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How Backpacking Changed My Gut Microbiome

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Before/after tests with uBiome show my gut biome is surprisingly stable despite a 2-week backpacking trip off the grid.

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How Backpacking Changed My Gut Microbiome

  1. 1. Backpacking and My Gut Microbiome Richard Sprague October 14, 2015
  2. 2. You Weight Human Non-Human Cells Human Non-Human Genes Human Non-Human 3 pounds
  3. 3. Find which microbes you have
  4. 4. Microbiome changes over time David et al: Host lifestyle affects human microbiota on daily timescales Genome Biology 2014, 15:R8
  5. 5. The QS Questions • What did I do? – Measured how my gut biome changed after a 2- week backpacking trip in New Mexico • How did I do it? – Gut tests before/after – Analysis with Python/R • What did I learn? …
  6. 6. Scout Ranch • High elevation: 8,000 – 13,000 ft • Rugged, pristine, natural • Microbes!
  7. 7. 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
  8. 8. Changes 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
  9. 9. Biggest Losers tax_name tax_rank May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jun-15 Aug-15 Diff % Faecalibacterium genus 10.753% 6.376% 0.642% 14.198% 20.374% 14.909% 18.539% 22.044% 7.621% -14.42% Bacteroides genus 14.631% 8.943% 21.508% 12.717% 10.396% 5.547% 8.061% 14.218% 6.494% -7.72% Lachnospira genus 0.919% 0.642% 0.388% 0.978% 0.137% 0.375% 1.729% 2.630% 0.470% -2.16% Pseudobutyrivibrio genus 0.594% 1.977% 1.252% 1.804% 4.134% 3.552% 2.502% 2.314% 0.402% -1.91% Coprococcus genus 3.986% 3.324% 3.579% 5.411% 2.574% 5.176% 2.250% 1.430% 0.693% -0.74% Bifidobacterium genus 0.847% 0.653% 5.875% 6.652% 0.692% 0.688% 0.005% 1.045% 0.540% -0.51% Parasutterella genus 0.749% 0.243% 0.037% 0.384% 0.661% 0.613% 1.217% 0.836% 0.437% -0.40% Lactobacillus genus 0.153% 0.000% 1.004% 0.144% 0.084% 0.713% 1.704% 0.568% 0.205% -0.36% Paenibacillus genus 0.005% 0.000% 0.000% 0.011% 0.000% 0.000% 0.000% 0.273% 0.000% -0.27% Brevundimonas genus 0.415% 3.665% 0.068% 0.045% 0.031% 0.075% 0.084% 0.327% 0.082% -0.24% Alistipes genus 2.026% 1.330% 1.670% 0.456% 0.626% 0.909% 1.634% 1.157% 0.995% -0.16% Top 10 most-depleted taxa (genus) Highest Abundance Least Abundance Abundance compared to all previous tests of that taxa
  10. 10. Biggest Gainers tax_name tax_rank May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jun-15 Aug-15 Diff % Blautia genus 3.240% 2.364% 3.808% 4.469% 8.585% 6.907% 1.895% 2.807% 9.705% 6.90% Odoribacter genus 4.104% 3.388% 0.800% 1.108% 0.842% 0.721% 0.242% 1.880% 7.106% 5.23% Ruminococcus genus 5.151% 3.596% 9.351% 8.383% 7.906% 7.749% 5.349% 4.430% 8.597% 4.17% Akkermansia genus 3.096% 1.965% 0.765% 0.627% 0.000% 1.129% 0.945% 0.236% 4.318% 4.08% Subdoligranulum genus 0.550% 0.543% 0.033% 0.099% 0.881% 1.200% 1.107% 0.541% 3.396% 2.86% Anaerostipes genus 1.139% 1.168% 1.234% 2.090% 0.789% 3.662% 0.072% 0.761% 1.788% 1.03% Anaerotruncus genus 0.153% 0.000% 0.166% 0.051% 0.075% 0.205% 0.082% 0.011% 0.854% 0.84% Roseburia genus 1.355% 1.116% 0.783% 4.278% 1.075% 0.773% 4.890% 2.448% 3.250% 0.80% Phascolarctobacterium genus 0.349% 1.520% 0.015% 0.039% 0.115% 0.310% 0.312% 0.027% 0.556% 0.53% Barnesiella genus 1.744% 1.179% 0.847% 0.466% 0.264% 0.566% 1.140% 0.804% 1.324% 0.52% Sarcina genus 0.385% 0.000% 0.271% 0.331% 0.026% 0.093% 0.193% 0.032% 0.545% 0.51% Methanobrevibacter genus 0.000% 0.000% 0.000% 0.000% 0.000% 2.399% 0.215% 0.145% 0.635% 0.49% Dorea genus 0.358% 0.636% 0.405% 0.744% 0.670% 1.057% 0.287% 0.096% 0.534% 0.44% Dialister genus 0.604% 0.000% 0.560% 0.319% 0.009% 0.290% 0.475% 0.064% 0.456% 0.39% Synergistes genus 0.199% 0.000% 0.019% 0.027% 0.000% 0.067% 0.124% 0.021% 0.273% 0.25% Bilophila genus 0.399% 0.000% 0.183% 0.063% 0.031% 0.161% 0.780% 0.080% 0.325% 0.24% Streptococcus genus 0.399% 0.231% 0.118% 0.263% 0.018% 0.133% 0.029% 0.011% 0.195% 0.18% Most-enriched taxa (genus) Highest Abundance Least Abundance
