Experiments With My Microbiome
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This document summarizes Richard Sprague's experiments with his own microbiome over time. He tracked changes in the composition of microbes and bacteria in his gut from May 2014 to July 2015. Sprague also conducted an experiment where he cleared out his gut biome using a colon cleanse to see how it would recover. He found that while the amounts and ratios of bacteria changed after the cleanse, the overall composition recovered quickly and most of the same organisms returned. A few taxa did change permanently in larger amounts. The document concludes that it is difficult to significantly alter one's microbiome in the long run.
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Experiments With My Microbiome
- 1. Experiments With My Microbiome Richard Sprague March 15, 2016 Hive-Bio Discussion
- 2. You Weight Human Non-Human Cells Human Non-Human Genes Human Non-Human 3 pounds
- 3. Find which microbes you have
- 4. Microbiome changes over time David et al: Host lifestyle affects human microbiota on daily timescales Genome Biology 2014, 15:R8
- 5. Overall: Pretty Stable 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jul-15 Phylum Composition Euryarchaeota Verrucomicrobia Tenericutes Actinobacteria Proteobacteria Bacteroidetes Firmicutes 0% 10% 20% 30% 40% 50% 60% 70% May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jul-15 Bacteroidetes/Firmicutes
- 7. Before/After Camping Firmicutes 72% Bacteroidetes 23% Verrucomicrobia 0% Proteobacteria 2% Actinobacteria 1% Other 2% BEFORE CAMPING Firmicutes 71% Bacteroidetes 20% Verrucomicrobia 5% Proteobacteria 1% Actinobacteria 1% Other 2% AFTER CAMPING Not much difference
- 8. 0 10000 20000 30000 40000 50000 60000 70000 May Jun Oct Jan Feb Bifidobacterium
- 10. Experiment: Gut Cleanse • What did I do? – Cleared my gut biome to see how it recovers • How did I do it? – Gut tests before/after – Colon cleanse – Analysis with Python/R • What did I learn? …
- 13. Reseeding Date Calories Carbs Fat Protein Cholesterol Sodium Sugars Fibre 15-Oct-15 2542 332 79 104 165 3339 53 48 17-Oct-15 1290 194 32 38 76 2907 58 19 18-Oct-15 0 0 0 0 0 0 0 0 19-Oct-15 0 0 0 0 0 0 0 0 20-Oct-15 2644 292 119 102 557 3266 61 41 21-Oct-15 2497 234 98 103 422 2593 89 44 22-Oct-15 2017 280 43 62 110 1577 58 29 23-Oct-15 2674 369 78 122 75 1305 49 36 24-Oct-15 2238 182 82 174 365 3123 62 30 25-Oct-15 1582 160 48 110 239 3084 38 19 26-Oct-15 1876 226 63 73 186 920 52 33 27-Oct-15 1771 173 62 97 767 1301 33 22 28-Oct-15 2190 291 88 100 252 1043 65 32 29-Oct-15 1768 161 88 90 267 1664 54 22 30-Oct-15 938 107 37 43 114 781 34 10 31-Oct-15 1637 251 42 94 223 4184 17 11 1-Nov-15 2133 198 69 100 380 1953 53 9 2-Nov-15 2142 269 76 60 306 2193 46 30 3-Nov-15 2019 300 97 70 255 2532 160 34 Cleans e
- 19. Conclusions • My gut microbiome recovers quickly • Amounts and ratios change, but not the organisms • A few taxa changed permanently, by a lot. • It’s hard to significantly change your microbiome
Notas del editor
- Quick review if you couldn’t attend my previous talks. I’ve always been interested in genetic testing, but I learned that most of the genes in our bodies is non-human! Trillions of living microbes, many of them co-evolved with humans, inhabit every space of our bodies, adding up to a total of 3-5 pounds, about as much as your brain!
- Each costs about $100 uBiome gives you results now in a few weeks (used to be months) uBiome gives you details about your own data, downloadable as JSON.
- My favorite academic paper that followed the details of two subjects to see how their microbiomes changed over a year. http://genomebiology.com/2014/15/7/R89#sec2
- Having taken many uBiome samples over the past year, one observation: my gut biome is surprisingly stable. Sure there are ups and downs, but in the broadest categories things don’t change that much. I’m an omnivore, and my Bacteroidetes/Firmicutes ratio is remarkably unchanged.
- Bottom line: at the highest levels, my 2 weeks in the back country didn’t do much. There are a few exceptions, though
- Like every QS talk, my remarks center around these three questions.
- I learned a few things as a result of this experiment, but…