Wednesday, January 28, 2015

Using tools to analyze my uBiome results

To study my uBiome samples more carefully, I’ve written a few tools that you may find helpful too. You’ll need to know a little about the statistical programming language R — just enough to load my scripts and enter a few commands at the prompts. The nice part is that you can easily read the results in Excel, letting you manipulate, sort, or graph the results to your heart’s content. Here’s an example comparing my uBiome samples taken in May and October.

These are the species that were found in both samples, and the normalized counts showing the relative increase for the second one:

SpeciesIncrease
Bacteroides plebeius
86248
Bifidobacterium animalis
37483
bacterium NLAE-zl-P430
17859
[Ruminococcus] obeum
9238
Lactobacillus rogosae
8726
Blautia faecis
6577
Clostridium baratii
4365
Corynebacterium freneyi
3940
Coprococcus catus
3420
bacterium NLAE-zl-H54
3077
Bacteroides salyersiae
2880

Here are the species that were still in the October sample, but at reduced count:
Roseburia sp. 11SE38
-5250
Barnesiella intestinihominis
-6780
Parasutterella excrementihominis
-6986
Coprococcus sp. DJF_CR49
-8958
Bacteroides massiliensis
-10835
Bacteroides uniformis
-11248
Clostridium clostridioforme
-13732
Odoribacter laneus
-28286
Faecalibacterium prausnitzii
-93781

I took several tablespoons daily of potato starch during the week before the October test, so those species were probably affected most.

Next, here’s a look at the gut flora that went extinct between May and October:
original count_normMissing
8295
Bifidobacterium tsurumiense
4650
Subdoligranulum variabile
2074
Dialister sp. oral clone BS095
780
Desulfovibrio sp. oral clone BB161
475
Adlercreutzia equolifaciens
459
Ruminococcus sp. ID1
328
Clostridiales bacterium 60-7e
305
Tannerella sp. 6_1_58FAA_CT1
194
[Clostridium] spiroforme
182
Clostridium disporicum
174
Lactobacillus paracasei

and some new ones that were not there originally but showed up in October:

CountNew species
92665
butyrate-producing bacterium A1-86
47129
Clostridium chartatabidum
19001
Bifidobacterium adolescentis
16245
Ruminococcus bromii
8495
Eubacterium siraeum
5929
bacterium NLAE-zl-H436
5803
Parabacteroides distasonis

The above examples were all done at the species taxonomic rank, but the tools let you look at other ranks, such as genus or phylum, just as easily.

The R source code, along with the data I used for this analysis are all available here on GitHub.  

(Huge thanks to Dr. Grace Liu and her Animal Pharm web site for help understanding what this stuff means).