Anthropology & Science: Is L. Plantarum a Keystone Bacteria for Human Health?

A quick catch up for anyone who is just tuning in:

Recently, I discovered that L. plantarum — the dominant bacterial strain in fermented plant foods like kimchi and sauerkraut — cures my hand eczema. I initially discovered this by noticing that I hadn’t experienced any eczema in the past two years, during which I consumed these foods on a near daily basis. And I then noticed that once I stopped consuming them last fall, my eczema returned. I hypothesized that not only was it these foods that kept the eczema away, but that it was specifically the probiotic bacteria that was creating the effect, because probiotic bacteria are known to primarily act through immune system modulation. And eczema is an allergy-related disease that is a product of an abnormal immune system response. So to test this hypothesis, I obtained a probiotic supplement containing a pure, isolated form of L. plantarum. Within three days of taking the supplement, my eczema had completely cleared.

Since then, multiple reports from readers of this blog (and elsewhere) have tried the experiment and replicated the results. And they have worked for other immune/allergy-related conditions as well, which was something I also hypothesized in my original report.

As you can imagine, since then I’ve been extremely interested in L. plantarum. Here’s why:

  • Anything that can have this kind of effect on the human body must hold some major significance for general human health.
  • Fermented foods have been a part of the human diet for a very long time, and are found throughout almost every culture. Humans are very likely adapted to eating them, which means the bacteria in fermented foods are important for human health.
  • Fermented foods, for the most part, fall into two categories: vegetables and dairy. Because L. plantarum is the dominant bacterial strain in fermented plant foods, this means that L. plantarum would account for a very significant proportion of the health benefit derived from fermented foods.

And it’s that last point that my mind has been focused on lately. I’ve been pretty satisfied with the explanation that L. plantarum must be important because it’s so dominant in fermented vegetables, which probably make up the majority of fermented foods (milk is just one food, but there are many types of plant foods you can ferment). But I haven’t been completely satisfied.

You see, I also very regularly consume fermented dairy, in the form of yogurt. But I never found yogurt to have any effect on my eczema. I’ll consume it for a while, stop for a while, and nothing. And it’s also the case that L. plantarum is not in yogurt. But fermented dairy must be important to human health as well. I guess L. plantarum can’t really explain its importance.

Or can it?

One thing I’ve known is that, while L. plantarum is never in any yogurt I’ve ever come across, it is found pretty often in kefir. Yogurt, on the other hand, has probably gone through quite an evolution in the past hundred years as it’s become a much more ubiquitous, mass produced food. Today, for a manufacturer to be able to call its fermented dairy product “yogurt,” it needs to contain just two bacterial species: S. thermophilus and L. bulgaricus. Whether this has anything to do with what constitues the ancient and ancestral formulation of yogurt, I do not know. But I very much doubt it.


Kefir production, on the other hand, very likely maintains much more of its traditional “ancestralness.” It isn’t as widely consumed, and can be considered much more of an artisanal food product. It is most often produced through the use of traditional kefir grains, which likely maintain a bacterial profile that is much closer to the kefir that’s been consumed for centuries. Kefir is always MUCH more diverse in its bacterial profile. Here is an example of the content of one widely available kefir grain starter set. You’ll notice it is much more diverse than your average yogurt product, and it contains L. plantarum.

And here is a study of traditional Tibetan kefir grains. Guess what bacterial species was isolated from them? L. plantarum.

Is it possible that the traditional yogurt consumed by ancient cultures also contained L. plantarum at one point? Kefir is known to have originated in the Caucasus. But yogurt, too, is known to have a strong connection to the Caucasus region, and perhaps originated there as well. Wouldn’t it be awfully likely that the traditional formulation of yogurt would contain a bacterial profile that is much more similar to kefir, and generally more diverse than what you find today on store shelves?

But there’s more.

I just came across this study (thanks Dr. BG!) that analyzes the fermented milk consumed by the Maasai tribe of Kenya. The Maasai are a beloved object of study by the paleo/ancestral health community, probably owing to the fact that they maintain a very traditional, ancestral way of life, and because they show that you can consume a ton of milk, blood, and meat all day and stay pretty healthy.

