Gut Healing and the Ultimate Probiotic

Gut Healing and the Ultimate Probiotic post image

Much has been written about healing the gut with diets such as SCD,  GAPS, Paleo and Paleo AIP. Many people can heal their leaky gut with these diets and other lifestyle changes. However, some people with more recalcitrant disorders, like autoimmune issues, may need some form of natural therapy to compliment the diet. That’s where the ultimate probiotic comes in, Fecal Microbial Transplant.

Fecal Microbial Transplant (FMT) is, in my opinion, the most promising treatment for a damaged gut, by far, as it is the ultimate probiotic. The transplant contains hundreds, if not thousands of strains of bacteria, many as yet unidentified. Compare that to the most powerful probiotic, that has, maybe up to 14 strains of bacteria.

The FDA has stepped in to control FMT when used in the clinical setting – limiting it to only resistant cases of C. diff. – after antibiotic treatment has failed at least 3 times (and the patient is near death).

There are clinics in the UK (Taymount) and Australia (Dr. Barody) where FMT is legal and has been practiced for years.

Because of the restrictions on the medical community, some people have opted to perform FMT at home with a local donor, thoroughly screened and tested. The Power of Poop website offers everything you need to know about FMT.

Additionally, there are now stool banks that supply donor stool for hospitals.

All of this is certainly progress towards a more effective and less risky form of treatment for autoimmunity that complements dietary and lifestyle changes very well. The future is bright! The challenge will be to move it along quickly and make it available to patients for many disorders other than just C. diff infection.

The Study of Poop

Jeff Leach is studying poop.

That’s right.


He is becoming quite the expert on poop. I’ll coin a term right here – poopology – the study of poop.

You may have heard about the American Gut Project and Jeff Leach. He has been living in Tanzania for over a year and studying the Hadza. The Hadza are one of the few thriving and surviving hunter/gatherer tribes left on this earth. They have a lot of fiber in their diet and possibly the healthiest poop around.

… we’ve collected nearly 2,000 human and environmental samples in an attempt to characterize the microbes on and within the Hadza and the microbes in their environment. The human samples have mostly included stool (feces), but also swabs of hands, foreheads, bottoms of feet, tongues (some spit), breast milk from mothers, and so on. Environmental sampling has included swabs of the plants and other foods they consume – like berries, roots, honey, etc. – and a dizzying number of animals ranging from Greater Kudu, Impala, Dik Dik, Zebra, various monkeys and birds, and so on. For the animals, we collect feces and when possible swabs of the stomach contents of larger animals – all of which end up covering the Hadza sooner or later during butchering (see little blurb in Nature titled Please Pass the Microbes). We also swab their homes – inside and out – along with the various water sources. In short, we swab everything including the researchers while in the field. (s0urce)

I am excited to report that Jeff Leach has performed FMT on himself using an adult Hadza hunter/gatherer as the donor. You can read more about that here. I just can’t wait to learn about the results of stool testing and how he feels.

Devastating Loss of Diversity

Interestingly, in studying the stool samples from the Hadza, Jeff and his team are finding extraordinary diversity in certain groups of bacteria. The Hadza harbor dozens of species of Prevotella, while in the typical western gut there have been only two species found (P. copri and P. stercorea).

Interestingly, Prevotella has been linked to greater potential for getting arthritis and other immune issues, so it is not clear how beneficial it is to have many more species.

Oxalobacter formigenes is an important microbe because it degrades oxalates – preventing problems with oxalates such as kidney stones and other gut issues. Apparently, the Hadza have plenty of Oxalobacter, while less than 15% of American still carry it.

Importantly, the Hadza seem to acquire Oxalobacter at a young age, while American children are not acquiring it at all these days, according to researchers at NYU who are working with Leach on this project.

Clearly, just by virtue of the findings of these two important groups of bacteria in the Hadza that are missing in our population – we can say that we are experiencing a devastating loss of the diversity of our microbiome.

Another finding that is quite interesting is that the genus Bacterioides, which is found in high levels in the guts of Americans, but is very minor in the guts of the Hadza. Leach speculates that this is due to the amount of dietary fiber in the Hadza – which is very high.

Compared to the amount of dietary fiber in Americans, which is very low – it may explain why Bacterioides is so high in Americans. This type of bacteria love alkaline guts which results from a lack of fiber. An alkaline gut also does not protect against pathogens as they tend to love more acidic environments.

Leach has even experimented on himself, (having access to all the stool testing one could ever hope for) and tested himself by increasing or decreasing the amount of fiber in his diet and getting a corresponding increase or decrease in Bacterioides. He speculates,

I think the dominance of Bacteroides in the western gut has to do with pH levels, which is “mainly” driven by fermentation of dietary fiber (fermentation of fiber equals more SCFAs {short chain fatty acids like butyrate} and thus a more acidic colonic environment which strains of Bacteroides don’t like). So with the average American eating less than 20g of fiber a day – pitiful – we are likely lugging around the most alkaline guts in human history which in turn is allowing certain species of Bacteroides (and some opportunistic pathogens) to flourish. Again, if we squint for a moment and lean on the gut of the Hadza, then maybe we shouldn’t let Bacteroides dominant our gut – and by doing so, who else is getting nudged out or down and potentially dragging us closer to ill health? I suspect the Hadza keep Bacteroides levels low with their high, daily levels of dietary fiber which keeps their colonic environment very acidic.(source)

All the experts notwithstanding, I am inclined to be influenced by what Jeff Leach is finding out from the Hadza population, what they eat and what microbes make up their microbiome.

After all, they represent what we have come from, what our microbiome should look like and how we should be eating.

… the Hadza literally hunt and gather many of the same animals and plants that humans and our ilk have subsisted on for millions of years – not too mention they are literally covered in the same dirt, drink the same water (save the occasional cow turd floating about), and practice the same central-based foraging that has brought people together in microbial-sharing camps/communities for the better part of the Pleistocene.

While the Hadza are not living fossils, nor in anyway represent a perfect referent population for early human evolution (but close), their hunting and foraging lifestyle and constant contact with the natural microbial world, natural births, extended breast feeding and limited to access to western medications, makes them one of the best – if not the best – population in the world for trying to understand what our ancestral microbes may have once looked like, where we got them and at what point in our life history we acquired them, before the rest of us ran gut first into the buzz saw of globalization. (source)

That said, these folks nurture their microbiome with plenty of environmental contact with plant and animal microbes and eat a high fiber diet. They have plenty of contact with the soil and the other microbes that thrive there as well. Something that is missing in the western diet for sure.

What do you think about these issues with fiber and feeding the microbiome? Would you seek out FMT for healing your gut? Let’s continue the conversation in the comments!

By the way, there is an amazing FREE online event coming up called the Digestive Sessions. My friend Sean Croxton is hosting and you know how great his events are!

If you have ANY digestive issues you want to reserve your spot in this event coming soon – Interviews with 25 experts and Functional Medicine Doctors all on the topic of digestive health!

Register here for the Digestive Sessions

Shared at: Real Food Wednesday, Allergy Free Wednesday

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Leave a Comment

  • Inner Clean October 10, 2014, 9:26 am

    Highly descriptive article, I loved that bit. Will there be a
    part 2?

  • Kim March 21, 2015, 1:01 pm

    Interesting article. I have many overlapping health issues and esp w my gut–including leaky and sibo…i am finding the different theories interesting..but NOT even if i was on my deathbed would i want to consider a Fecal transplant? Gross. I understand the theory but i advise caution sometimes theories change based on new information and find they were way wrong…that is a place i wont go. Caution and moderation in all things.