How Backpacking Changed My Gut Microbiome
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Transcript of How Backpacking Changed My Gut Microbiome
Backpackingand
My Gut Microbiome
Richard SpragueOctober 14, 2015
YouWeight
Human Non-Human
Cells
Human Non-Human
Genes
Human Non-Human
3 pounds
Find which microbes you have
Microbiome changes over time
David et al: Host lifestyle affects human microbiota on daily timescalesGenome Biology 2014, 15:R8
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?…
Scout Ranch
• High elevation: 8,000 – 13,000 ft
• Rugged, pristine, natural• Microbes!
Overall: Pretty Stable
May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jul-150%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Phylum Composition
EuryarchaeotaVerrucomicrobiaTenericutesActinobacteriaProteobacteriaBacteroidetesFirmicutes
May-14 Jun-14 Oct-14 Jan-15 Feb-15 21-Apr 28-Apr Jul-150%
10%
20%
30%
40%
50%
60%
70%
Bacteroidetes/Firmicutes
Changes
Firmicutes72%
Bac-teroidetes
23%
Verrucomicrobia0%
Proteobacteria2%
Actinobacteria1% Other
1%
Before Camping
Firmicutes70%
Bac-teroidetes
20%
Verru-comicrobia
5%
Proteobacteria1%
Actinobacteria1%
Other2%
After camping
Not much difference
Biggest Loserstax_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
Biggest Gainerstax_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
Top Unusualtax_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
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%
Diversity Increased
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
Conclusions
Thank you
@sprague
Odoribacter
What to track May Jun Oct Jan Feb 21-Apr 28-Apr Faecalibacterium prausnitzii 99571 62316 5790 95382 136354 106400 165582 speciesRoseburia 13554 11157 7825 42782 10750 7952 49379 genusChristensenellaceae 82585 39713 40290 40977 13530 familyChristensenella 269 NA 38 17 NA 126 92 genusAkkermansia 30960 19654 7648 6269 NA 11611 9538 genusBifidobacteria Longum 32 NA 1858 9571 2115 452 0 speciesBifidobacterium 8473 6532 58747 66516 6919 7072 49 genus B. Longum as % of total Bifido 0.38% NA 3.16% 14.39% 30.57% 6.39% 0.00% Bacteroidetes/Firmicutes ratio 41.09% 64.58% 47.09% 22.84% 21.93% 12.10% 19.74% Clostridium 35012 41679 71326 66114 17628 37684 2486 genusC. botulinum NA 25 128NA 7 speciesC. clostridioforme 28902 35372 15170 24128 16747 speciesC. baratii 1223 NA 5588 30543 132 282 species