Dear American Gut & uBiome: You Have Some Explaining To Do.

Uh oh.

This is concerning. Apparently, a science writer had her gut sequenced by the two popular gut sequencing services in the market right now — American Gut and uBiome. Not only that, but she had both done at the same time, from the same sample. Meaning, they should show the exact same results.

They didn’t. Not even close:

As you can see, the the ratio between the two predominant phyla, Firmicutes and Bacteroidetes, are almost flipped. FROM THE SAME SAMPLE.

Either one service’s sampling/sequencing method is faulty, or the general method that is being used by both services to do the gut sequencing is highly unreliable.

Either way, they’ve got some explaining to do. If this has legs, a lot of people will be — and should be — demanding their money back.

Video on Autoimmune & Bacteria + Best Eczema Report Yet

Moises Velasquez-Manoff is one of my favorite writers on the topic of the microbiome and health. Below is a video that covers the basic idea behind the hygiene hypothesis and the interaction between bacteria and our immune system. If you are a reader of this blog, chances are you are already pretty familiar with what he talks about, but it still has some really interesting tidbits that make it worth watching.

Oh, and Moises is planning to trek out to Hadza territory to cover Jeff Leach’s work out there for the American Gut project. I’m pretty excited to see the fruits of that, to say the least. Moises is crowdfunding the project, and you can help here.

If you’ve been following the Eczema + L. plantarum science experiment we’ve been running here, you’ll know that what Moises talks about in that video is very real. And to really put it into context, here’s a new report that just came in the comments:

I’m pleased to announce my two year old daughter’s eczema is almost completely gone after 1 week of Jarrow’s Ideal Bowel Support. She hasn’t scratched her skin at all starting on day 2 of the treatment. Now all of her scabs and scaly patches are healing. Poor girl would scratch herself until she’d bleed on a daily basis. Her doctor suggested we stop bathing her as often and apply lotion. Well that didn’t do a thing for her.

The directions on the probiotic say 1 pill twice daily. She’s little so I’ve been giving her one pill (pulled apart, powder mixed into full fat yogurt) in the a.m. only. I am amazed and so grateful I read this blog. She’s so much happier now. Thank you thank you.

I really don’t see how we can top that one. In fact, I think it’s time to close up shop here at Heisenbug headquarters. Mission accomplished. It’s been fun, folks.

Ok, ok. Not really. We’ll keep going. We have to. Why?


— Heisenbug


Female Gut, Fiber, Autoimmune: Do Women Need More Fiber Than Men?

A study on the effects of prebiotics on satiety and hunger came across my radar the other day. It had an interesting finding — that increased fiber had opposite satiety effects in men and women:

Over the remainder of the day, the high dose of scFOS reduced food intake in women, but increased food intake in men, suggesting a gender difference in the longer-term response.

I filed it away as interesting. Do women somehow extract more energy from fiber than men? Maybe.

But then, today, I came across a piece of info that I’m familiar with, but never really connected to anything: gender differences in colonic transit time. In short, it’s been found that women generally have a markedly longer colonic transit time. Average transit time for men: 33 hours. Average transit time for women? 47 hours.

That’s quite a difference. This study showed that when men and women are placed on an identical diet, women have lower stool weight and longer transit time. This study also confirmed longer transit time in women. And this study showed that the gender/transit time discrepancy was due to colonic transit time, and also that menstrual cycle was not the reason for the discrepancy (as was previously thought).

As we all know by now, the colon is where all the microbiota and fermentation action is. If we were to draw some kind of hypothesis from this, this one would be the most obvious: perhaps women derive more energy from fiber. The longer fiber remains in the colon, the longer the microbiota have to break it down, and thus produce more short-chain fatty acids. And if women do indeed derive more energy from fiber, then, just maybe, there’s a reason women might be built to do that? Do women need to support a larger/more diverse gut microbe community?

