Saturday, November 1, 2014

The "Perfect" Microbiome

I would be a bad blogger if I didn't respond to this article that appeared today in the New York Times.

There is no "Healthy" Microbiome

Take the Hadza. Their microbial roll call is longer than a Western one, with both omissions and additions. They are the only adult humans thus far sequenced who are devoid of Bifidobacteria — a supposedly “healthy” group that accounts for up to 10 percent of the microbes in Western guts. But they do carry unexpectedly high levels of Treponema, a group that includes the cause of syphilis.

 Science Writer Ed Yong discusses Jeff Leach's recent travels with the Hadza where he gave himself a fecal transplant using a turkey baster and a Hadza 'donation.'  I, personally, didn't like what Mr. Leach did, nor the message it sends. I think it was reckless and a waste of his resources at American Gut. Leach has an inside track when it comes to gut testing and seems to be able to test whatever, whenever he pleases.  The rest of us have to wait over six months for our results.  I would have thought a better plan for Leach would have been to thoroughly examine the Hadza diet and test his microbiome frequently while eating as they do and living amongst them.  Now we will not know the extent of microbiome transference that occurred naturally in Leach's experiment.

This all brought back memories of the scientists living in the University of Arizona's Biosphere, a closed, self-sustaining ecosystem designed to test the possibilities of living in outer space in a controlled environment.  They quickly realized the CO2, oxygen, and humidity were all wrong and began pumping in fresh air while continuing their experiments.  A cloud was cast over these and all future experiments carried out in the Biosphere.

I never really got the impression that Leach was striving for a perfect blend of certain species he deems 'correct' for a human microbiome, rather he is just trying to manipulate his gut to resemble that of the Hadza and see how he fares with this new microbiome.

But Yong goes on:

Is this menagerie worse than a Western one? Better? I suspect the answer is neither. It is simply theirs. It is adapted to the food they eat, the dirt they walk upon, the parasites that plague them. Our lifestyles are very different, and our microbes have probably adapted accordingly. Generations of bacteria can be measured in minutes; our genomes have had little time to adapt to modern life, but our microbiomes have had plenty.

This shows the ignorance of the microbiome that plagues our current medical establishment.  The present way of thinking is that the microbiome "is what it is." Doctors have no problem prescribing round after round of antibiotics to pregnant women, children, and people of all ages. While many of us see this as a travesty, we also live in a world where people live and eat with absolutely no concern for fostering a healthy microbiome.

I think that we can, in fact, look at someone's microbiome and make observations on whether it is "bad" or "good." A microbiome dominated by pathogens or low in overall diversity is "bad." A microbiome dominated by butyrate- and lactic acid-producing bacteria is "good." The former is a result of years of poor diet and/or antibiotic use, the latter the result of eating a human-appropriate diet and exposure to the microbes found all around us.

The microbiome is the sum of our experiences throughout our lives: the genes we inherited, the drugs we took, the food we ate, the hands we shook. It is unlikely to yield one-size-fits-all solutions to modern maladies.

So true, and I really like this thought!  Our microbiome is partly due to our individual genes as well as external factors like food, drugs, and social interactions. Even fecal transplants will fail if not followed-up with the proper diet.

In concluding remarks, Yong says:
We cling to the desire for simple panaceas that will bestow good health with minimal effort. But biology is rarely that charitable. So we need to learn how tweaking our diets, lifestyles and environments can nudge and shape the ecosystems in our bodies. And we need ways of regularly monitoring a person’s microbiome to understand how its members flicker over time, and whether certain communities are more steadfast than others.  

I didn't get the impression that Jeff Leach was searching for simple panaceas when he basted his bum with Hadza poo, I think Leach is after knowledge and using the tools he has available at American Gut to test his theories.  I think it's great that we can now see what we have living in our microbiome by examining a fecal sample sent through the mail with a check for $99 attached, but I also think it is giving us a false sense of thinking we can define what a perfect microbiome looks like.

There are too many problems associated with looking at the microbes on a fecal swab to make blanket statements.  Looming over all of this is the fact that fecal samples don't show all of the diversity in the large intestine. There are colonies of all types of bacteria living deep in the mucosal layers and within biofilms that don't show up on fecal samples. We've also seen that a microbiome report can have differences and errors that are acceptable to the company providing the report. In this respect I don't think we are anywhere near using an American Gut or uBiome report to tailor one's microbiome.

Using American Gut and uBiome as our barometer for gut health also has another major completely neglects the mycobiome...the fungi and yeast that inhabit our intestines and form commensal relationships with us and our bacterial/viral counterparts. The mycobiome may, in fact, be way more important to our health than, and a main determinate of, the microbiome. 

Now, don't get me wrong!  I've done two uBiome tests and two American Gut tests and I'm still waiting on several of these to come back.  When I get them all together, I will try to make sense of the results and post my thoughts here.  I doubt that you will see me saying that you need to strive for one or another specific gut microbes, but I will point out the ever-changing nature of our microbiome.

The 800 pound gorilla in the room in all of these discussions is diet.  In Yong's article today, I saw no mention that our gut microbes need to be fed real food.  Jeff Leach "gets" it, but then he goes and pulls the turkey baster stunt.  I think the panacea to great guts is actually simple:

Eat a diet that human beings are designed to eat, one filled with vegetables, fruit, fungus, and animal products.  But more importantly, devoid of artificial colors, flavors, and man-made chemicals and low in refined sugars, flours, and oils.

Avoid antibiotics and get dirty now and then.  Exercise.  Sleep.  Avoid stress.




  1. I sent in a sample to American Gut in September 2013. Still waiting on my results. I periodically email them and they keep telling me results in a couple weeks and check back. Humph.

    1. Wow! really? A whole year?? That's bloody ridiculous. Email me when you get your results if you don;t mind sharing, I'd love to see.

  2. "I didn't get the impression that Jeff Leach was searching for simple panaceas when he basted his bum with Hadza poo." Nice turn of a phrase! I sent my sample in to uBiome a couple weeks ago. Anxious to see what they find.

  3. This is a test, because I can never seem to post here.

  4. I get this fabulous paper delivered to my door every day so I saw this, and was steaming. It's so typically patronizing and diluted for the susceptible masses. I suspect Yong knows there is beneficial bacteria, but he feels he's doing us a service to prevent us from running out like lunatics to buy probiotics in a delusional attempt to cure ourselves of every disease. That's what I got from this - it was more of a hey guys, don't do anything yet! We don't know enough, we haven't studied enough, wait for us to prescribe!

    1. I think that we need some studies done to show the optimal amounts and types of fiber to produce the perfect amount of butyrate, pH, and other gut-bug gifts. It's fun to speculate and argue the finer points of Methanobrevibacter smithii, but we really don't know what a perfect microbiome looks like!

      My thought is that it will be different for everyone, but with a common theme: Eat real foods and plenty of diverse fiber types.