A first look at my microbiome

UPDATE: I’m not doing science here, the word “hacking” is deliberate. Also, know the facts about FMT. There’s a lot of risk. At the very minimum, ensure that the donor material is properly screened.

Today is an exciting day. I received my first set of results from uBiome, and I launched this blog! The blog is a journal of my investigations into my microbiome.

What’s the microbiome? Well, it turns out that the human body contains ten times more microbial cells than human cells (1), most of which reside in the gut. The bacterial composition of the human gut may have an impact on things like obesity and various chronic illnesses.

In this post I’ll briefly cover my motivation and then share a few interesting findings in my first set of test results.

Why I care about my microbiome

I have moderate psoriasis on my arms and legs. Psoriasis is an autoimmune disease, and recent research suggests that gut flora may impact autoimmunity (2). My psoriasis developed after I underwent several heavy doses of antibiotics. I suspect that the antibiotics changed my gut biome, and may have caused or accelerated my psoriasis.

I decided to run some tests and experiments on my body to see if there’s any merit to my suspicion, and to see if by modding my microbiome I can affect my psoriasis.

The procedure

Last December I learned about uBiome and the possibility of sequencing my gut biome. Around the same time I learned about recent research into fecal microbiota transplantation (FMT) (3). I realized that I could alter my gut biome via FMT and measure the affects with uBiome.

I took an initial gut sample and mailed it to uBiome. I then performed an at-home FMT, with a close friend acting as the donor. A few weeks later I sent in another sample, and so did the donor. Since then we’ve been anxiously waiting for our results from uBiome.

I’m hoping that I’ll learn a few things:

  1. Is my gut biome normal?
  2. Can I change my gut biome, and how drastically?
  3. If I change it, will I notice a difference? Will it improve my psoriasis, or other aspects of my life?

uBiome results for my first two samples

After a long wait, I received my first set of results this morning. I haven’t have time to dig into the details, but wanted to document my initial reaction. I’ll follow up with more info as I investigate further.

Note that the data is from uBiome’s beta service. I’m pretty excited to have early access.

Overview

Here are the overview graphs of my microbiome, before FMT:

… and after FMT:

The post FMT sample shows more Bacteroidetes, fewer Firmicutes, and a minor reduction/rearrangement of the next few phyla.

Firmicutes and Bacteroidetes are the most common bacteria in humans, and may play a role in obesity. Generally, a higher ratio of Firmicutes to Bacteroidetes is associated with higher obesity (4, 5). In my case the ratio of Firmicutes to Bacteroidetes dropped.

Here’s a graph prior to the FMT showing my Firmicute and Bacteroidete proportions. The green bar represents the range of normal values, and the white mark is my sample. You can see that the Firmicute proportion was on the high end of normal, and Bacteroidete was near the low end.

After the FMT, both had moved closer to center.

Wrap up for now

The big question is, was I able to affect my microbiome with an FMT? It wouldn’t be surprising if that were the case, but it will require a more controlled experiment to determine. However it’s remarkable that there are low-cost tools becoming available for this kind of at-home exploration.

There’s a lot more to unpack from the results. I haven’t begun to look at the diversity of my initial sample, or searched for irregularities. In addition, the donor’s sample hasn’t been sequenced yet. I’m very excited to see how it compares to mine.

In the next few weeks I plan to run another test to see if my gut has continued to change, or is holding steady. I’m looking forward to learning more, and sharing it here. Thanks for reading!