Maasai bebiendo sangre

For the Maasai, milk is an extremely important food source. Probably the most important. And the majority of it is consumed in fermented form. And guess what bacterial species was found to predominate in the Maasai’s fermented milk:

Lactobacillus plantarum was the major species among the lactic acid bacterial strains isolated from traditional fermented milk of the Maasai in Kenya.

Or how about this: Dadiah is a traditional fermented buffalo milk drink consumed by the Minangkabau tribe of Indonesia. In other words, another excellent way to see what traditional dairy fermentation really looks like.


And once again, we find L. plantarum to be a major component of this product. Not only that, but when analyzed, it was found to be the bacterial strain that had the greatest anti-colonization effect on pathogens in the fermented drink:

The most adhesive Lactobacillus plantarum strain was IS-10506, with 9.8% adhesion. […] All tested LAB strains displaced and inhibited pathogen adhesion, but the results were strain-specific and dependent on time and pathogen strains. In general, L. plantarum IS-10506 showed the best ability against pathogen adhesion.

As you can see, not only did the traditional fermented drink contain L. plantarum, but when compared to other Lactic Acid bacterial strains, it was shown to be the one with the strongest impact on host health.

Which brings us to the second part of our exploration. I think we’ve established a pretty good anthropological case for L. plantarum’s importance for human health. But what about some hard, scientific data? Well, that last study on Dadiah isn’t bad. And my own experience with eczema is pretty darn good proof, too. But are there any other studies comparing L. plantarum’s immune modulation abilities to other bacterial strains? Would I even be asking that question if there weren’t any!?

Here’s an interesting one: researchers took a look at which bacterial strain had the best ability to reduce an allergic reaction to soy. They fermented soy with various bacterial strains, including Bacillus subtilis and, of course, L. plantarum. The use of B. subtilis is especially interesting, because it is the traditional bacteria used to ferment soy into Japanese Natto. The results: fermentation by all bacteria reduced allergy response significantly, but L. plantarum did the best:

L. plantarum fermented soy flour showed the highest reduction in IgE immunoreactivity (96-99%) depending upon the sensitivity of the plasma used.

But here’s an even better one. It isn’t even about L. plantarum. It’s about Bifidobacterium infantis. The study examined B. infantis’s ability to protect the gastrointestinal barrier through its immune modulating effects. But before it did so, it first did a comparison among bacterial strains to see which had the strongest effect. The one with the strongest effect was the one chosen to be further examined. B. infantis was the winner, so that’s the one that was chosen to study further.


As you can see, B. infantis came in first. And Bifidobacterium breve came in second. Third place: L. plantarum! Why does this vindicate what we’ve been saying? Because out of the three, only L. plantarum is a probiotic bacteria found in fermented foods. The other two are bifidobacteria — they are the commensal bacteria that reside in the human body. Of course these would show the strongest effect! B. infantis, specifically, is the dominant strain of commensal bacteria found in human infants. This is like comparing the importance of a micronutrient to a human organ. Exogenously consumed probiotic bacteria like L. plantarum can be thought of as a very important nutrient like, say, Vitamin D. But your commensal microbiota are a part of you. So sure, Vitamin D is important for human health. But you know what’s even more essential? Your spleen.

So from this graph, on the specific, narrow measures that this study uses, we see that L. plantarum is indeed a major player in human host health. And probably THE major player when it comes to fermented food consumption. And it’s quite likely that this study alone doesn’t get at the entire unique nature and capabilities of L. plantarum.

And now a final, meta note to end this post. As you can see, both anthropology and scientific data are vital tools to figure out the human health puzzle. This post, and this blog in general, are a pretty good testament to that, I hope. But in the end, when it comes to practical matters of health, I have to vouch for the superiority of anthropology, for a very simple reason: despite what many “experts” would have you believe, there is so much more we don’t know than we do know. When it comes to human health, anthropology is a map of the unknown.

Take my eczema example, for instance. I consumed fermented foods for over two years. Why? Not because I had any scientific proof that they would help me. I didn’t even know how, exactly, they could improve my health. I simply observed that they seemed to be an immensely important part of traditional human food consumption. So I took it on faith. For a while. (It also helps that I grew to like them.)

