A quick summary of my efforts up to this point to restore my intestinal tract to a more pristine state. In 2005, I traveled to the East Horn of Africa to self inoculate with a beef tapeworm. There was obvious signal as I experienced improvement in a number of allergy related conditions. I ended that infection at day 107 due to side effects of a mature beef tapeworm (motile proglottids). In 2006, I traveled to Amazon Basin to self infect with human hookworm. I used seven Necator americanus and was well below the carrying capacity of my gastrointestinal ecosystem as there was no obvious improvements in my allergic or autoimmune conditions. So in 2007, I went to Central America and increased my population of hookworm by 60.
This population resulted in dramatic improvements in both my allergic and autoimmune conditions. Since 2007, I have hosted from 67 to 227 hookworms. I have found, by experimenting, I do best with 40-60 hookworms. Below that lower threshold and my immune dysregulation gives me trouble and above I notice metabolic deterioration. Tinkering with the worm populations no longer gives perceivable improvements in my immunologic or metabolic function. Simply put, even though I am dramatically healthier with a worm population, I have lost the signal using only worms, diet and lifestyle modification. Adding multiple species of worms makes no significant improvement.
One of the most interesting observation in the near decade of hosting large eukaryotes in my intestinal tract is that antibiotics will cause whatever benefits I am experiencing to temporarily disappear; the longer and more broad the exposure to antibiotics the more dramatic the return to my baseline prior to the self-infections. It is obvious that the health of the bacterial lawn is essential for the benefit provided by the worms.
This makes sense, in that, the bacterial lawn is required to fully activate regulatory immune cells derived from the GI tract (1). In 2014, I tested my microbiome using uBiome. Here are those results:
There is obvious room for improvement and this is when I became interested in seeding my bacterial lawn with a Non-Western biome. In my interpretation the dominance of Firmicutes is a simple hyper-nourishment bloom. Under such eutrophic conditions one or two species will come to dominate with a concurrent loss of biodiversity. I think that is what is happening in my gastrointestinal tract combined with the immune dysfunction developed in early childhood. I would like to disturb my ecosystem towards a more evolutionarily congruent state to see if that offers any further improvement to my immunological or metabolic functions.
Acknowledging the limitations of bacterial assays (which tell you the populations but nothing about behavior), I looked for a source from a more biodiverse ecosystem that were displaying the properties I am most interested in improving. I have been a runner most of my life and the cultures of indigenous people that were generating superior runners was where I focused my search. Having done field work in the East Horn of Africa I could have sourced from there but to be honest Africa scares me. It seems there are patterns of ecological filtering that are selecting more pathogenic strains. For instance, I am hosting Necator americanus which has taken a more commensal path than the old world cousin Ancylostoma duodenale. The forms of malaria in the New World tend to be less pathogenic than the forms that are endemic to Africa.
Mexico has a population of world class runners living in primitive conditions. In late 2014, I went to the San Madre mountains of central Mexico to collect some samples and run with the Tarahumara.
I can confirm that the Tarahumara that I ran with are superior metabolically to me when it come to transforming food energy into kinetic energy. In addition to biodiversity and robustness, metabolic efficiency is a measure of the health of an ecosystem. Here is what the uBiome assay of a metabolically fit Tarahumara runner looks like:
As you can see there are non-trivial differences in this assay from mine. The most obvious being the inversion of the Bacteroidetes to Firmicutes ratio. After extensive and expensive testing I have identified a donor that passed the screening protocols (there is always risk as the testing protocols were designed for a Western biome, but my hope is to have mitigated the risk to well tolerated, self-limiting infections). My plan is to introduce small amounts of this inoculate orally (top-down) for two weeks and re-test my bacterial lawn. Due to the nature of inoculate it will be frozen at -50 degrees celcius. This is done to ensure that the samples are sero-surveilled and as an additional safety step to ensure the death of possible parasitic contamination (Entamoeba and Strongyloides). My null hypothesis is that daily use of this bacterial inoculate with not result in any detectable change in my bacterial assay. I will be recording and logging my progress on this blog.
1. Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses.