What do you think of Epimicrobiomics?

by 10194 · July 17, 2010 1:11 AM

What is epimicrobiomics? Read on and find out...(prepare for a circuitous explanation)

A few weeks ago, I had the pleasure of having lunch with Richard from Free The Animal. As we were talking, Richard mentioned the tendency of some bacteria/viruses to actively alter their immediate environment to their benefit – potentially to the detriment of us and/or our beneficial-symbiote-bacteria.

Richard specifically mentioned that H. pylori actively increases pH in the stomach (making it less acidic) as H. pylori does not tolerate “normal/natural” stomach pH levels very well. I didn’t know this and found it quite interesting as the ramifications are interesting.

H. pylori does this, presumably, for two reasons:

1) “Climate-control” the environment for its own benefit

2) Perhaps injure/kill competing bacteria, which we might have a symbiotic relationship with (they, again, presumably, would likely be better off at lower pH levels) - again to its benefit, and to our potential detriment.

A bit more background: Some of the evolutionary psychology folks posit that diarrhea may not be induced by the human body to discharge bacteria/viruses but the other way around --- that some micro-organisms may induce diarrhea in our bodies to help them spread to other hosts. That is to say, a micro-organism radically shapes and alters its hosts behavior to its benefit.

Another vivid example, I recall reading about is “brain-jacking” and Thorny-Head Worms: http://en.wikipedia.org/wiki/Acanthocephala

[More interesting examples of this here: http://www.dawntoduskpublications.com/html/Brain_Robbery_Long.htm -- however, please ignore the “Intelligent Design” angle of the article. The examples, without the author’s commentary, are actually quite good.]

What I am driving at is the following thought-experiment (I am painting with a very broad brush here):

What if recent years of eating low-fat SAD has altered the micro-biota landscape of our collective GI tracts such that evolutionary processes have brought about micro-biota that not only alter their immediate environment (e.g. the GI tract’s pH levels), but also actively affect their hosts’ behavior to the bacteria’s benefit. i.e. bio-chemically and metabolically encourage their hosts to continue eating SAD, by making them crave carbs/wheat/sweets/whatnot and “punish” their hosts for not doing so.

If this idea holds any water at all, the ramifications are tremendous. When you bite into a piece of white bread at a restaurant, and it pops your insulin, and you crave more carbs/sweets. It may not just be a function of the bread sugars hitting your metabolism – it may also be our micro-biotal puppet-masters also pulling the strings as well....which suggests that tackling this (if it even exists) is paramount and underpins all of Paleo eating.

Maybe the "Carb Lust" referred to here: http://theorytopractice.wordpress.com/2010/06/02/6210-some-tul-intensive-vertical-pushing-and-pulling-and-severe-case-of-carb-lust-wtf/

is a function of micro-biota manipulating us to their own benefit!?!

This is what Brent Pottenger has termed "epimicrobiomics" -- to wit, epigenetics meets our GI micro-biota. In plain English, maybe we should be feeding our micro-biota such that they express their genes in a way that is mutually beneficial to us and them.

PS See Brent Pottenger's post on this here:


I also found this fascinating NYT piece from 2006:


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10750 · June 07, 2010 5:08 PM

I believe that there is something to what you are describing.

I would encourage everyone to check out Bonnie Bassler on this subject. http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

I'm also intrigued by the section of the Japanese population that carry gut flora that can Digest seaweed, a trick that the rest of humanity is missing. http://www.npr.org/templates/story/story.php?storyId=125675700

But an even better artcile discussing what you are trying to point out is at NPR: The Gut Response To What We Eat by Nell Greenfieldboyce http://www.npr.org/templates/story/story.php?storyId=120318757&ps=rs -=- I think that is also a part of why it takes some people langer than others to adjust from SAD to Paleo. If you already have the 'right' bacteria on board, your jump to a keto-adapted paleo diet would be smoother.

Hmm, it this plays out well, there might someday be a targeted probiotic capsule to make for an easier transition to Paleo eating.