But I’m also a pretty skeptical person. After a while, I started to wonder if there really was any benefit. So I stopped consuming them. And that’s how I made my discovery. The dots were all there, of course — the fact that eczema is an immune condition, that probiotic bacteria modulate the immune system. Even studies showing L. plantarum treating eczema in mice and humans. But seeing the dots and connecting them is easy in hindsight (in fact, that’s how most experts make their livings, and then pretend it was foresight).

Anthropology was the map. It allowed me to follow a healthful trail without seeing the dots. And then a healthy dose of skepticism and personal experimentation turned on all the lights.

In conclusion: eat your damn kimchi!

— Heisenbug

Gut Bacteria & IQ: Could It Really Be?

Back to our regularly scheduled program. We left off at a bit of a cliffhanger last time. And as with any cliffhanger, we need to follow with a recap. Here’s what we’ve done so far…

…We noticed that smoking, which is the number one predictor of heart disease, causes a microbial shift. Not only that, but a specific one.

…We noticed that plant fiber consumption, or the lack of it, causes a shift as well. The same one we see in smoking.

…And we realized that both plant fiber consumption and smoking are both considered to be not only related to overall health, but they are also both correlated to heart disease. Which is just a little too convenient.

…Along the way, we noticed that transplanting the microbiota from healthy people to people with metabolic syndrome restored insulin sensitivity. And it was due to the same microbial shift that we see in plants & smoking. And we also noticed that smoking seems to be related to some other conditions that have a strong microbial connection. And that smoking introduces pathogenic, gram-negative bacteria directly into smokers. And that nicotine probably doesn’t explain any of this. That was all very interesting.

Finally, we presented a pretty solid base of research on the microbiome/brain connection. And we surmised that, since we established a pretty good microbiome/heart disease link, then if there were some kind of brain factor closely correlated to heart disease, it too would be under suspicion of having a microbial link. Turns out: low IQ is the second strongest predictor of heart disease. And then, lo and behold, we were handed a hot-off-the-presses rodent study showing that the feeding of prebiotic, fermentable fiber leads to changes in the brain.


OK. That should catch us up. Now where were we? Oh right: IQ. Could microbiota, and its primary modulator (fiber), really have an impact on IQ?

I think I know what most people were thinking last time: “Yeah, ok. Cute. But let’s be honest: dumb people do dumb things. If you have a low IQ, you’re probably less cognizant of the fact that cigarettes, ho ho’s, big macs, and spending all day on the recliner are slowly going to kill you.”

That’s certainly one explanation. And it’s an intuitive one. It’s the explanation that is widely cited in most of the reports by the epidemiologists themselves. But it’s not the only one. In fact, it didn’t even seem to be the most emphasized one by the epidemiologists in these reports. Here’s the explanation that got the most attention. I’ll quote from the NYT report:

“I.Q. is a marker of lifetime insults, physiological insults. We know kids with poor diets, kids who have repeated infections, have a lower I.Q., so it could be an I.Q. is capturing something about lifelong misery.”


“It may also be that a high I.Q. is associated with better overall neurological and physiological “wiring,’’ meaning all the body systems, from brain to heart to liver to kidneys, function at a more efficient level.”

So, we now have the two possible explanations of the IQ/Heart disease correlation, from the researchers themselves.

The Bad Behavior theory: Heart disease and low IQ track closely together because low IQ can cause heart disease. People with low IQs are more likely to engage in unhealthy behaviors because they don’t know that they’re hurting themselves when they smoke, consume an unhealthy diet, don’t exercise, etc.

The Bad Wiring theory: Heart disease and IQ track closely together because a low IQ is caused by all of the same things that cause heart disease — a series of physiological insults from the environment, poor diet, toxins, infections, etc.

There isn’t much to say of the Bad Behavior theory, other than that it is plausible, but by no means a sure thing. If you ask me, there is a whiff of condescension and misunderstanding about health-based decision making. To quote again from the NYT article:

It may be that people with low I.Q. have a more difficult time understanding complex health messages and don’t fully understand the long-term health effects of an unhealthy lifestyle.

