When I was 13, I started to get really sick, really frequently. Strep throat would take me down so often that I was taking antibiotics more months than I wasn’t. It got to the point where I was nearly constantly on antibiotics, and I still got sick all. the. time! About to embark on my second attempt at college at age 19, after 6 years of this nonsense I was ready for a break!! So when my doctor recommended I get my tonsils out, I was like see ya, tonsils! A tonsilectomy was supposed to get rid of the strep problem, and it did...but plenty of other sicknesses swarmed in to fill its place.
Little did I know, my gut microbiome was seriously on the struggle bus from being beaten back by so many antibiotics. Colds & flus were normal, and I remember teachers remarking that I must have a weak immune system because I was out sick so much! And I had digestive problems I honestly don’t even want to talk about! But one thing was clear, as I moved into my 20s, the ill health trend continued. I took up everything from juicing to organic farming to medicinal mushroom tinctures by the mouthful, but still I would get sick at the drop of a hat.
At the time I came up with the idea to experimentally inoculate myself with indigenous microorganisms (IMOs), my boss was an insightful, ecologically-literate designer. My shoddy immune system was definitely affecting our workflow & productivity, since I would get sick literally every time we traveled (which was a lot)! Remarking on how often I seemed to be stricken down with plague, he guessed it could have to do with my gut health and asked me if I’d taken antibiotics before. I was like, ?!?!? Have I…!!!
As it turns out, taking any antibiotics, let alone downing handfuls of them month after month for years, can really compromise the immune system because of what it does to the gut.
Image credit Jane Barthelemy
Our gut has the most nerve endings out of the whole human body, and it’s directly connected to our brain, so it’s extra sensitive in perceiving discomfort. Bacteria & yeast (a kind of fungi) in the stomach produce enzymes & different chemicals that help break food down, and if they can’t break down & absorb food efficiently -- like if they’ve been decimated by antibiotics -- this process causes discomfort & provokes immune response over time. This was news to me!
“A huge proportion of your immune system is actually in your GI tract,” says Dan Peterson, assistant professor of pathology at the Johns Hopkins University School of Medicine.
"'Asked about their immune system, most people might think of white blood cells, lymph glands or vaccines,'
said Dr. Natalia Shulzhenko, author of a new report in Clinical Reviews in Allergy and Immunology, and assistant professor and physician in the Oregon State University Department of Biomedical Sciences.
'The human gut plays a huge role in immune function,' Shulzhenko said. 'This is little appreciated by people who think its only role is digestion...They do help us digest food, but they do a lot more than that.'"
My interest was piqued!
“An emerging theory of disease, Shulzhenko said, is a disruption in the "crosstalk" between the microbes in the human gut and other cells involved in the immune system and metabolic processes.
‘In a healthy person, these microbes in the gut stimulate the immune system as needed, and it in turn talks back,’ Shulzhenko said. 'There's an increasing disruption of these microbes from modern lifestyle, diet, overuse of antibiotics and other issues. With that disruption, the conversation is breaking down.'"
At that same time I was also learning about Korean Natural Farming online, because I am a plant nerd & therefore eternally curious about soil health & structure. I learned so much via this excellent youtube channel.
Korean natural farming was basically saying to me, Hey! Honoring & using what’s naturally around you for health is really freaking important, AND here’s how we literally collect & use this biology. This fit in well with the systems thinking approach to ecology that I was learning about (and will probably never be done learning about!). One of the key practices in Korean Natural Farming is collection & proliferation of indigenous microorganisms found in areas of healthy natural soil. I decided it was very interesting but sort of obscure, so I didn’t immediately prioritize collecting IMOs, though I did start practicing other parts of natural farming with great success.
Meanwhile, led by curiosity in my microbiome, I started digesting all the web could give me on the subject. I came across information like this Harvard study:
“Harnessing naturally occurring microbes or molecules and using them to modulate immune response holds the promise of providing better precision-targeted immune therapies. Such therapies, the researchers say, carry the promise of optima benefits with minimal to no toxic side effects.
‘Because we observed microbial effects mainly in the gut, we believe that a microbe-based therapy would avoid the collateral damage seen with drugs that wipe out classes of immune cells across the body,’ said Christophe Benoist, a professor of microbiology and immunobiology at Harvard Medical School.”
Methanobrevibacter smithii, the primary archaea of the human gut.
Soil & the human gut are two of the most microbially diverse environments on Earth. Gut and root microbes both suppress pathogens. So although there is scant published research on the overlap between microbiota in our guts & microbiota in the soil, I thought welp, since Korean Natural Farming has now taught me exactly how to collect soil microbes, why not see if anything in the soil will fill the missing niches in my gut microbiome?
And just like that, I had an actionable starting point; collecting those microorganisms moved to the top of my priority list!
(Really, I had stacked in a function of experimentally inoculating and hopefully healing my microbiome with the IMO collection I was already planning on doing because of what it does for soil & therefore plant health.)
Now, I needed to decide what locations I would collect these indigenous microorganisms from. Since I grew up basically covered in dirt on our family farm, and to my knowledge this contributed to my lack of allergies, I figured the microbes there were probably my best bet. Also, I had land access and assurance no one would mistake my collection sites for trash and interrupt my experiments.
It was early August 2017. Using the general process outlined by many online IMO collection guides, I prepared my rice & set up five different collection sites.
IMO collection, beginning the process. Image credit
After four days of waiting, I returned & excitedly collected my cultures. One had been chewed through by some sort of animal, but I still had four viable samples! Weighing out the proportionate amount of brown sugar to store the IMO in a shelf-stable form, I ate small pieces of each rice collection right away, and smeared a good bit of it on my hands and arms as I worked (in case transdermal absorption was the thing!). In the days that followed, I inoculated myself twice with half a teaspoon of culture mixed into a large glass of water, prepared fresh each time.
What have my results been?
Nothing short of freakishly effective. Before, shaking hands with a single person, or one trip to the grocery store could result in my coming down with a cold that would put me in bed for a week. I used to actually avoid shaking hands with people if I could help it just because I didn’t want to get sick!
Since my inoculation, life has changed dramatically. I’ve traveled everywhere from Pennsylvania to the West Coast without so much as a cough!!! And I rarely have any gas or stomach upsets. I’ve hugged & kissed strangers and shared drinks with dozens of acquaintances with no ill effects. It’s honestly shocking what a huge difference this experiment has made in my life!!
I wish I knew more about what’s really going on in my microbiome now versus before this citizen scientist experiment. Honestly, the truth is that I really have no idea what I took or exactly how or why it’s working. But what I do know? Is my quality of life is so much higher than it was before. And that? Is worth it to me to write up & share with you.
DISCLAIMER: Pathogenic microbes can live in unhealthy soils, especially anaerobic soil. Caution should be taken to make sure you're choosing good quality soil.
Would you try this experiment? If you do, or have done anything similar, I would LOVE to know! Share your experiences with working with your own microbiome in the comments so we can all learn more together!
You can also DM me on Instagram 
Special thanks to Leif Olson & Craig Trester for their knowledge & support.
Happy inoculation, friends!
Xoxo J