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Biohacking: Comparing Multiple uBiome Samples

uBiome is offering the much needed service of telling us the make up of our microbiome. They provide friendly user interfaces to review the results. Despite beautiful charts and comparison tools one of the limitations of uBiome’s web services is that you cannot compare three or more samples at once. This is a bummer for biohackers who are regularly submitting samples and want to see their changes over months and years. uBiome has posted some python tools through github to allow users to go further. Special thanks to Richard Sprague for contributing to so many microbiome tools on GitHub and a Microbiome Hackers Guide.

In order to merge three or more ubiome results  we will need to do the following five steps:

  1. download uBiome JSON file results
  2. install the uBiome python library
  3. install csvkit
  4. create a python script to merge the files
  5. view the results on the command line

Download uBiome JSON file results:

  • Login to uBiome
  • Click on Advanced
  • Download Taxonomy JSON
  • repeat for each date results are available for

 Install the ubiome python library:

$ pip install ubiome

Install CSVKIT:

$ pip install csvkit

$ cat ubiome-multi-merge.py

Create a python script to merge the files:

#!/usr/bin/env python

from ubiome import *

f1 = UbiomeSample(“2016-11-21”)

f2 = UbiomeSample(“2017-04-01”)

f3 = UbiomeSample(“2018-01-29”)

m = UbiomeMultiSample(f1)

m.merge(f2)

m.merge(f3)

m.write(“merged-files.csv”)

Run the merge script and view the results:

$ ./ubiome-multi-merge.py

csvsort -c 3 -r merged-files.csv | csvlook

Once you have a merged the CSV file you could of course use Google Sheets to view and sort the columns. My preference is for the command line so I use csvkit to compare my three years of microbiome results. The shifts I’ve seen over two years of testing are huge.

 


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