But are these messages so complex? The idea that you should not eat unhealthy food? Sit on the couch all day? Smoke cigarettes? Or are these decisions more about basic willpower? Don’t we all know smart people who engage in these types of behaviors? Is understanding how or why they are “bad” even relevant? After all, even most children understand the basic “badness” of these types of things by a certain age, and they know you should avoid them without knowing the why or the how. And yet we’re to believe that adults could have a difficult time making the same basic connection? I’m willing to bet the average person, of average intelligence, doesn’t truly understand the why’s and how’s of unhealthy behaviors. We just know you aren’t supposed engage in them or our health will suffer. And yet many of us continue to do so — not because we lack basic intelligence, but because these activities challenge a fundamental part of human nature.

So color me skeptical. But alas, it isn’t something we can outright disprove. We’ll have to let this stand as one plausible explanation. For now.

Which brings us to the Bad Wiring theory. The idea that IQ is a reflection of overall “wiring” — that all the different physiological assaults that lead to heart disease can also, separately, lead to worse cognitive performance — is an intriguing but not so controversial idea. I think most people wouldn’t be too surprised to hear that an accumulation of negative health factors throughout life will lead to a deterioration in overall functioning, and that brain functioning would be a reflection of that deterioration.

But when viewed within the context of our investigation here — that heart disease may have microbial origins — then things become much more interesting.

You see, if heart disease has a microbial origin, then all of the “physiological assaults” that contribute to it — smoking, diet, infections, toxins, etc. — must share some sort of microbial mechanism themselves. In fact, we’ve shown here how smoking and diet (fiber, specifically) do so.

But if those same set of physiological assaults also contribute to worsened cognitive performance, then isn’t it reasonable to conclude that the same microbial mechanism is at play in that effect? What are the chances that they would all share a completely different mechanism?

In other words, with the Bad Wiring theory, the epidemiologists have essentially made the case for us.

So that’s where we find ourselves now — still two possibilities. If IQ is simply a predictor of unhealthy behavior, then that’s that. Our investigation has hit a dead end. Fun while it lasted.

Or….it could be the other thing.

So, what now? Do we just all place some bets and wait a couple of decades to see how it all shakes out? Not quite.

First, it turns out that IQ can do a lot more than predict just cardiovascular-related death. It can predict all death. That would suggest that something other than the inability to make good, “healthy” decisions is at work in the IQ connection. But it gets better.

In 2005, researchers set out to see if reaction time had the same predictive association with mortality. Reaction time can be understood as a cognitive subset of IQ. Reaction time is inversely correlated with cognitive ability. People with higher cognitive ability have shorter and less variable reaction times.

And here’s what the researchers found: reaction time did have the same correlation, and not only that, but when reaction time was factored out, the IQ correlation no longer held up.

Then, in a study by the same researchers who discovered that IQ was the second strongest predictor of heart disease, it was found that reaction time was, in fact, the critical element — reaction time was found to be the second strongest predictor in heart disease.

And finally, in a study published just a few weeks ago, those same researchers, wanting to eliminate confounding variables that can be involved in tests of intelligence (knowledge, education, culture), sought to replicate the effect using an even simpler reaction time test designed to be a raw measure of neuropsychological functioning — of one’s “wiring,” if you will. The effect, again, was replicated.

In other words, the IQ correlation is really a reaction time correlation.

With all this in hand, let’s now ask ourselves the million dollar question: what does reaction time have to do with understanding “complex” messages about health and avoiding behaviors that would lead to heart disease? NOTHING. That’s what.

And what would something like the speed with which your brain can react to something indicate about, say, your overall…”wiring”? Oh, maybe everything?

Bad Wiring: We have a winner.

Which means….

OK. This is all a little too heavy for me. Someone get me a stiff drink. FOS, Psyllium, and Raw Potato Starch. On the rocks.

— Heisenbug

Microbiome and Meat: Let the Silly Season Begin

I’ve been meaning to get this one out of the way. As the microbiome and the importance of our gut microflora composition begins to get more attention, it will become, as all things do, subject to preconceived notions and biases about health. And perhaps nothing is as preconceived and biased in the world of diet and health as the idea that intake of meat and its associated saturated fat are inherently unhealthy.

