Personal Science and the Microbiome
Intro
1
What is Personal Science?
1.1
Reference Values
1.2
Quantifying the anecdotal
2
Getting Started
2.1
Raw data for your microbiome
2.1.1
uBiome
2.1.2
Thryve
2.1.3
American Gut
2.1.4
Other
2.2
Using uBiome
2.3
Download your uBiome Data
3
Using Personalscience.com
4
Microbes to Watch
4.1
Phylum
4.2
Genus
4.3
Species
5
The Science of the Microbiome
5.1
Microbes everywhere
5.1.1
Microbes above and below
5.1.2
Microbes around you
5.1.3
Microbes within you*
5.1.4
Microbes and food*
5.2
Microbes and you
5.2.1
The promise and disappointment of genetic testing
5.2.2
Most of your DNA is not fixed
5.2.3
Microbes are older than any of us
5.2.4
What they want
5.2.5
Who’s in charge?
5.2.6
What is health?
5.3
Microbes and health
5.3.1
Gluten
5.3.2
Other conditions
5.3.3
Hygiene**
5.3.4
Diversity and health
5.3.5
Microbes and behavior*
5.4
Microbe technology
5.4.1
The 16S rRNA Gene
5.4.2
Limitations of 16S
5.4.3
Limitations of collection
6
My Experiments
6.1
Summary of My Experiments
6.1.1
Diversity
6.1.2
Variability through time
6.2
Kefir and the Microbiome
6.3
Traveling to China
6.4
Exercise and the microbiome**
6.5
Do Probiotics Work?
6.5.1
VSL
6.6
Experiment: Gut Cleanse*
6.7
Kombucha
6.8
Hacking my sleep
6.9
Other foods and my microbiome
6.10
Diet Change
6.11
Collection methods
6.12
The Skin Microbiome*
6.12.1
Body odor
6.13
The Oral Microbiome*
6.14
The Nose Microbiome
6.15
Are my Dialister levels normal?
6.16
Omega-3 and the microbiome**
6.17
Soylent
6.18
Conclusions
7
Case Studies
7.1
Healthy People
7.2
Family members
7.2.1
My sister
7.3
Alzheimers and the microbiome
7.4
Colorectal Cancer
7.5
Ketogenic Diet
7.6
Parkinson’s Disease and the Microbiome
7.7
Lyme Disease
7.8
Gut Issues
7.8.1
CB
7.8.2
NJ1
7.8.3
Ed
7.8.4
Celiac Patients
7.8.5
SJ
7.8.6
U5
7.8.7
Mr. C
7.8.8
FF
7.8.9
High Proteobacteria
8
Using uBiome
8.1
Find more details in your uBiome results
8.2
How are you different?
9
Go Further*
9.1
Microbes and genes
9.2
Beyond Bacteria
9.3
Fermented Food
9.3.1
Yogurt
9.3.2
Pickling
9.3.3
What’s happening in sauerkraut
9.4
Annotated References
9.4.1
Authors
9.5
Best Academic Papers
9.5.1
Popular Topics
9.5.2
Academic Papers
9.5.3
General Overview
9.5.4
Microbes and Behavior
9.5.5
Historic Papers
9.5.6
Self-tracking
9.5.7
Diet
9.5.8
Population studies
9.5.9
Enterotypes
9.5.10
Large population summaries
9.5.11
Methods
9.6
Other Resources
9.6.1
Software
9.7
Coming Soon
10
Appendix
10.1
Gut Microbiome
10.2
Healthy ranges
10.3
Mouth Microbiome
10.4
Skin Microbiome
10.5
Nose Microbiome
10.6
Lab Tests Compared
10.6.1
Thryve
10.6.2
DayTwo
10.6.3
Viome
10.6.4
Gencove
References
Richard Sprague (c) 2019
Personal Science Guide to the Microbiome
Chapter 8
Using uBiome
Tips and tricks for getting as much as possible out of your uBiome results.