Boost Gut Diversity With Exercise. Or More Protein. Or Not.

This NYT article got me thinking about other ways to boost gut diversity, ways that have nothing to do with actual ingestion of different bacterial strains or even prebiotics and polyphenols (read: plants) that feed them. The researchers found significantly higher gut microbe diversity in exercisers (albeit extreme ones) vs. non-exercisers.

Correlation. Zero causation, and lots of confounders, rendering this whole article kind of a non-starter.

The study discussed, comparing rugby players to couch potatoes, suffers from more than a few design problems. First of all, how do you control against the possibility that rugby players are simply rolling around in the dirt more than the non-exercising control group? I mean, just look at the game itself. They’re covered in mud, inhaling and inadvertently swallowing millions of soil-based organisms while crushing and pummeling each other on the pitch.

And that’s leaving out the fact that athletes tend to have special diets with higher amounts of protein (known to change gut bacterial populations), representing a whole ‘nother variable that has broad potential to skew results.

In short, nice idea guys, but all you did was piss me off. More refinement needed, and a laboratory setting wouldn’t hurt either. It’s very simple: Just two groups kept at the clinic, ON THE SAME DIET, for christ’s sake. Exercise one of them, let the other play cards and call their moms all day. Analyze their crap before and after the exercise period. Do you really need me to tell you this?



Glyphosates, gut biodiversity, and kinda sorta maybe a Unified Theory of Modern Disease?

I was a long-time sufferer of celiac disease. Since identifying it in my thirties, I spent 8 years avoiding all gluten, being a general pain in the ass at every dinner party and restaurant. Any accidental crumb of bread would almost immediately send me dashing to the john for a painful session that, depending on the contamination level, could be repeated for up to 48 hours.

About 2 years ago, in an unrelated move, I started eating only food that came either from our garden, local farmers who didn’t treat their crops, or the nearest organic supermarket here in Normandy.

So it was last week that I started reading about the link between glyphosates (think RoundUp or other herbicides) and celiac disease. Wait a minute: this wasn’t something I was born with after all? Was the problem not the wheat but what had been sprayed on the wheat?! By going organic, I had effectively avoided herbicides and pesticides for the last 2 years, so I tried a wacky, cutting-edge experiment: I had a beer, after first making sure I was sprinting distance to a bathroom. And the weirdest thing happened:


And you won’t know how great that is unless you’ve got celiac. The experience was so astonishing, I decided to try some bread. Again, no symptoms.

Not long afterwards, my sister-in-law sent me this review on the relationship between celiac incidence and glyphosate-based herbicide use over the last 20 years. You can’t overlook this pretty striking association, as shown on page 2. Ok, that’s correlation. Interesting but not enough to catch glyphosates red-handed. Gotta pathway, tough guy? You betcha.

None of you will be surprised to note that this has something to do with gut bacteria. While we destroy diversity planet-wide, we are also doing it inside ourselves. Wouldn’t it be logical that an herbicide created to destroy diversity on a crop field (also known as “killing weeds”) would do the same thing in your colon? It’s killing off beneficial bacteria and leaving you with mostly baddies. (Yes, I realize those are chickens in the study, but those are all bacteria housed in the human intestine too.)

So once you’ve got serious dysbiosis down under, you’ve got problems. First off, none of the hormone signalling usually taken care of by your resident healthy gut bacteria is taking place. Secondly, you’re developing holes in your gut wall, since the protective bacteria aren’t there, or aren’t there in big enough numbers. You’re opening yourself up to tons of other diseases since your shizz is now getting through to the Other Side. Wanna keep your immune system wired all day, overzealous, trigger-happy, overworked, and generally unprepared to meet the demands of protecting your body? Get some bodywide toxemia from bacteria entering your bloodstream through your gut endothelium. We’re not talking simple IBD or colitis anymore. The downstream effects will be felt everywhere.

So, commence extrapolation to all autoimmune disease. Damn, I’m late to the party, as the science journal Nature already did that. So did the Centre for Research on Globalisation, who went as far as to name glyphosates as a causative factor in all modern disease, period.

I’ll leave you with this interview by Jeffrey Smith, who you may know from his book, Genetic Roulette. If you have an hour to spare, it’s well worth it. Here he lets researcher Dr. Stephanie Seneff tell you first hand all about what she learned regarding glyphosates and what they do to us, our resident bacteria, and our health.

The Unified Theory of Modern Disease comes into sight when you throw in a lifestyle involving frequent therapeutic antibiotic use, low-dose antibiotic ingestion in your meat, milk and water, and modern ultra-high levels of hygiene with not enough exposure to natural soil bacterial communities. You’re decimating your gut biome, and your health. Get dirty and get organic, and get on it now to prevent diseases of civilization.