  11. 11. Top Unusual tax_name tax_rank Aug-15 Diff % Blautia genus 9.705% 6.90% Odoribacter genus 7.106% 5.23% Akkermansia genus 4.318% 4.08% Subdoligranulum genus 3.396% 2.86% Anaerotruncus genus 0.854% 0.84% Sarcina genus 0.545% 0.51% Synergistes genus 0.273% 0.25% Collinsella genus 0.188% 0.18% Sutterella genus 0.031% 0.03% Allisonella genus 0.027% 0.03% Top 10 taxa after camping that were found in highest abundance among all my tests. “may mediate obesity, diabetes, and inflammation” • Consumes H2 • Probably contributes to a family of organisms • Characterized, but unknown function
  12. 12. My Microbiome Through Time tax_name tax_rank May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jun-15 Aug-15 Highest Diff % root root 100.000% 100.000% 100.000% 100.000% 100.000% 100.000% 100.000% 100.000% 100.000% 100.00% 0.00% cellular organisms no_rank 0.000% 0.000% 0.000% 0.000% 0.000% 99.644% 99.253% 99.245% 99.762% 99.76% 0.52% Bacteria superkingdom 100.000% 100.000% 100.000% 100.000% 100.000% 97.219% 99.026% 99.020% 99.125% FALSE 0.11% Verrucomicrobia phylum 3.135% 1.965% 0.770% 0.664% 0.013% 1.155% 0.957% 0.236% 4.418% 4.42% 4.18% Clostridia class 59.443% 44.506% 56.495% 70.663% 67.494% 77.062% 66.026% 66.738% 61.692% FALSE -5.05% Clostridiales order 59.417% 44.506% 56.487% 70.622% 67.423% 77.037% 66.019% 66.727% 61.680% FALSE -5.05% Ruminococcaceae family 24.727% 18.175% 17.022% 30.217% 38.711% 32.624% 34.518% 40.258% 30.487% FALSE -9.77% Lachnospiraceae family 13.842% 14.637% 13.106% 23.755% 23.093% 27.560% 16.830% 15.793% 20.475% FALSE 4.68% Bacteroidetes/Chlorobi group superphylum 25.573% 29.927% 27.489% 16.434% 14.918% 9.684% 13.602% 21.760% 18.290% FALSE -3.47% Euryarchaeota phylum 0.000% 0.000% 0.000% 0.000% 0.000% 2.425% 0.227% 0.225% 0.637% FALSE 0.41% Bacteroidia class 25.554% 16.284% 27.470% 16.319% 14.852% 9.660% 13.578% 21.519% 18.259% FALSE -3.26% Bacteroidales order 25.532% 16.284% 27.446% 16.234% 14.843% 9.651% 13.566% 21.412% 18.253% FALSE -3.16% Porphyromonadaceae family 7.619% 6.012% 3.585% 2.285% 3.054% 2.596% 3.097% 4.280% 10.103% 10.10% 5.82% unclassified Bacteria no_rank 3.347% 2.231% 6.011% 2.132% 8.633% 3.330% 9.972% 5.164% 9.719% FALSE 4.55% unclassified Bacteria (miscellaneous) no_rank 3.347% 2.231% 6.011% 2.122% 8.633% 3.328% 9.971% 5.164% 9.719% FALSE 4.55% Blautia genus 3.240% 2.364% 3.808% 4.469% 8.585% 6.907% 1.895% 2.807% 9.705% 9.71% 6.90% bacterium NLAE-zl-P430 species 2.067% 1.491% 3.853% 1.487% 7.959% 1.912% 8.529% 3.680% 8.963% 8.96% 5.28% Dysgonomonas genus 0.000% 0.000% 0.000% 0.012% 0.000% 0.000% 0.000% 0.000% 0.000% FALSE 0.00%
  13. 13. Diversity Increased
  14. 14. What I Learned • My microbiome is quite robust – Big groupings don’t change much over time • Camping helped my Akkermansia • Camping is good for diversity
  15. 15. Conclusions
  16. 16. Thank you @sprague
  17. 17. Odoribacter
  18. 18. What to track May Jun Oct Jan Feb 21-Apr 28-Apr Faecalibacterium prausnitzii 99571 62316 5790 95382 136354 106400 165582species Roseburia 13554 11157 7825 42782 10750 7952 49379genus Christensenellaceae 82585 39713 40290 40977 13530 family Christensenella 269NA 38 17NA 126 92genus Akkermansia 30960 19654 7648 6269NA 11611 9538genus Bifidobacteria Longum 32NA 1858 9571 2115 452 0species Bifidobacterium 8473 6532 58747 66516 6919 7072 49genus B. Longum as % of total Bifido 0.38%NA 3.16% 14.39% 30.57% 6.39% 0.00% Bacteroidetes/Firmicut es ratio 41.09% 64.58% 47.09% 22.84% 21.93% 12.10% 19.74% Clostridium 35012 41679 71326 66114 17628 37684 2486genus C. botulinum NA 25 128NA 7 species C. clostridioforme 28902 35372 15170 24128 16747 species C. baratii 1223NA 5588 30543 132 282species

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