Archive: Notes &amp; Microbiome

R tutorial on autocorrelation analysis for personal health data, using resting heart rate and weight time series to find hidden patterns.

Jul 20, 2020

Testing myself for COVID-19

First-hand experience with at-home COVID-19 testing through the Seattle SCAN study, including kit unboxing, nasal swab process, and results.

Jun 17, 2020

Quick look at Psomagen GutBiome+

Detailed review of Psomagen GutBiome+ whole genome sequencing microbiome test, including gut health scores, metabolites, and dietary advice.

Jun 5, 2020

New results from Viome

In-depth Viome review covering transcriptomics technology, clinical trials, and personal experience using FODMAP diet to treat post-surgery SIBO.

Jun 5, 2020

Coronavirus and the microbiome

Evidence linking COVID-19 and the microbiome, including GI symptoms, fecal virus detection, loss of smell, and the Prevotella hypothesis.

Mar 23, 2020

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.

Feb 21, 2020

Nature Outlook special microbiome issue

Key takeaways from Nature Outlook’s January 2020 special issue on microbiome science, diet, and future microbiome-based medicines.

Jan 29, 2020

Microbiome testing with Psomagen

My experience using the Psomagen Gene and Biome test

Jan 9, 2020

Understanding my heart rate

How to optimise exercise through monitoring your heart rate

Jan 5, 2020

Viome and DayTwo Updates

Updated 2019 results and dietary recommendations from Viome and DayTwo microbiome-based personalized nutrition tests.

Oct 12, 2019

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.

Jun 27, 2019

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.

Jun 15, 2019

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.

Jun 9, 2019

Continuous Glucose Monitoring

Pointers to everything I know about CGM

Jan 19, 2019

Viome and DayTwo Updates

Comparing updated food recommendations from Viome and DayTwo microbiome tests, including major changes to personalized diet advice.

Jul 7, 2018

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.

Jun 11, 2018

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.

Jun 7, 2018

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.

Jun 6, 2018

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.

May 21, 2018

Deep learning and the microbiome

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Summary of links about how to apply AI to studying the microbiome.

May 18, 2018

How to think about microbiome diversity

Understanding microbiome diversity metrics like Shannon Index, Inverse Simpson, and alpha vs beta diversity for gut health analysis.

May 10, 2018

Sonification of the microbiome

Guide to converting microbiome data into sound using R, with a survey of sonification packages, tutorials, and a working example.

May 5, 2018

An interesting high fiber experiment

Analyzing Prashanth Rao’s self-experiment comparing gut microbiome changes from high-grain versus high-vegetable fiber diets.

Apr 13, 2018

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.

Apr 8, 2018

What little I know about nutrition

Brief overview of what I know about nutrition science

Apr 8, 2018

My Microscopic Fellow Travelers To China

How international travel to China affected my gut microbiome, tracked through daily sequencing samples during the trip.

Apr 2, 2018

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.

Mar 15, 2018

Sleeping better on a different diet

Exploring the connection between dietary changes, gut microbiome composition, and sleep quality through personal tracking data.

Richard Spraguer

Mar 6, 2018

Watching Microbiome Changes in Mexico

Tracking gut microbiome shifts during travel to Mexico, observing how diet and environment change bacterial composition.

Feb 24, 2018

Does kombucha change my microbiome?

Personal experiment testing whether drinking kombucha produces measurable changes in gut microbiome composition over time.

Dec 14, 2017

Do Probiotics Really Work For Me?

Testing whether probiotic supplements actually change the gut microbiome by tracking daily samples before, during, and after use.

Nov 29, 2017

Ochrobactrum Sniffles

Tracking nose microbiome changes before, during, and after a rhinovirus cold using daily 16S sequencing with uBiome data.

Nov 28, 2017

How a Citizen Scientist Will Win a Nobel Prize

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How democratized data and citizen science are transforming hypothesis generation, enabling breakthroughs beyond traditional research.

Nov 3, 2017

Frozen blueberries are better for me

DayTwo microbiome analysis shows frozen blueberries score better than fresh for my gut, backed by anthocyanin research.

Oct 17, 2017

Soylent and my microbiome

Tracking my gut microbiome daily to see how drinking Soylent affected my Bacteroidetes/Firmicutes ratio compared to a clinical trial.

Oct 16, 2017

Best Academic Papers About the Microbiome

Essential academic papers on microbiome science, including the Firmicutes/Bacteroidetes ratio debate and key research reviews.

Oct 16, 2017

Richard Sprague Clifton Strengths Inventory

Results from the CliftonStrengths personality assessment: Input, Intellection, Analytical, Responsibility, and Strategic.

Oct 15, 2017

Best references about 23andme

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Curated guide to the best resources, tools, and utilities for analyzing your raw 23andMe genetic data and SNP results.

Oct 14, 2017

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.

Oct 1, 2017

Recommended books about nutrition and health

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Annotated list of the best books on nutrition, diet, and health including paleo, fermentation, and germ theory of disease.

Aug 17, 2016

Bacteroides plebeius and me