Case in point. A writer for The Guardian reports on having his gut bacteria sequenced and drops a couple of misconceptions that really need to be cleared up:

At the broadest level, the phylum level, my microbiota, in common with everyone else’s, was dominated by two types: firmicutes and bacteroidetes. The western diet, by which we tend to mean the North American diet, is high in fat and protein. In this diet bacteroidetes usually make up more than 55% of the gut microbiota, and sometimes, in North America itself, as much as 80%. In Europe, the average numbers vary from country to country. In my case I had 34%.


Again these were positive results. Lachnospira degrade pectins and ferment dietary fibres and I have three times more than typical. And bacteroides are often associated with meat-based, high-protein, high-fat diets, just as alistipes tend to be more present in people who eat less plant-based food. In sum that meant my gut – the lack of six-pack notwithstanding – was probably in good shape.


But by then he had managed to make a blind prediction of my diet that was uncannily accurate. He saw very little evidence of meat-eating – I haven’t eaten meat for 30 years.

Where to even start? The idea that specific colonic bacteria are enriched by meat and fat consumption is reflective of having missed a third grade lesson on anatomy. Meat and fat are, by and large, absorbed in the small intestine. Non-digestible carbohydrates — fiber — pass into the large intestine to be fermented by bacteria. In the context of diet, the composition of your microflora will be a reflection of the amount and type of fiber ingested.

Tell me how, exactly, one would see “evidence” of high or low meat consumption in this scenario. High meat and fat consumption and high plant consumption are not mutually exclusive. In fact, there is an entire diet devoted to this eating pattern. I forget the name.

To make it even clearer, I’ll once again highlight the evidence that I talked about in this post, showing what plant fiber — and plant fiber alone — can do to your gut microbiome:


Notice what doesn’t change in this experiment? Meat and fat consumption. Because it doesn’t matter. While it’s true that, on a personal level, your decision to eat meat and fat may lead you to eat less plants, that is a personal decision. And this may in fact explain the oft-cited correlation between high meat (red meat, specifically) intake and diseases like heart disease and colorectal cancer. In other words, “high meat & fat” may have really been “low fermentable plant fiber” all along. But again, these are not mutually exclusive eating patterns. Sure, at a certain point, meat and fat intake can begin to “crowd out” plant consumption to a level that is not optimal for gut health. But that is a far cry from saying that meat and fat themselves cause disease. Advice like that could lead one to cut meat and saturated fat out of one’s diet, and instead increase their intake of sugar, processed grains, and industrially-processed oils. Theoretically. Failure to make important, nuanced distinctions could, say, lead us down a 40-year road that results in no improvement in disease prevalence.


Of course, our diet-nutriton-health industrial complex can’t allow for such a nuanced idea. It’s all a one-or-the-other, good vs evil, science-illiterate holy war, isn’t it?

It’s the omnivore’s dilemma.

— Heisenbug

Update: An exchange in the comments led me to realize a further piece of evidence showing how useless it is to focus on meat & fat: the chart above shows that a high meat + fat + plant fiber diet produces MORE Firmicutes and LESS “meat & fat loving” Bacteroidetes than the author of the Guardian piece reports for himself. He reports 51% Firmicutes and 34% Bacteroidetes. From the chart above, it looks like high meat/fat/fiber produces around 75% Firmicutes, and less than 25% Bacteroidetes. I’m willing to bet that the Actinobacteria (good guys, Bifidobacteria) in that chart are much higher than in our intrepid reporter as well.

Eczema & Probiotics: Personal Update, Reader Reports, and the Respiratory Connection

Good news: my hand eczema is back!

Why is that good news? Because I stopped taking the probiotic a week and a half ago. I did so for two reasons. The first is that I want to try out a single-strain probiotic with a different bacterial species to see if it has the same effect. To do that, I need to induce the eczema again. More on that soon.

The second reason is that I wanted to see how long it would take for the eczema to return, in order to establish a minimum effective dose. My guess has always been that once I achieve a certain concentration, I probably don’t need to take it every day (probiotic pill or sauerkraut/kimchi). Well, it looks like it took about three days for it to start appearing very, very mildly — I had to pay close attention to notice. This itself is extremely strange — my eczema never pops up “mildly.” If it’s there, it’s very obvious.  It’s been a week and a half now, and I have to say, it’s still nowhere near the level I’m used to. In fact, the pattern I’m experiencing is unprecedented. I’m now getting extremely mild flare ups that disappear within a day or overnight. In other words, a very muted inflammatory response, which is what I’d expect as my concentration of L. plantarum lowers but is not completely diminished. If my immune system is slowly returning to its “overactive” state, then this is exactly how I would expect the eczema to return.