Chock fulla Whodathunkit: Bacteria in your BLADDER.

For years we were told that urine is sterile. It was a foregone conclusion that things like overactive bladder, cysts and bladder cancer couldn’t be a result of infection, because hey, no bacteria.

I’m sure by now you can guess what I’m going to say about why we had the blinders on: we couldn’t culture them using standard lab environments, mediums, temperatures, pH levels, gas mixtures and CO2 contents, anaerobic vs. aerobic settings, etc. The labs also have pretty high cutoff limits on bacterial quantities in order for them to be considered statistically significant. Anything lower than these were considered too low to have any clinical effect. Meaning they were treated as if they weren’t there.

We didn’t see them. Hence they didn’t exist.

But URINE LUCK. (Sorry. How was I going to pass that up?)

Have a nice warm, yellow cup of proof that they do. Along with lots of indications their dysbiosis is what may be causing many bladder diseases and even bladder cancer, even when present in vanishingly small amounts as compared to the intestines (remember there aren’t really any fibers or sugars for bacteria to thrive on in the bladder).

All it took were a few scientists who had the cojones to question their own methods instead of following protocol. And of course their findings are not catching on in the scientific community. Who wants to admit they’ve been wrong for generations?

As for practical implications for the patient… You thinking what I’m thinking? Yep, this raises the issue, yet again, of a Disturbed Microbiome as a, if not the, culprit in yet another spectrum of diseases.

And what disturbs it more than antibiotics??

The Incredible Exploding Kitchen Effect (Soil Culturing Experiment Update)

The best thing I can say about this experience is that I wasn’t wearing white. I should add the miracle that Nine Months Pregnant Wife Upstairs somehow remained asleep when I squealed in horror as the first gush of red sludge hit the spotless white ceiling, and then during the ensuing banging and clanking as I frantically wiped down kitchen appliances, the countertops, the windows, the ceiling, the floor, the walls, the cat…

But I’m getting ahead of myself. Let’s back up a bit to my brilliant idea a few weeks ago.

I was going to cleverly and deviously save tons of money on soil-based probiotics by growing my own from cultured soil. My first mistake was trying to grow it as if it were beer or spumante in a pop-top bottle like this. My drenched kitchen and pajamas are testament to the fact that the gas created by your brew inside the bottle will result in a lovely, heartwarming this when you open it.

My second mistake was thinking beets would be such an AWESOME additive for the organisms to feed on. Are you prepared to hose down your house afterward? And your kids and your neighbors? Because that shit is BRIGHT RED. Use sugar, syrup or something else to feed your bugs. If you’re looking for a starch, cellulose or plant fiber to add, try white rice or cabbage.

And finally, I was just harebrained enough to pop the bottle in the house. The thought of turning your interiors into a scene from Dexter should tell you all you need to know: open your concoction @OUT. SIDE. But I’m not against “burping” your bottle daily if you can remember, and are sufficiently pathetic. Alternately you could just place the cap on the bottle but don’t “pop” the latch down. This will allow gas to escape but keep bugs and most other bacteria out.

So after spending my first hour of the day scouring and mopping, there was thankfully about a fifth of the bottle left inside for sampling. The liquid smells pretty rank, kind of like cow patty on a hot day, and comes out kind of thick. I’ll let you imagine the taste then (think nuanced hints of colostomy bag with a faint background of septic tank). And I can’t be sure I cultured all the SBOs I was looking for. But I definitely grew something funky, so I’m calling the experiment a success.

I’m currently growing the remains with a kinder, gentler color (just a few tablespoons of maple syrup) and making sure to keep the bottle unpopped overnight.

Take care when you do this. Your ceiling will thank you.




Dahling, What IIIIIS That Dirt You’re Wearing?

This is a quickie since I’m super busy these days. A NYT Magazine article on a company trying to market a soil-based bacteria you spray on instead of bathing, presumably to mimic the natural microbiotal pattern we once had on our skin. They are wondering about “probiotic” topical treatments like this for inflammatory conditions such as eczema too.

Can’t roll around in dirt before your morning commute? Well, consider AO+ Refreshing Cosmetic Mist.

Yes, our body’s largest organ evolved over millions of years covered in a universe of living organisms. Bacteria, viruses, fungi, yeasts and just plain ol’ insects. We were crawling in critters, or them on us, or em… Some of them good, some of them not so good. But ALL of them in balance.

Our modern habits of cleanliness basically demand slathering ourselves with antibiotics several times a day. Considering that we don’t know how these skin bacteria signal our bodies, how they protect us, or how they cause disease, once again it seems we’re in over our heads.