If that’s the case, we might observe something indicating increased fiber preference from females in the anthropological record. Do we?

We’ve talked about the Hadza quite a bit here — they are an African tribe and one of the last remaining true hunter-gatherer groups in the world. And they are the major subject of inquiry by the American Gut project. We’re going to learn a lot about the human microbiome through that work.

A lot of study has been done into the foraging and food preferences of the Hadza. Their diet is highly seasonal, and relies on a handful of staples whose availability changes season to season. We’ve discussed previously their strong reliance and preference for honey. Honey is the Hadza’s top-ranked food, and in some months out of the year, it accounts for up to 70% of their energy intake. The reason for honey being their top preference is quite clear: it is the most energy dense food in the world. As such, the Hadza’s second-ranked food is meat. Third is baobab fruit. Fourth is berries.

If we’re just talking about men, that is.

One of the most fascinating things about Hadza food preference research is the fact that women rank berries above meat. For women, berries are the second-ranked food. Not only that, but meat ranks fourth — after baobab fruit. That seems significant. Berries and baobab are not very energy dense — they are largely composed of dietary fiber. It seems that, after honey, men continue to prefer energy density, while women shift to a preference for fiber.

What’s more, the overall eating pattern of Hadza women shows that while men tend to consume infrequent but high energy foods, women eat far more frequently than men, and are consuming “low quality” (read: lower energy density, higher fiber) foods throughout the day. To me, that sounds like a diet geared toward deriving energy from a continuous, steady fermentation of fiber from colonic microbiota. 

Hadza men, on the other hand, are largely tasked with the job of hunting game — leading to an obvious situation in which they kill, prepare, and consume meat (and are the exclusive consumers of organ meat) much more often. Does this point to an evolved gender dimorphism, in which women have a greater capacity for energy harvest from fiber, an enhanced gut microbiota, and a greater need for fiber?

And lastly, this all seems to comport with studies of gender food preferences in modern, Western populations: research has shown that men have a greater preference for meat, while women have a greater preference for fruit and vegetables. On their own, these studies might not exactly be perfect, given the role of culture and other factors, but the fact that they line up with what we find in a non-industrialized, hunter-gatherer population is relevant, I think.

So that’s all pretty fascinating. And adds quite a bit of fuel to this women/fiber hypothesis fire.

Now I’ll go ahead and heap another log. A pretty speculative one.

As you should know by now, a major area of interest for this blog is the role that the human microbiome might play in chronic disease. And there’s a pretty specific class of chronic disease that is particularly under the microscope. Given that we know what an important role microbiota play in our immune system — they are major regulators of immune activity, and about 70% of our immune system is considered to be in our gastrointestinal system — there’s no wonder that autoimmune diseases are at the top of the list when looking at the microbiome and human disease.

Now, let’s see. If women have a greater need for dietary, fermentable, prebiotic, gut bacteria-feeding fiber, would it perhaps stand to reason that they might suffer disproportionately from a modern Western diet devoid of that? Ummm:

Taken together, autoimmune diseases strike women three times more than men. Some diseases have an even higher incidence in women.


The fact that women have enhanced immune systems compared to men increases women’s resistance to many types of infection, but also makes them more susceptible to ADs.

All very interesting.

— Heisenbug

More on Probiotic Timing

Reader Matt asked a good question in the comments:

What’s with the time factor – before vs. after the meal? Stomach emptying is in terms of hours. Seems like if consumption of probiotics 30 minutes before was within the optimum timing, maybe something other than raising the ph could be going on?

I wondered the same thing – why is 30 minutes before a meal optimal? According to the study, before and during a meal were both better than after a meal. But survivability was best before a meal. Well it turns out the answer is pretty simple. Probiotics come in capsules, and it takes a little bit for the capsules to open and release the probiotics:

The bacteria survival, when given before a meal, can be explained by the fact that the pH in the stomach remained higher for a longer period of time after the probiotic capsules opened due to the important buffering effect of the spring water and the saliva. The saliva secreted in response to the intake of the capsules, taken with water, raised the gastric pH and then when the meal entered the stomach, 30 minutes later, the gastric content was further buffered. When the capsules were given after the meal, the number of bacteria surviving stomach and duodenal passage was greatly reduced as the bacteria arrived about the same time as the pH of the system began to decrease.