I never imagined I’d be broadcasting my daily hand eczema updates to the world, but there you have it. Science! Now for some reader updates.

In the last post, I noted that reader reports reflected a very clear pattern: slow but noticeable improvement. And if this was due to fermented food consumption, it was likely due to the fact that fermented foods have lower bacterial concentrations than the probiotic supplement I took. Sure enough, in a comment on that post, reader dojodelft reported similar results on what sounds like a classic, but pretty extreme, case of hand eczema:

I don’t care for sauerkraut much. So I was reluctant to join this experiment. However I suffer from hand eczema badly for 3 years now (I’m a desk worker). It appeared out of nowhere and it is controlling my life ever since. It’s got a (about) 4 week cycle, winter or summer. It flares up for about 3 to 4 nights in a row with extreme ichtiness. After I (of course) scratch the hell out, it resides. Leaving my hand intensely dry, red and very very calloused on the inside and outside. Even my fingertips are effected. Which is very inconvenient since I drop things out of my hands because of it. It feels like I have hardened melted candle wax on it. I always wonder if it could be something else, but my doctor insists it is hand eczema. Nothing seems to elevate the symptoms, accept antihistamine against the itch attack.

I now struggle every day to eat 4 forks of sauerkraut for 3 days. Conclusion: I really hate sauerkraut. But I’ve noticed that the skin on my fingertips is getting softer and sensation is somewhat returned. Still a long way to go, maybe even the full 50 days you mentioned, but I’m going for it. No prescription ever had the same effect for me.

Again, slow but noticeable improvement with fermented foods. There was also a second report from Wilbur noting continued improvement in one family member:

Patient 1 recovered from the asthma and cold, and likewise the (likely) new patch of eczema went away. This has never happened before! There is a confounding variable because I also increased the dose of radish kimchi by 50% or so.

Wilbur plans to try the probiotic pill in a second family member, who did not seem to get results from the foods. After one bag of sauerkraut, Jason H has yet to experience any significant effects:

As for the eczema, I don’t believe that there has been any significant improvement on my hand or my ankles. We did get hit by extreme cold this past week. My plan is to try the supplement after I finish bag #2.

Lastly, commenter libfree notes some dramatic changes:

Just a quick update. I’ve been taking the probiotic for just this week (twice a day plus some kimchi when I can + I started eating Kimchi at the beginning of last week) and I’ve seen some dramatic improvements. My feet have always had dry, itchy skin which has just disappeared. I have a cronic bunionette, a bunion on the outside edge of the foot, that has softened dramatically. My Rosacea hasn’t changed at all. Sinuses seem better but I’m still holding off on weather this intervention is helping. The most dramatic change has been in my lower respiratory area. My lungs are nearly free of mucus. I don’t remember a time that they were this clear.

If you remember, I speculated in my original post that, perhaps, this same intervention holds promise for other allergy-related conditions, such as asthma and other respiratory problems. So that’s a promising sign. But there’s more.

From a post on Seth Roberts’s blog, I came across a news report showing that a bacteria from Japanese fermented turnip called Suguki prevents flu in mice. The bacteria is Lactobacillus brevis, which is also a constituent of other fermented foods like sauerkraut and kimchi. L. brevis appears in lower numbers than L. plantarum and begins to grow toward the end of the fermentation process. But here is the interesting part: a commenter (Peter) on Seth’s blog post notes almost the exact same respiratory improvement that commenter libfree did:

Lactobacillus brevis also is found in pickled turnips. I’ve used it for weeks and noticed a difference. It seems to clear my lungs.

The one thing we can’t be sure of is whether it really is L. brevis that’s causing the respiratory improvement, because pickled turnips will almost surely have L. plantarum as well. In fact, my guess is they will probably have more L. plantarum than L. brevis (yup). But it is also very possible that L. brevis and L. plantarum have very similar characteristics, given that they seem to thrive in identical environments.

Fermentation cycle

Oh, and wouldn’t you know it, L. plantarum seems to protect against the flu as well.