Aside from the fact that your antibiotic soaps and shampoos go right down the drain after you use them and wreak havoc on the planet as they alter natural microbiotal and fungal ecologies in the environment, we don’t even know if they’re good for us. There’s got to be a better way.

Even L’Oreal, Clinique and Estée Lauder are jumping on the “skin probiotics” bandwagon trying to sell dirt for your skin without saying you need dirt for your skin. They are, predictably, using the old chestnuts Lactobacillus and Bifidobacterium. Those choices reek of a marketing decision as opposed to an actual health one, since consumers recognize those bacterial strains from their yogurt labels. I have a hunch there are thousands more (and more important) strains that we don’t know about since you can’t culture them in a lab. Which means you can’t sell them in a bottle.

Strange days.






Back2Back Backs The Quest!

If you don’t know Moises Velasquez-Manoff, you really should. He is a science and technology journalist for the NYT, among other papers, and wrote the great book I am presently tearing to shreds called An Epidemic of Absence (expect a full review on this in upcoming weeks).

He’s looking to crowdsource for a new article he’s working on about anthropologist Jeff Leach’s “Quest for Our Ancestral Microbes”, so lick your thumbs and snap out some fresh benjamins to help out please:

Ancestral Microbes Article Proposal

Using the Hadza as our nearest living hunter-gatherer model, the idea is to profile (yet another) thing that is fast going extinct due to encroachment and pollution by the industrial world: the microbes that live in and on us when we live the way we did during our evolution. Scoff you may, but we are only beginning to scratch the surface regarding how our gut microbes control, alter and shape our bodies. By the time we have things figured out (if that’s even possible), these ancient microbe populations will surely be gone forever.

You didn’t think civilization would discriminate as it kills planet-wide diversity, did you? Why stop at animals and plants? Why leave out the most major player of all?

Jeff Leach is planning to live with the Hadza and document what that does to his microbes. Lucky SOB! His and Manoff’s working theory is that the dirtier and less sanitized the environment (read: the lower the antibiotic exposure), the less susceptibility to autoimmune disease and allergies: that means the stronger the organism.

Here’s a scrumptious mouthful of dirt to get you oriented: The Hygiene Hypothesis.

At the very least, this project will raise awareness about how important it is to preserve diversity both around us and INSIDE us. Both Leach and Manoff are personally affected by autoimmune disease. Even if you don’t have a personal dog in this fight, knowing the ancestral microbe populations will give us a base for developing an understanding of autoimmune disease and why it’s skyrocketing in the “modern” world.

And I know I don’t have to tell you how bad it’s getting

Soil Culturing Experiment for Daily Mud Slugging

And with great effort, a yellowed, spotted lightbulb painfully flickered, popped and buzzed, ever so dimly illuminating the dusty and cobwebbed barn attic he called his noggin…

It came to me suddenly the other day, just as I was about to click “Buy” on Amazon: why shell out another 57 Intergalactic Space Credits on soil-based probiotics when I live right here in the fields of Normandy, treading every day over some of the best soil there is? If they can grow these bugs in huge drums somewhere in an industrial park off the highway thousands of miles away, I can most surely find a way to get these critters humming naturally in my kitchen.

Here‘s what I’ve been taking for the last few weeks. This brand seems to have the most diverse array of bacteria and yeasts I’ve seen in a supplement. If you’re not hitting the soil-based, you are not creating the gut biome diversity you need to be healthy. Just popping some L. acidophilus or falling face first into a bowl of Danone will help your endothelial function a bit and even lower your fasting blood sugar, but if you take anything from this blog, it should be that NOTHING in bacteriology can be seen in isolation.

Taking one strain is certainly not going to introduce the diversity we had as hunter gatherers, who were pretty much covered in mud and shizzaz all the time.

I can hear you saying “Alright wise ass, why don’t you just go outside and eat a spoonful of dirt every day”. I suppose any organic salad is going to have a fair amount of soil bacteria on it, no matter how much you wash it. But necking a whole spoonful of Backyard every single day risks the ingestion of the many parasites that come along with your beneficial bacteria. We can leave the discussion of whether that may be good for you or not to another post. I’m skipping the whipworm for now to just culture the bacteria in a little sipable brew I can replicate at will (without the parasites).

Anyway, Day 1 of Operation Home Grown Biome went like this: Brought back a ziploc bag of freshly scooped earth from the prairie right next to our house. Put it in an airtight pop-top cider bottle, added half a finely cut beet, two tablespoons of sugar, and filled the rest up with filtered water. (Filtered to get the chlorine out.) Shake lightly and let it stand in the cupboard. I figure I’ll wait about 2 weeks before pouring it through a fine-knit filter, throwing out most of the original and then re-culturing with just a bit of it as starter so I can be fairly sure any possible parasites are left behind.

We meet back here in about a month for the taste-test.



