My Best Posts
Note: I’m working on a major new project to make it easy for normal people to understand their microbiome test results. Meanwhile, if you’ve tested yourself with uBiome or others, please contact me and I’ll be happy to help you (if you give me your data!)
For “final” versions of my microbiome experiment summaries, please see my entries at Personal Science and the Microbiome on Medium.
Personal Science Guide to the Microbiome: an ebook summary of everything I know about the microbiome. Eventually this will replace everything on this page.
Microbiome Labs: How Actionable Are They Today? In the Future?: Podcast interview with Damien Blenkinsopp
Surfing the Microbiome: Interview with Mark Swanson in Naturopathic Doctor News & Review.
“So Should I Eat Apples or Not?” My review of the Viome microbiome gut test.
“When a Double-Chocolate Brownie is Better for You Than Quinoa” My review of the new DayTwo microbiome testing app. Published by NEO.LIFE
Fusicatenibacter Is Associated With Kefir Drinking My preprint academic paper, submitted to peer review, about a microbe association I discovered in a self-experiment.
How to interpret your uBiome results: My article in O’Reilly’s BioCoder.
How does kombucha affect the microbiome Tracking my microbiome while drinking kombucha.
uBiome official Python Utilities Open source Python module for analyzing your uBiome results.
Peeking into a Baby Biome: Investigating a baby and her mother.
Posts to the uBiome blog
Experimenting with a gut cleanse: before/during/after results from a one-month experiment.
Hacking my sleep with uBiome and an update.
Looking into my mouth microbiome: testing myself at the dentist.
One week change in my microbiome: a before/after test with detailed food tracking.
My microbiome in the jungle: how my gut biome changed during a trip to Central America.
Technical uBiome posts
What do I do with my raw data?
Invitation to the uBiome open source repository
How to make a single table of your uBiome results
How to analyze a uBiome sample in Excel
Other Quantified Self
Richard Sprague: "Fish Oil Makes Me Smarter" from Quantified Self on Vimeo.Following an experiment originally proposed by the late UC Berkeley psychologist and Quantified Self pioneer Seth Roberts, I tested the effect on brain reaction time (BRT) of taking fish oil supplements. Surprisingly, periods of taking fish oil corresponded to significantly higher scores on the test, even when controlling for sleep and other factors such as alcohol consumption. I speculate on why this effect may be real, and suggest how the BRT may be useful in discovering similar effects. I wrote up my results here and you can run the same experiment using Seth’s original R code kept on Github.
- 2018-07-07 Viome and DayTwo Updates
- 2018-06-11 A dictator can’t be too careful
- 2018-06-07 My nose microbiome throughout the seasons
- 2018-06-06 Convert uBiome files to Phyloseq with Actino
- 2018-05-21 Measuring sample variability: uBiome BioRxiv paper
- 2018-05-10 How to think about microbiome diversity
- 2018-05-05 Sonification of the microbiome
- 2018-04-13 An interesting high fiber experiment
- 2018-04-08 Which microbes go with each other?
- 2018-04-02 My Microscopic Fellow Travelers To China
- 2018-03-15 What’s happening to my mouth microbiome?
- 2018-03-06 Sleeping better on a different diet
- 2018-02-24 Watching Microbiome Changes in Mexico
- 2017-12-14 Does kombucha change my microbiome?
- 2017-11-29 Do Probiotics Really Work For Me?
- 2017-11-28 Ochrobactrum Sniffles
- 2017-10-17 Frozen blueberries are better for me
- 2017-10-16 Soylent and my microbiome
- 2017-10-16 Best Academic Papers About the Microbiome
- 2017-10-01 My favorite books about the microbiome
- 2015-05-11 Bacteroides plebeius and me