Personal Science
Intro
1
What is Personal Science?
2
The Science of the Microbiome
2.1
Microbes everywhere
2.1.1
Microbes above and below
2.1.2
Microbes around you
2.1.3
Microbes within you*
2.1.4
Microbes and food*
2.2
Microbes and you
2.2.1
The promise and disappointment of genetic testing
2.2.2
Most of your DNA is not fixed
2.2.3
Microbes are older than any of us
2.2.4
What they want
2.2.5
Who’s in charge?
2.2.6
What is health?
2.3
Microbes and health
2.3.1
Food Allergies
2.3.2
Gluten
2.3.3
Obesity
2.3.4
Other conditions
2.3.5
Hygiene
2.3.6
Diversity and health
2.3.7
Microbes and behavior*
2.4
Microbe technology
2.4.1
The 16S rRNA Gene
2.4.2
Limitations of 16S
2.4.3
Limitations of collection
3
My Experiments
3.1
Summary of My Experiments
3.1.1
Diversity
3.1.2
Variability through time
3.2
Kefir and the Microbiome
3.3
Traveling in Mexico
3.4
Traveling to China
3.5
Camping
3.6
Exercise and the microbiome**
3.7
Do Probiotics Work?
3.7.1
VSL
3.8
Visiting the dentist
3.9
Experiment: Gut Cleanse*
3.10
Kombucha
3.11
Hacking my sleep
3.12
Other foods and my microbiome
3.13
Diet Change
3.14
Collection methods
3.15
My Skin Microbiome*
3.15.1
Body odor
3.16
My Oral Microbiome*
3.17
My Nose Microbiome
3.18
Are my Dialister levels normal?
3.19
Omega-3 and the microbiome**
3.20
Soylent
3.21
Conclusions
4
Case Studies
4.1
Healthy People
4.2
Family members
4.2.1
My sister
4.3
Alzheimers and the microbiome
4.4
Colorectal Cancer
4.5
Ketogenic Diet
4.6
Parkinson’s Disease and the Microbiome
4.7
Lyme Disease
4.8
Gut Issues
4.8.1
CB
4.8.2
NJ1
4.8.3
Ed
4.8.4
Celiac Patients
4.8.5
SJ
4.8.6
U5
4.8.7
Mr. C
4.8.8
FF
4.8.9
High Proteobacteria
5
Getting Started
5.1
Raw data for your microbiome
5.1.1
uBiome
5.1.2
Thryve
5.1.3
American Gut
5.1.4
Other
6
Using Personalscience.com
7
Microbes to Watch
7.1
Phylum
7.2
Genus
7.3
Species
8
Go Further*
8.1
Microbes and genes
8.2
Beyond Bacteria
8.3
Fermented Food
8.3.1
Yogurt
8.3.2
Pickling
8.3.3
What’s happening in sauerkraut
8.4
Annotated References
8.4.1
Authors
8.5
My favorite books about the microbiome
8.5.1
Other Books Worth Having in the Pile
8.5.2
Not about the microbiome
8.5.3
Other
8.6
Best Academic Papers
8.6.1
Popular Topics
8.6.2
Academic Papers
8.6.3
General Overview
8.6.4
Microbes and Behavior
8.6.5
Historic Papers
8.6.6
Self-tracking
8.6.7
Diet
8.6.8
Population studies
8.6.9
Enterotypes
8.6.10
Large population summaries
8.6.11
Methods
8.7
Other Resources
8.7.1
Software
8.8
Coming Soon
9
Appendix
9.1
Gut Microbiome
9.2
Healthy ranges
9.3
Mouth Microbiome
9.4
Skin Microbiome
9.5
Nose Microbiome
9.6
Lab Tests Compared
9.6.1
Thryve
9.6.2
DayTwo
9.6.3
Viome
9.6.4
Gencove
References
Richard Sprague (c) 2020
Personal Science Guide to the Microbiome
Chapter 9
Appendix
Here are summaries of the overall results of my own testing.