the behaviors and mental distortions experienced.

    This post brings to mind a chapter on gut health in “The Ultramind Solution – fix your broken brain by healing your body first” by Dr. Mark Hyman. He gives examples of some cases where the patients suffered from OCD, or erratic, disruptive behavior and part of the solution was giving them selective, nonabsorbed antibiotics to remove pathogenic bacteria (and in some cases antifungals also). One woman was harboring a bacterium that produced ammonia, which was at the root of her OCD. Imagine what a difference healing the gut can make for people!

    People with mental health issues also often have problems with their HPA axis. I have found posts here: helpful in making connections between the endocrine system and gut health.

    Keep joining the dots. It is very helpful!

  3. As I just related on Melchior’s blog : the plot thickens.
    But what if it is not a two-way street Shant? What if it is a matter of greater or lesser presence of microbiota? We all know by know that we are completely and utterly outnumbered by our microbes, so I am beginning to think that there could quite well be a lot brain volition than we like to assume. We may be thinking with our gut. I think our dog thinks with his gut too 🙂

    • It really does make you wonder who is in the driver’s seat. While I’m not quite ready to completely hand over the keys, we’re clearly going to need some type of sharing agreement. 🙂

  4. What are the mechanisms of smoking disrupting the microbiome?

    Is it the nicotine specifically, or a combined attack by the hundreds of others chemicals in cigarettes?

    I’m asking because I occasionally chew nicotine gum as a stimulant. I find isolated nicotine to be quite a cognitive boost and have never found it addictive (because it lacks the MAOIs, see here if interested

    • I don’t think we know what exactly is causing the microbial effect. But the available evidence suggests it isn’t the nicotine. As I mentioned, tobacco smoke has been found to introduce gram-negative bacteria and endotoxins directly into smokers, so that’s one possible clue. Also, nicotine patches have not been found to have the same correlation with heart disease. Lastly, pipe smoking, which exposes smokers to much less nicotine, has been found to be no safer than cigarettes in terms of heart disease risk (in one study, anyway.)

  5. I am just learning about probiotics and other gut microbes. Not even sure I an using correct terms. I have OCD and find this info very helpful and would like to learn more. Can taking bifidobaterium infantis actually help my OCD.Where can I find a dr. to talk to or get to work with me.

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