Microbiome
50 posts · all topics
Personal Science Guide to the Microbiome
The definitive guide to microbiome testing
Viome Recommendations
R code to compare Viome food recommendations across multiple tests and track changes over time.
Microbiome
Richard Sprague's microbiome research and personal science experiments tracking gut bacteria over hundreds of tests.
Microbiome Reviews
Richard Sprague's hands-on reviews of microbiome testing services including Bristle Health, ZOE, Viome, and DayTwo.
My Results
Full microbiome test results from Richard Sprague's hundreds of gut health tests across Tiny Health, Bristle, ZOE, and other providers.
Podcasts
Podcast interviews with Richard Sprague on microbiome science, personal science, and gut health.
Science
Microbiome science experiments and detailed analysis by Richard Sprague, including kombucha studies and academic research.
Read Bristle Health Raw Data
R tutorial for reading Bristle Health oral microbiome data, creating tree maps, and comparing with 16S mouth microbiome samples.
New results from Viome
In-depth Viome review covering transcriptomics technology, clinical trials, and personal experience using FODMAP diet to treat post-surgery SIBO.
Quick look at Psomagen GutBiome+
Detailed review of Psomagen GutBiome+ whole genome sequencing microbiome test, including gut health scores, metabolites, and dietary advice.
Coronavirus and the microbiome
Evidence linking COVID-19 and the microbiome, including GI symptoms, fecal virus detection, loss of smell, and the Prevotella hypothesis.
How effective is the flu vaccine, really?
Analyzing CDC flu vaccine effectiveness data for the 2019-2020 season, showing 45% efficacy and what it means for healthy individuals.
Nature Outlook special microbiome issue
Key takeaways from Nature Outlook's January 2020 special issue on microbiome science, diet, and future microbiome-based medicines.
Microbiome testing with Psomagen
My experience using the Psomagen Gene and Biome test
Viome and DayTwo Updates
Updated 2019 results and dietary recommendations from Viome and DayTwo microbiome-based personalized nutrition tests.
Viome Presentation at Personalized Nutrition Summit
Notes from Viome CSO Momo Viyusich's presentation at the 2019 Personalized Nutrition Summit on transcriptomics and diet predictions.
Could my gut microbes change my blood type?
Exploring Flavonifractor plautii, the gut bacterium whose enzymes can convert Type A blood to Type O, with personal microbiome data.
Studying back-to-back microbiome results
Comparing back-to-back gut microbiome samples to study day-to-day variability and the effect of Reducose on gut bacteria composition.
R-tude: My Bifido Levels by month
R tutorial creating a calendar heatmap visualization of Bifidobacterium gut microbiome abundance levels tracked over multiple years.
Viome and DayTwo Updates
Comparing updated food recommendations from Viome and DayTwo microbiome tests, including major changes to personalized diet advice.
A dictator can’t be too careful
What can spy agencies learn from microbiome analysis? Examining gut bacteria linked to mood and personality, from Kim Jong-un to Mao Zedong.
My nose microbiome throughout the seasons
Tracking 50+ nose microbiome samples over three years to find seasonal patterns in nasal bacteria like Corynebacterium and Moraxella.
Convert uBiome files to Phyloseq with Actino
How to convert uBiome microbiome data to R Phyloseq objects using the Actino package for advanced gut microbiome analysis.
Measuring sample variability: uBiome BioRxiv paper
Analyzing uBiome's BioRxiv paper on gut microbiome sample variability and reproducibility, with independent replication using 25 duplicate samples.
How to think about microbiome diversity
Understanding microbiome diversity metrics like Shannon Index, Inverse Simpson, and alpha vs beta diversity for gut health analysis.
Sonification of the microbiome
Listen to a year's worth of my microbiome results.
An interesting high fiber experiment
Analyzing Prashanth Rao's self-experiment comparing gut microbiome changes from high-grain versus high-vegetable fiber diets.
Which microbes go with each other?
Using R and correlation analysis on daily gut microbiome samples to find which bacterial genera rise and fall together.
My Microscopic Fellow Travelers To China
How international travel to China affected my gut microbiome, tracked through daily sequencing samples during the trip.
What’s happening to my mouth microbiome?
Mysterious Streptococcus species shifts in my oral microbiome detected through regular 16S testing of cheek, tongue, and lip sites.
Sleeping better on a different diet
Exploring the connection between dietary changes, gut microbiome composition, and sleep quality through personal tracking data.
Watching Microbiome Changes in Mexico
Tracking gut microbiome shifts during travel to Mexico, observing how diet and environment change bacterial composition.
Does kombucha change my microbiome?
Personal experiment testing whether drinking kombucha produces measurable changes in gut microbiome composition over time.
Deep learning and the microbiome
Summary of links about how to apply AI to studying the microbiome.
Do Probiotics Really Work For Me?
Testing whether probiotic supplements actually change the gut microbiome by tracking daily samples before, during, and after use.
Ochrobactrum Sniffles
Tracking nose microbiome changes before, during, and after a rhinovirus cold using daily 16S sequencing with uBiome data.
Frozen blueberries are better for me
DayTwo microbiome analysis shows frozen blueberries score better than fresh for my gut, backed by anthocyanin research.
Best Academic Papers About the Microbiome
Essential academic papers on microbiome science, including the Firmicutes/Bacteroidetes ratio debate and key research reviews.
Soylent and my microbiome
Tracking my gut microbiome daily to see how drinking Soylent affected my Bacteroidetes/Firmicutes ratio compared to a clinical trial.
My favorite books about the microbiome
Ranked list of the best books about the gut microbiome, from beginner introductions to advanced science and practical guides.
Experimenting with a gut cleanse
Your gut microbiome changes constantly in response to everything from diet to exercise, so when looking at multiple uBiome test results side-by-side it can be complicated to figure…
Microbes on my skin
For some reason I haven’t had good luck getting uBiome to process my skin microbe samples. I swab the skin under my ear, just as directed, back and…
I'm a secretor
The Gut Guardians podcast interview with Alanna Collen included an interesting reference to the FUT2 gene, which the podcast hosts says has been linked to response to high…
Measuring my uBiome diversity
While there are few agreed-upon standards for what constitutes a good or bad microbiome, nearly everyone agrees that a diverse microbiome is better than one that is less…
A gut bacteria for caffeine metabolism?
23andme says I’m a slow caffeine metabolizer because I have the AC genotype at SNP rs762551 . You’d think that means I’m extra sensitive to caffeine before bedtime,…
My QS Seattle Talk: Cholesterol and my Microbiome
My presentation at the July meeting of Quantified Self Seattle , with more details about the A/B experiment I wrote about on the uBiome blog . Embedded content…
Overselling the microbiome
Here’s the cover of a magazine I saw yesterday in the grocery store checkout lane: I thought about submitting it to Jonathan Eisen's list of Overselling the Microbiome…
Which species do I track?
At the Microbiome breakout during last week’s Quantified Self Conference , several people were interested in the list of organisms I track. Here’s the list, along with my…
Bacteroides plebeius and me
How I found Bacteroides plebeius in my gut microbiome despite having no Japanese ancestry, likely from years living in Tokyo.
Using tools to analyze my uBiome results
To study my uBiome samples more carefully, I’ve written a few tools that you may find helpful too. You’ll need to know a little about the statistical programming…