That’s all for now.

— Heisenbug

Exactly What We Expected: “Bacterial Signature” Found in Colicky Babies

A few days ago, I noted that the association between smoking and baby colic was another piece of evidence pointing to a broader smoking/microbiota link.

A couple of commenters, drawing from familial experience, helpfully pointed out that colic isn’t always a result of smoking during pregnancy — it wasn’t the case in their experience. This is a very well-taken point, and I responded that in the specific case of colic, the microbiota link is much more important than the smoking link. Smoking may be just one of many ways to achieve the dysbiosis that may be at the root of colic.

Well, now we see a new report showing just that:

The research identified a distinct bacterial “signature” in the guts of infants with colic, a term that describes babies who cry for more than three hours a day without a medical reason.

In the first few weeks of life, the research found, colicky babies had higher numbers of bacteria from a group called Proteobacteria in their guts compared to babies without colic. Proteobacteria include bacteria known to produce gas, which may cause pain in infants and lead to crying, said study researcher Carolina de Weerth, a developmental psychologist at Radboud University Nijmegen in the Netherlands.

Once again, our good friends the Proteobacteria. As we’ve noted plenty of times now, bacteria from the Proteobacteria phylum go down when you stop smoking, and probably go up when you do smoke (they also go down when you eat plant fiber, and vice versa). Not only that, but we’ve shown that smoking directly introduces live pathogenic bacteria into smokers. What phylum do all of these pathogenic bacteria belong to? Take a wild guess.

Is it really any wonder that smoking is a great way to induce colic in newborn babies? It’s almost certainly not the only way. But it’s clearly a very, very good way.

Oh, and once again we see the “golden ratio” of microbiota — or at least a significant part of it — implicated in another disease. So there’s also that.

— Heisenbug

Kimchi & Sauerkraut Experimenters: A Distinct Pattern Emerges

I’m really happy to see that some reader reports from Kimchi and Sauerkraut experimenters have started to pop up in the comments — people looking to repeat my L. plantarum & eczema experiment to see if they get similar results. And I’ve noticed that a distinct pattern has emerged from these reports: slow but noticeable improvement. Progress seems to be slower than mine. And for that reason, there’s a less definite causal link. When progress is slower, it’s much harder to connect it to a specific cause. After all, skin conditions progress in waves and are expected to both improve and worsen over time. But if the sauerkraut or kimchi that readers are consuming are the cause of this slow but noticeable improvement, then there is probably a good explanation for why my experiment produced quicker results, and thus more defined causality.

First, the reports. Reader Wilbur first reported that he, too, struggled with eczema in the past but that this winter was the first where he did not experience the symptoms. This happened to be the first winter that Wilbur was consuming sauerkraut and kimchi. Because Wilbur’s family members were also suffering from eczema, he decided to see if kimchi would help them:

I’ve only been able to work with one person, but I can say after 5 days of radish kimchi that the eczema in that person is very clearly receding and, in a few spots, is completely gone. From prior experience, it would not have done this on its own. This person also did not use any of the usual medical remedies.

Wilbur then followed up:

We’ve had an odd set of results. Patient 1 described above does indeed have receding eczema except that we noticed a new patch today. It’s possible we missed it before, but I don’t know how. Patient 2 has seen no effects from kimchi, and a new patch appeared today. I, on the other hand, have the best skin I’ve had in many years.

Reader Jason H. reports:

Day 5 – I’m eating 4-5 fork loads of the Farmhouse kraut per day and I believe that my knuckle has improved a small amount. I’m also keeping an eye on my ankles. They get dry and scaly in the winter and I never even thought of it being eczema related. There has been no improvement so far.

And reader Hielkje then reported:

For a while now a have one finger with eczema. Not very extreme, just a slightly more red, dryer en the lines more pronounced. Sometimes gaps arise, especially after cleaning. A few weeks ago, I had a small pimple underneath my finger. It itched for three weeks and very slowly disappeared. The day before I read this article, came another. Since I had sauerkraut in the fridge, I immediately started eating a couple of spoons. Raw of course. Now I have eaten it six out of the seven days. After the second day I saw the pimple became soft and smaller. The third day it was gone. Great, very happy. The skin of my finger has become a little more softer but is still dry. The color is now almost identical to my other fingers.

