Heisenbug lives.

Hi all.

Just wanted to let you know that regularly scheduled programming will return shortly. Apologies for the blackout — got swallowed up by some consuming projects over the past couple of months. But rest assured, Heisenbug lives.


Seth Roberts

It is with a very heavy heart that I share the news of Seth Roberts’s passing.

As many of you probably know, Seth was an early champion of this blog and was very encouraging of the ideas contained in it. Had it not been for Seth, I might not have continued past the first few posts. In fact I sometimes found myself writing posts imagining Seth to be the entire audience.

I only got to know Seth personally at the beginning of this year, but we struck up a friendship by email and Skype very quickly. We emailed frequently, often daily, and were deep into a writing project together. Sadly that won’t reach completion now.

We never met in person, but planned to soon given that we both had roots in California. I’m very sad that we won’t be able to. You’d think that only knowing someone via the Internet and not having met in person makes it easier to deal with their passing, but in reality it’s quite difficult, because there’s no one else to share the sadness and grief with.

The deep sense of loss I feel is one for the world. Seth had an extremely unique perspective on very big and important ideas. He said things no one else was saying, and understood things in a way no one else did. The commonality we found on ideas about human health, personal science, innovation, and societal progress is one that I’m not sure I will find again. The phrase “Yes, I agree with that” was probably a part of every exchange we had. Losing the only person who you feel understood certain ideas is very difficult, and the importance of keeping those ideas alive is now felt very acutely.

Learning about his passing late last night made for a horrible night of sleep — one that none of Seth’s discoveries could have made better. Rest in peace, Seth. I will do my best to advance the ideas we found so much agreement on, in some small way.

– Shant


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