lassesen 8:24 pm on January 1, 2018  

Comparing uBiomes from different dates

A reader sent me over two uBiomes taken 3 months apart and was confused by the results. Fortunately, I could upload her data and do some quick analysis (which will eventually be available as a web page).

Phylum Level Is Improving

The numbers below are the counts. It they are getting closer to normal, it is improving. If further away then a loss.

October December Normal tax_name tax_rank Change
15453 10574 45026 Actinobacteria phylum Loss
701911 424855 271874 Bacteroidetes phylum Improved
60 9124 38 Euryarchaeota phylum Loss
269622 527597 561301 Firmicutes phylum Improved
12694 22898 32511 Proteobacteria phylum Improved
271 512 4200 Synergistetes phylum Improved

We see a rare phylum (Euryarchaeota) was one of the two losses, so we really had 4 gains to 1 loss.

Class Changes

The dominant change at the class level are improvement if we take by raw counts. Both Clostridia and Bacteroidia (the two biggest classes have improved). The third largest class Erysipelotrichia has had a loss.

October December Normal tax_name tax_rank Change
15453 10574 45026 Actinobacteria class Loss
120 3024 24677 Alphaproteobacteria class Improved
15544 8799 20967 Bacilli class Loss
701911 424855 270991 Bacteroidia class Improved
527 12086 12351 Betaproteobacteria class Improved
221346 469302 511846 Clostridia class Improved
1191 6249 3903 Deltaproteobacteria class Improved
5367 1337 7271 Epsilonproteobacteria class Loss
15785 36597 10249 Erysipelotrichia class Loss
5488 199 24696 Gammaproteobacteria class Loss
60 9124 38 Methanobacteria class Loss
16946 12899 24121 Negativicutes class Loss

For this overgrowth, we have some suggestions.

class

NOTE: Walnut is reported at two places. We have contrary results from studies 😦

Order Changes

We see gain and loss here too.

October December Normal tax_name tax_rank Change
5261 2899 23920 Actinomycetales order Loss
346 249 15243 Bacillales order Loss
701911 424855 268676 Bacteroidales order Improved
527 11974 11721 Burkholderiales order Improved
5367 1337 7271 Campylobacterales order Loss
221346 468964 512463 Clostridiales order Improved
2140 7674 21896 Coriobacteriales order Improved
1191 6249 3544 Desulfovibrionales order Loss
15785 36597 10192 Erysipelotrichales order Loss
15197 8549 19016 Lactobacillales order Loss
60 9124 38 Methanobacteriales order Loss
180 199 6984 Pasteurellales order Improved
120 24 41600 Rhizobiales order Loss
16946 12899 24121 Selenomonadales order Loss
271 512 4200 Synergistales order Improved

The worst loss was for Rhizobiales, with the following suggestions coming from the website

order

It is now clear that walnuts should be avoided.

Bottom Line

One concern that I have asked is about undergrowth. Working at the genus level gets very complex here. Working at higher levels like phylum, class and order is simpler.

With this new comparison page proposed, you get better clarity of the numbers and can focus on the highest count targets.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.