As suspected, there was a glitch in my latest uBiome results. Apparently a server hiccupped, so the scientists there recomputed my sample and sure enough, the new data is much more believable. Here is the single chart summary of all four of the uBiome tests results I’ve received so far:
You can see a number of changes, but what’s exciting about this one is that it’s the first sample where I was deliberately trying to test something: the effect on my gut of taking potato starch to hack my sleep.
A few details about this sample:
- Taken on Jan 19th, almost exactly 3 months after my Oct 17th sample.
- During the 94 days between samples, I had 31 days where I took a dose of potato starch, a total of about 80 tablespoons.
- I had been taking 1 T daily, an hour before bedtime, for a week before this sample.
To analyze my results, I first popped into my publicly-available uBiome utilities, using the data I had already downloaded from the site. If you want to follow along at home, here are some of the commands I typed.
To answer the question: Which new species appeared in January?
head(uBiome_sample_unique(jan,oct),topN)## missing.count_norm missing.tax_name
## 1 1257 Arthrobacter albus
## 2 573 Bacillus amyloliquefaciens
## 3 530 Enorma massiliensis
## 4 376 Ruminococcus lactaris
## 5 188 Subdoligranulum variabile
## 6 163 Adlercreutzia equolifaciens
## 7 145 Oligella urethralis
## 8 137 Clostridium sp. NML 04A032
## 9 137 Desulfovibrio sp. oral clone BB161
## 10 111 Streptococcus rubneri
and which went extinct (are no longer in January sample?)
head(uBiome_sample_unique(oct,jan),topN)## missing.count_norm missing.tax_name
## 1 5929 bacterium NLAE-zl-H436
## 2 114 Dialister micraerophilus
## 3 101 Peptoclostridium difficile
## 4 88 Dehalogenimonas lykanthroporepellens
## 5 76 Bifidobacterium catenulatum
## 6 51 unidentified bacterium ZF5
## 7 51 Veillonellaceae bacterium canine oral taxon 211
## 8 51 Ruminococcus sp. 25F8
## 9 51 Clostridium leptum
## 10 38 Peptoniphilus sp. gpac018A
Here’s the overall picture of what changed between Oct and Jan:
Positive numbers indicate something that is more plentiful in January than October:
tail(octVsJan,topN)## tax_name count_change
## 24 Bifidobacterium longum 7713
## 39 Clostridium clostridioforme 8958
## 78 Ruminococcus bromii 10663
## 20 Bacteroides uniformis 11036
## 23 Bifidobacterium animalis 13578
## 69 Peptostreptococcaceae bacterium TM5 14151
## 47 Coprococcus sp. DJF_CR49 19000
## 36 Clostridium baratii 24955
## 76 Roseburia sp. 11SE38 35712
## 57 Faecalibacterium prausnitzii 89592head(octVsJan,topN)## tax_name count_change
## 17 Bacteroides plebeius -90998
## 30 butyrate-producing bacterium A1-86 -88414
## 38 Clostridium chartatabidum -41972
## 11 bacterium NLAE-zl-P430 -23659
## 22 Bifidobacterium adolescentis -18334
## 10 bacterium NLAE-zl-H54 -9970
## 62 Lactobacillus rogosae -8575
## 27 Blautia faecis -7693
## 56 Eubacterium siraeum -6040
## 5 Alistipes onderdonkii -5878
See the difference?
Let’s look at the genus level:
(again, positive numbers are more plentiful in January)
tail(octVsJan,topN)## tax_name count_change
## 27 Dorea 3396
## 42 Parasutterella 3473
## 48 Pseudobutyrivibrio 5523
## 34 Lachnospira 5895
## 14 Blautia 6612
## 12 Bifidobacterium 7769
## 7 Anaerostipes 8565
## 23 Coprococcus 18317
## 52 Roseburia 34957
## 29 Faecalibacterium 135557head(octVsJan,topN)## tax_name count_change
## 10 Bacteroides -87903
## 3 Alistipes -12141
## 41 Parabacteroides -9820
## 53 Ruminococcus -9685
## 35 Lactobacillus -8601
## 28 Eubacterium -5785
## 21 Clostridium -5212
## 11 Barnesiella -3809
## 17 Butyricimonas -2702
## 26 Dialister -2410Summary
| Organism | May | Jun | Oct | Jan | Rank |
|---|---|---|---|---|---|
| Faecalibacterium prausnitzii | 99571 | 62316 | 5790 | 95382 | species |
| Roseburia | 13554 | 11157 | 7825 | 42782 | genus |
| Christensenellaceae | 82585 | 39713 | 40290 | 40977 | family |
| Christensenella | 269 | NA | 38 | 17 | genus |
| Akkermansia | 30960 | 19654 | 7648 | 6269 | genus |
| Bifidobacteria Longum | 32 | NA | 1858 | 9571 | species |
| Bifidobacterium | 8473 | 6532 | 58747 | 66516 | genus |
| B. Longum as % of total Bifido | 0.38% | NA | 3.16% | 14.39% | |
| Clostridium | 35012 | 41679 | 71326 | 66114 | genus |
| C. botulinum | NA | 25 | x | 128 | species |
| C. clostridioforme | 28902 | 35372 | 15170 | 24128 | species |
| C. baratii | 1223 | NA | 5588 | 30543 | species |
The units are all uBiome’s “count_norm” field, which you can think of as, roughly, a percentage (a fraction of one million). Items in italics are “good”.
