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:
| Species | Increase |
| 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_norm | Missing |
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:
| Count | New 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.
