If the oceans are the final unexplored regions of Earth and space is the final frontier of the universe…then the gut biome is one of the last great mysteries of the human body.  Running through our intestines are hundreds of bacterial species, some of which are yet undiscovered.  Nurturing these critters can yield vitamins, energy, better immune function and more.  Neglecting or destroying the gut bacteria can precipitate a collapse of the fragile gut ecosystem, opening the door to opportunistic pathogens.  Plenty of misunderstood diseases (with autoimmune at the top of the list) are very likely due to bacterial imbalances in the intestines.


In this post, I won’t get too technical (promise!).  I want to talk about some current and fascinating research and hopefully clear up some misconceptions about our gut bacteria.  Their interaction with our bodies remains a complex mystery, so I’ll try to ask the right questions…”hey bacteria, what’s gut?” (I’ll try harder next time).


Jeff Leach’s Gut Crusade

Jeff Leach… man, myth, explorer, scientist, hero… all of these terms have been linked  to him (by me at least).   On January 1st, 2014, Mr. Leach embarked on a one-year tour to, in his words, “undertake a series of dramatic shifts in my diet and lifestyle in attempt to whack my microbiome around”.   During each shift, Jeff will collect stool samples to measure the percentages and absolute levels of his gut bacteria species.  Poop is mostly gut bacteria, by the way.  Not fiber.  Not starch.  Not mysterious brown entity (ok, it is brown).

Before his quest, Leach’s diet included generous amounts of meat, supplemented with fermentable plant material like soluble fiber and resistant starch (I’ll talk about resistant starch later).  His pre-quest colon is represented by the first circle below and is full of Firmicutes bacteria (the red).  On January 1st, Leach removed the plant element from his diet and went 2-3 weeks on nearly meat and fat alone.




As you can see, Bacteroides took over (see the blue).   Bacteroides are survivors.  They are highly resistant to antibiotics.   They (B. Fragilis specifically) are linked to colon cancer.   In the gut, they are typically benign and often beneficial, but they clearly don’t need a lot of nurturing to survive.

On the other hand, Leach’s fragile Bifidobacteria (represented in purple) were nearly wiped out by the plant-less diet.  Leach postulates:

In the case of Bifidobacterium levels taking a hit – note I like Bifidobacterium as they are often cited as being part of a healthy and balanced gut flora – I would go out on a limb and suggest they were suppressed due to my lack onions, garlic, leek etc.

It’s incredible how much change can occur in the gut biome in just 2 or 3 weeks!  Even a cursory glance at these charts should convince us that dietary modifications can cause MAJOR and RAPID shifts in our gut bacteria.  There is no consensus on exactly WHICH strains we want down there, though.

Some of the other diet / lifestyle modifications that Leach will try in 2014 include:

  • Raw food diet
  • Juicing diet
  • Mediterranean diet
  • High fermented foods diet
  • “Copious amounts of weed” trial period
  • Living with the Hazda hunter gatherers in Tanzania

Leach’s research is breaking exciting new ground here, as we will now be able to measure what bacteria flourish under varying conditions.  Leach also founded American Gut, a project to collect thousands of volunteers’, ahem,  samples analyze the bacteria, and gain a better understanding of how diet and lifestyle impact the gut biome.  I plan on participating.


Butyrate…it’s great!

Let’s circle  back to a major question I asked: – what species of bacteria do we absolutely want in our gut?  One feature stands out…  we want the bacteria that produce butyrate.  The scientific community seems in agreement on the importance of butyrate (a short chain fatty acid) to provide a whole slew of health benefits and maintain healthy intestines.  From a recent paper:

In vitro data indicate that SCFA are important metabolic fuels for colonocytes with butyrate being their preferred substrate (Roediger 1982) and that their capacity to oxidise butyrate is modulated by the microflora (Cherbuy et al., 1995). Cell culture studies show that the presence of butyrate at physiological concentrations enhances growth of normal cells and inhibits that of malignant ones.


Resistant starch increases butyrate

Ok, so the next question is… how do we reliably get our microscopic buddies to infuse us with the all-important butyrate?   Richard Nikoley and Dr. BG have been shouting it from the mountaintops of late.  Resistant starch!  Despite loads of research on RS over the past 20-30 years, it has only recently come into the limelight.  I suspect this is due to:

1)   The usual Paleo community aversion to the word “starch”

2)   A burgeoning array of research on the gut biome

The reasons why are not really that important here.  In numerous human and animal studies (explore the above link if you’re interested) resistant starch supplementation has definitively caused higher levels of butyrate production.  Lower blood glucose levels too – probably from the increased butyrate.   Resistant starch feeds more types of gut bacteria than other prebiotics (like soluble fiber)…plus it’s easier for the bacteria to break down, making RS an ideal food for promoting bacterial diversity in the gut.  Oh, and it’s zero calories and doesn’t feed bad bacteria.   Raw potato starch is the simplest way to supplement RS.

Admittedly, the research on resistant starch doesn’t tell us the exact bacteria that reliably produce butyrate (there are a few types, like Clostridia, but science is still far from a deep understanding).  The research does tell us that supplementing with RS produces beneficial outcomes AND that the outcomes are due to gut bacteria fermenting the RS.


Probiotics… definitely room for improvement

Broad spectrum probiotics with soil-based-organisms are, in my opinion, the best vessel to increase bacterial diversity in the gut.  Unfortunately, most probiotic studies are inconclusive.  The mish mash results are probably due to:

1) Improper strains and concentrations of bacteria in the pills

2) Not enough food (like RS) for the bacteria to ferment.

3) Organisms not surviving the stomach acid – it’s designed to keep bacteria / viruses out after all!

Another possible snag – recent research shows that a mismatch between host / bacterial ancestral origins can lead to problems.


Personally, I’ve been experimenting with fixing my gut bacteria ever since a stomach virus and several courses of antibiotics turned my intestines into a warzone.  I will be watching like a hawk as Jeff Leach and other pioneering researchers unravel the mystery of the gut biome.  The more we find out about gut bacteria, the more I’m convinced that they’re an underappreciated, yet fundamental, part of human health.  Treat them well.


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