So it turns out that 30 minutes before provides just the right timing for the probiotics to be released into the buffered pH of the stomach. Remembering to take something 30 minutes before a meal is a bit much for me, so as far as I’m concerned, taking them right before a meal, or perhaps right as I’m starting to prepare a meal, should probably do just fine.

But I don’t regularly take probiotics anyway, unless I’m curious about experimenting with something. I prefer to consume fermented foods. And guess what doesn’t come in a capsule? Fermented foods. And how are fermented foods usually eaten? Not 30 minutes before a meal. We traditionally eat them with a meal.

Sometimes it all makes so much sense it hurts.

— Heisenbug

Eczema & L. Plantarum Success Stories

Thought I’d do a roundup of some of the reader reports that popped up throughout the past month…

After not achieving any success with the standard dermatological approaches, Mary has cleared up her eczema completely using the L. plantarum probiotic:

Thank you for the advice on taking probiotics for eczema. My dermatologist prescribed creams and soap alternatives and it didn’t seem to be doing much good at all. I’d had very strong symptoms of eczema since last September – including severe itching and bleeding. Since I’ve started taking the probiotics, it’s cleared up completely. And it just took a week. Could not be more grateful to you or to the friend who directed me to your blog!

Reader Gestalt reports that he cured his girlfriend’s eczema with the L. plantarum protocol:

Just wanted to report I put my gf on the L.plantarum after reading your first post about curing eczema. She has had severe eczema on her hands arms, shoulders eyes and lips for about 1.5 years. It took 2 weeks of the Jarrow’s formula, 2 capsules a day before it started diminishing. This is the best improvement she has seen in a long time and I have you to thank for this discovery. She looks like maybe after another week or so she will fully recovered at this rate. Keep up the blogging, I look forward to your every new post.

Janet noted improvement after just two doses of the probiotic:

I took my second L plantarum this morning and it looks like my hand eczema is already improving! Definitely clearing up. No itching around the margins. Number of bumps decreasing and there is just one small “colony” left in the flare that was at least 2 inches in diameter. I haven’t been drinking my homemade kombucha because I thought that was the cause of the rash, but I have realized for awhile that it wasn’t. So hurray! I can begin my KT factory again. Also, I am ready to start some other fermentations. I am amazed.

And Janet followed up that her hand eczema is now completely clear.

Reader T.J. seems to have made a major improvement in his psoriasis. Psoriasis and eczema are not the same thing. However, like eczema, psoriasis is a skin condition with a strong immune system component:

Taking L. plantarum probiotics has much reduced the severity of my psoriasis. We’re experimenting to see if it has an effect on arthritis inflammation as well.

And now the best for last. Out of all the experimenters, reader dojodelft definitely stood out as having one of the more extreme and intractable cases of hand eczema, which has been plaguing him for years. Despite not having a taste for it at all, he decided to begin a daily sauerkraut regimen.

One non-scientific observation I’ve made is that most success cases seem to come from those using the probiotic therapy rather than fermented foods. This certainly seems to be the case with the most dramatic reversals. As I mentioned, this would make sense — given the difference in bacterial concentration, doing this with fermented foods was likely going to be a longer process. When I first made my discovery, it was after having consumed fermented foods repeatedly for months, likely building up an adequate concentration. When I stopped (and the eczema returned), I took the probiotic and noticed results almost instantaneously.

