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