I, Roving Fermentation Vat

Anyone suffering from a serious case of hubris should take a look at a phylogenetic tree sometime. Kinda puts your big life problems into perspective. You’ll notice most of the tree are bacteria and archaea, and even among the eucaryota, animals are squished somewhere between slime molds and fungi. Oh but even then, most of these animals are insects. Humans, but one branch of the primates, are pretty small beans if you’re looking at this from an overall diversity perspective.

And I don’t have to remind you that in your own body, only about 10 percent of the cells are even human at all. So not only are you small and fairly insignificant in the grand scheme of things, there’s actually no You in the first place.

Aaaaaand cue the Galaxy Song, just to make our point.

They control your tissue growth and development, digest most of your Happy Meal, and determine if you’re going to succumb to that virus you just breathed in from Annoying Close-Talking Coworker. You are their bitch. So chill out and start enjoying the ride.

Here’s a primer by Noah Fierer:

Exploring Terra Incognita: The Extraordinary Diversity of Microbes On Us, In Us and All Around Us


Sub-Therapeutic Antibiotics and Obesity: You Are The Cattle

This is a quick one and it relates to the previous post. Martin Blaser, director of the NYU Human Microbiome Program, on the microbiome and how we futzed with it (unwittingly through antibiotics seeping into our diet and environment) and are now making ourselves obese. And who knows what else.

Microbiome and Obesity

And here’s his website, where you’ll see he recently wrote a book about all this called “Missing Microbes”:

I will review the book in a subsequent post.

What’s great about the studies he shows here is that he gave the EXACT SAME SHORT ANTIBIOTIC TREATMENTS WE USE ON OUR KIDS to animals in the first few months of life, and they grew up to be mice with metabolic syndrome. Ditto when they used sub-therapeutic amounts of antibiotics in the mice’s drinking water, mimicking the stuff you’ve been drinking for years as our industrially-raised cattle and chickens pee it right out so it can eventually pollute the groundwater.

And don’t forget your municipal drinking water is already treated with chlorine or fluoride, or both, depending on where you live. They are anti-microbials. Do you know what they do to your gut microbiota and what effects changing our natural flora balance could have?

Antibiotics, or “We have no idea what we’re doing”

This dropped out of Ye Ol’ YouTubes yesterday. It was so fascinating, I thought I’d kick off the blog with it. You’ve got Julian Davies, head of the microbiology department at the University of British Columbia, saying that antibiotics don’t just go away once they’re in circulation, among other things.

Pharmaceutical companies produce millions of tons of antibiotics every year. How about hundreds of millions of people and probably billions of industrially-raised livestock and fish pissing out antibiotics every day, which go right into the water and soil? How about the antibiotics that get thrown away by the ton once they pass expiration? And that’s not counting the tens of millions of antibacterial soaps, lotions, sprays, dishwashing liquids, deoderants, pet shampoos and toothpastes (did you even realize that was an antibiotic? Did the manufacturers ever bother to tell us?) produced every year as well.

You wash your hands, brush your gob, flush your toilet, and that stuff goes right back into the biosphere. With profound effects on the natural world.

Only 30 minutes, and well worth the click:

Harvesting the Molecular Wealth of Microbiomes

The take-home, besides the fact that we’ve been playing with fire for decades, is that microbes are a COMMUNITY, not something to be seen in isolation. In the natural world, they live and exert their effects in concert with others, while in an ecological balance with hundreds or even thousands of other strains. They live off each other’s excretions. They signal each other constantly. They toss molecules and chromosomes back and forth. Context is everything when it comes to bacteria.

Assigning “bad” and “good” effects to one single strain is naive, and extremely dangerous.

Paracelsus is all fine and dandy, but we’re not talking about a single human patient here. That’s pretty easy to gauge. No, see, this is about worldwide inter-relationships that are TOO COMPLEX FOR YOUR PUNY KNOW-IT-ALL NOODLE. We have been sub-therapeutically dosing the world with antibiotic mixtures since around the 50s. And if we had pretty much no idea what we were doing with high doses to eradicate pathogenic strains, we have even less idea what low doses over long periods of time are doing as they seep into our lakes, streams and soil.

One man’s dose only stays his dose for a short while; once he pulls the chain, it becomes his neighbor’s (diluted) dose. Have you thought about what something as innocuous as your hand soap could be doing to him? I chose your neighbor as an example because you actually see him. What about the other 99.9% of the natural world you don’t see?

When it comes to the planet, we don’t know the dose.



Edit: I can hear the comments already that he’s talking to a roomful of scientists interested in exactly the kind of reductionism I’m railing against. But you have to give Davies credit for trying to introduce an ounce of environmental responsibility and a more community-centered spirit into the Human Microbiome Project.