754 · June 07, 2010 9:43 AM

Both the cooling inflamation and hyperlipid blogs have covered this in passing but yes its scarey that our gut bacteria can be puppet masters.

the series on hyperlipid about FIAF I believe covers the most but the idea is this: when we aren't eating carbs that bad gut bacteria crave, they send signals to the body saying "we are starving! release the fat stores, and tell the brain to gets some carbs STAT!". When we are eating carbs they basically say to your body and brain "store fat! we are getting fed! and keep sending the carbs!"

Part of the adjustment period to full paleo or a keto diet is apparently passing out/replacing this part of you gut flora which can take 1-2 weeks. In the case of people who still have massive cravings some of the carb hungry gut flora could be hiding out in gut biofilms (covered in great detail at cooling inflammation as well, also has implications in autisim treatment as they can be reservoirs of ingested heavy metals ).

The good news is going paleo and/or using avc/komboucha/fermented foods, pre and probiotics, and pectin from fruits tends to all be things that can get your gut health back into balance and degrade gut biofilms as well.

80 · June 16, 2010 at 12:19 AM

Functional intestinal microbiome, new frontiers in prebiotic design. http://www.ncbi.nlm.nih.gov/pubmed/20471127

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. http://www.ncbi.nlm.nih.gov/pubmed/20368178

10170 · June 07, 2010 2:29 PM

Really interesting and a bit scary as well!

This great interview with the always fantastic Robert Sapolski will probably interest you too (on Edge), on the effects of toxo on behaviour:


Not only are our own genes using us as a survival machine (dixit Richard Dawkins), but genes of other organisms could be as well.

People finally have come to accept that our genes have a major influence on us, that we're not born blank slates. And now we have to take this one step further.

Daniel Dennet also talks about this in his famous TED-talk and he links it to memes:


Nice topic! Nice expansion into other aspects of evolutionary medicine. The paleo diet is all about the mismatch between the present and the past, but there are other really interesting things about evolutionary medicine.

4888 · June 07, 2010 at 12:31 PM

I heard a programme on the radio some time ago related to this. It mentioned a parasite that lives in rats, and makes them go seeking cats in order to get eaten, as the 2cnd part of the parasites life cycle takes place after being eaten by the cat! I don't remember the details, but it sounds as though the concept of "free will" may have to be modified to allow for manipulation by microbes / parasites!

"I didn't mean to do it, officer - it was the parasites made me!"

7709 · June 07, 2010 4:05 PM

I'd be a little cautious when using terms that ascribe conscious purpose or intent to the actions of a bacteria. They aren't doing things for their benefit any more than they're doing things for any reason at all - bacteria act the way they do because they evolve to respond to environmental stimuli in certain ways. There is no intention or thought or pulling strings, etc. It's not like they get together and plan anything. So, yeah, beware the metaphor used to describe what's going on lest it convey something more than what you intend.

That said, I would agree with the basic thesis that eating SAD alters your gut bacterial balance over time, and that righting that balance can be a slog. Bacteria are pernicious little bastards. Many bacteria actively alter their environment to be more suitable to them - see all cultured foods - and the pathogenic ones are likely no different.

Bacteria causing people to crave something seems a bit far fetched. I'm not sure how they would accomplish this. A bacteria which absorbs much of what you eat might make you crave food as a side-effect (your body feels as if it is being starved), which helps feed the bacteria, or it might change the pH of its environment, but that's a far different claim from them actively interfering with the endocrine system or somehow altering your brain. There are parasites which do that, of course, but I'm not aware of any that act in humans in the manner described. A mechanism for their action would need to be found before it could be considered plausible.

I think a lot of people probably experience the effects of gut flora rebalancing/dieoff if they radically alter their diet, and that this probably contributes to diet failures as they think, "ick, this isn't working." It's a shame there hasn't been more research done on gut bacteria to create a narrative helpful for those feeling such symptoms.

22684 · June 06, 2010 at 11:59 PM

This would also explain why forced healthy eating both adapts our systems to not have the carb craving, as well as why we feel really bad if we do cheat, our good bacteria "punish" us for giving ammo to the enemy. The "fight of good vs evil" is not fun in my gut...

I plan on reading Alot more about this... Thanks for sharing!!!

I believe gut balance is of utmost importance to health

118 · June 07, 2010 at 10:49 AM

The gut flora and/or infectious theory of calorie partitioning may just be one answer to the phenomena of the Paleo non-responder. Fascinating area of study.

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