In my experiment, I noticed clear and dramatic results within 3 days. Why might this be? Well, the main difference between my experiment and the experiment of these readers is that, instead of consuming fermented foods, I instead took a probiotic pill that solely contained L. plantarum — the primary bacteria found in sauerkraut and kimchi. This pill contains 10 billion colony forming units of L. plantarum.

How does that compare to sauerkraut and kimchi? The data on this is extremely sparse, and considering how much fermented products can vary, we’ll have to assume that what we come up with is a very ballpark number. But from this sauerkraut production study, which I’ve repeatedly found to be one of the only studies that delves sufficiently into this question, we find that L. plantarum is a) the predominant bacterial species in sauerkraut; and b) is found to be at a concentration of 10 million CFU per ml of product. (I was also able to find some real-world confirmation on this product page, which states that based on independent lab tests, this brand of sauerkraut contains about 7.8 million CFU. So we really might not be that far off).

One standard serving of sauerkraut or kimchi comes out to about 4 tablespoons, which is about 60 ml of product. That is very close to my stated daily average of about four forkfuls. I assume readers are consuming around the same amount. We’ll also have to assume that, on average, sauerkraut and kimchi do not have widely divergent concentrations (sourness/acidity is a pretty decent measure of fermentation, and I’ve never noticed a big difference in sourness between the two). So given those numbers, here is the comparison:

Fermented food: 600 million CFU of L. plantarum / day

Probiotic capsule: 10 billion CFU of L. plantarum / day

Why does this make a difference? It’s quite likely that, as with any kind of intervention, to achieve a clinically significant effect you’d have to reach a specific concentration. When I first experienced remission from eczema in the winter, it was after consuming these fermented foods for months on an almost daily basis (I started consuming them in the spring of 2011). I had plenty of time to build up a concentration of L. plantarum in my body from these foods. From this study, we see that there was a significant difference between groups who were administered L. plantarum for 15 days and 30 days. And it found that it takes about 15 days after the discontinuation of L. plantarum administration for the bacteria to become undetected. So it does seem that administration has a cumulative effect, and slowly diminishes after consumption ends.

My experiment showed that it took three daily doses of 10 billion CFU to eradicate the eczema. At that rate, for those attempting the same with sauerkraut or kimchi, it would take 50 days to achieve similar results.

Now, I actually think it might not take quite that long — we have to allow for the fact that, regardless of reaching the right concentration, human skin can only heal so quickly. Perhaps I reached the required concentration on the second day. Maybe even the first. But regardless, these two different interventions will likely require different durations to achieve the same result.

This is also the reason I tend to favor interventions that will achieve results as quickly and dramatically as possible when engaging in personal experiments. That’s one of the reasons I decided to use a probiotic pill this time, rather than simply eating the fermented foods again. It’s really important to establish causality first — I can always go back to the fermented foods later. Delayed results can decrease motivation in continuing the experiment, and will result in some level of questioning. Now that I’ve established causality to a sufficient degree, I can freely go back to the fermented foods.

— Heisenbug

Chronic Diseases Can’t Be Cured?

I was just doing a little side-digging on rheumatoid arthritis — an autoimmune, inflammatory condition — and came across this line on the Arthritis Foundation website

“Rheumatoid arthritis is a chronic disease, meaning it can’t be cured.”

Who decided that the definition of a chronic disease is one that can’t be cured? Why?

The “incurableness” of chronic diseases is a pervasive and, in my opinion, pernicious belief. It’s the foundation and subtle undertone for any conversation about treating and dealing with chronic disease. But there’s nothing about chronicity, per se, that lends itself to the inability to cure it. Chronicity can end. A sentence is a chronic series of letters that eventually ends. Like that one right there.

By the way, guess who tells me that eczema can’t be cured? The National Eczema Association. Feel free to check them out so you can learn all about how to “live with eczema.” (This is how I decided to live with eczema.)

Maybe it’s a bad idea to set up and devote precious resources to organizations that would have to shut down if a disease was cured?

Our health care system treats chronic disease like it’s a club membership.

Animals get cures. We get organizations and welcome pamphlets.

I know, I’m so cynical. But I can’t help it. It’s chronic.

— Heisenbug