Well a few weeks ago, dojodelft did note slow progress:

Though for me it doesn’t seem to disappear over night, slow progress is still noticeable. I’m eating kraut for about 4 weeks now. My skins slowly seems to heal. It started at my fingertips, then some small patches of skin started to renew (pink and soft  )and now the deep cracks and groves are starting to fade. I haven’t had the crazy itch on and between my fingers for 4 weeks.

Well I’m now excited to see that his eczema seems to have completely cleared:

Though it is maybe early to tell… but my hand eczema has vanished… gone… as in not there any more. An end to years of torture. I can’t believe it. The skin is still a bit dry and recovering from years of insane scratching, But no more itchy patches and night time finger scratching.

Pretty incredible!

— Heisenbug

Probiotics Survive Better with Some Fat: It’s the pH

If you haven’t noticed yet, a running theme/theory on this blog is the importance of pH in determining the microbial makeup of a person’s GI. The acidity level of one’s gut is what gives rise to particular species of bacteria, and I now believe it is the main determinant of whether one maximizes the benefits of supplementing with Resistant Starch and other fibers. The human gut is full of saccharolytic (carbohydrate-degrading) bacteria, and I believe what determines which ones get fed is pretty simple: whichever ones happen to be present. And again, it’s pH that largely decides that. If a bacteria is not adapted to a particular pH, it won’t survive, plain and simple. Like putting a human on a planet that doesn’t contain any oxygen. Now, this may sound a little circular — after all, it’s fermentable fiber that lowers pH. We’ll get to that soon, I promise!

For now, I wanted to do a quickie post that I think will give another angle on pH that I think is a little more tangible, since people are quite familiar with probiotics and fermented foods.

For a while now, I’ve been aware of research showing that the survivability of probiotics is greatly increased when taken with, or just prior, to a meal. And it is particularly the fat in the meal that increases the survivability. This study showed that quite clearly:

Enumeration during and after transit of the stomach and duodenal models showed that survival of all the bacteria in the product was best when given with a meal or 30 minutes before a meal. Probiotics given 30 minutes after the meal did not survive in high numbers.


The protein content of the meal was probably not as important for the survival of the bacteria as the fat content. We conclude that ideally, non-enteric coated bacterial probiotic products should be taken with or just prior to a meal containing some fats.

I hadn’t given this a ton of thought, until recently, when it occurred to me that the same pH principle applies here. The reason Lactic Acid bacteria (LABs) in probiotics and fermented food survive better is because of the pH buffering effect of food, and particularly fat. The stomach and its acids provide a very harsh environment for bacteria, as they should — that’s how we keep a lot of pathogens out. The stomach’s fasting gastric pH is about 1.5. That’s very low, even for the acid-loving LABs. What’s ideal? Broadly speaking, it looks like survivability grows and hits its peak at around a pH of 5. L. plantarum hits its peak at 4.8, in that study. And here’s a chart of L. plantarum growth in sauerkraut, which confirms that.




How does that line up with the effect of food on stomach acidity? Like so:

Humans secrete approximately 2.5 liters of gastric juice each day, generating a fasting gastric pH of 1.5, which increases to between pH 3.0 and 5.0 during feeding.

Well would you look at that. And when you look at how fermented foods are traditionally consumed, it makes perfect sense. Fermented dairy seems like quite a probiotic package, with its protein and fat content providing what is likely a pretty good pH buffer for LABs. And in the case of sauerkraut and kimchi, we know that these foods are traditionally consumed as condiments as part of larger meals that most often include meat and fat.

So it seems that if you are looking to maximize the effect of fermented food consumption it would be wise to consume some sausage with that sauerkraut, and some Korean BBQ with that kimchi.

More broadly, I think this illustrates what an important and universal principle pH is for the gut microbiome. What I found interesting in researching this was that among LABs, L. plantarum (who we’ve talked about quite a bit) seemed to be one of the most acidophilic. Which is in keeping with what’s been argued here — that L. plantarum is a pretty important commensal, and that acidophilia is a pretty good determinant of commensalism. Looks like L. plantarum is pretty well equipped to survive GI passage (but not without a little fat!).

