Ok, here comes a big dump of information (pun intended, har har har)…

Here’s what i found (and I am a little surprised):

my ubiome wellness score was 88% for one sample and 96% for the other. In my mind, a big difference.

ubiome diversity was 20th and 53rd percentiles. Also a big difference in my mind.

F/M ratio was 0.9:1 and 1.4:1

no akkermansia and very little probiotics detected in the one sample, the other sample had good amount of both.

How about compared to your full sample history spanning months.

See plots here, specifically, the last 2 samples are from the same piece of stool sampled at 2 different sites, roughly first quarter and last quarter (also added inline to message): https://github.com/isaacgerg/ubiome_longitudinal_analysis/tree/master/sample_data

If you look at the genus Almplot and the genus heatmap of the last 2 samples, you can see the differences most clearly in my mind.

I just upgraded to matplotlib 2.0 so my stylessheet is messed up. Please bear with me (for example not grids on plots).

Any idea what meal the samples were taken from (markers like beet coloring or undigested corn kernels)?

No idea. Nothing stood out to me. I have pictures of the sampling process if are really interested so you can see for yourself.

Can you associate the samples with different Rx intake?

I am in the process of looking at this now. So far, the anova hasnt shown anything but i just got back 3 more samples. I likely wont have this analysis done until later summer since Im working on another paper at the moment.

Was your health status stable during the time frame for digestion and sampling?

Mild IBS

Do you have any information on the Measurement System Analysis (reliability and repeatability) of the sample analysis done in uBiome’s lab?

Nothing but anecdotes so I will not say anything. You can see the number of reads for each sample in the .json files. The first part of the stool had worse diversity score of the 2 (ref comments above) and the number of reads was:82321. the second part of the stools had 73785 reads. So both seem fine to me in terms of quality. In my plots, the first part of the stool occurs first in time of the 2 samples. (json files 101419 and 101960 respectively in my repo – they are also labeled in the json notes).

I assume both samples were taken at approximately the same time so that should not be a factor. (I recall that exposure to oxygen is problematic for some of the microbes). I also assume the sample storage tube has a preservative that fixes the relative counts so they don’t grow on the way to the lab, both samples arrived on the same day and were tested on the same equipment by the same person.

Both taken at the same time. My hypothesis is that the biome of the outer part of the stool differs significantly from the inner part of the stool. My next samples will specifically test this.