And of course, LABs like L. plantarum seem to return the favor. If they can make it past that harsh acidic environment, their lactic acid production has a pH-lowering effect in the gut. We’ve gone at length about immunomodulation as the primary benefit of probiotic consumption, but I have to believe that this is a major benefit as well. But probably not to the same extent as fermentable fiber consumption.

Lastly, the effect of fat on pH lines up pretty well with the research showing the darker side of that effect — that meals with fat can increase circulating endotoxins, and that the consumption of fiber along with the fat negates this effect. In other words, this isn’t an excuse for a fat free-for-all. I’ve been running a personal experiment to test out this phenomenon, and it’s been quite interesting. I’ll post on that soon. In the meantime, I’ll leave you with Heisenbug’s corollary:

Eat fat. Always with plants. Sometimes the fermented kind.

— Heisenbug

Why Medicine Dabbling In The Microbiome Scares Me

One side effect of my dive into microbiome research is the startling realization that experts in medicine and health know much, much less than we think they do. Heck, even within microbiome research, it’s amazing how researchers seem to not keep up very well — I see so many studies premised on not very solid, and often outdated, assumptions. And often premises that completely conflict with one another. Ie, “Because Firmicutes are associated with obesity, we wanted to…” and “Because Bacteroidetes are the result of an unhealthy Western diet, we wanted to see if…” It’s as if they don’t talk to each other. But that’s a discussion for another time.

I bring all of this up because I came across this report: Cancer scientists seek to stop radiotherapy’s side-effects on ‘friendly’ gut bacteria.

When I first read that headline, I expected a report about how doctors are becoming more sensitive to the effect their treatments and procedures have on the microbiome. Which is a very positive thing to see. But if you actually read the article, that doesn’t seem to be the case at all:

“One possibility is that different populations of bacteria in a person’s guts are making them more or less susceptible to radiotherapy.”


“The aim is to build up a profile of gut bacteria which will allow us to predict who will suffer side-effects that might limit the effectiveness of the radiotherapy. Then we can think of finding ways to treat people in advance of radiotherapy in future.”

Mmhmm. Please, go oooooooon……

One technique would involve administering medicines that would alter the makeup of a patient’s population of gut bacteria. Alternatively their entire population of gut bacteria could be removed and replaced with another from a donor, a technique called a faecal transplant.



Call me crazy, but this sounds to me like the opposite of what the title suggested. What these doctors seem interested in is modifying gut bacteria — perhaps drastically — in order to make radiotherapy more effective.

And that’s scary. The idea that these people will figure out the “right bacteria” any time soon, and then try to proactively alter or demolish someone’s gut based on that, is very scary. Why? Because this is the same person who, in this article, said:

“Men and women have a startling amount of bacteria in their stomachs…”

Yeah. I bet he can also see Russia from your colon. The stomach is notable for being a place in your GI that is extremely hostile to bacteria. Too acidic. It has a startlingly low amount of bacteria.

It’s truly astounding to me just how strong of a proclivity these people have toward not only intervention, but extreme intervention. You can sense how titillating it is for them. A real chance to “geek out.” Even if they do identify an enterotype that is more amenable to radiotherapy, how do they know that enterotype won’t produce other side effects in an individual? How do they know that enterotype will be compatible with that person’s genotype?

If anything, emerging microbiome research teaches the opposite lesson: We don’t know as much as we think we do, so tread lightly. But some people just aren’t built to understand that lesson, I guess. No, they’re built to get really “science-y” and bring us things from the future. Hammer, meet nail:

“The crucial point is that we are now becoming aware of how important the bacteria in our guts are to our general health – and that should help direct us to a range of new drugs and treatments for all sorts of different conditions in future,” said Dearnaley.

Thank you, doctor from the future! See? Where we’re going, we won’t need common sense and a basic understanding of human anatomy…

— Heisenbug