This post is intended to educate people more on the technical aspects of the microbiome. I am not talking about taking 4 samples from one stool and sending it to 4 different testing company. I am talking about one sample sent to one testing company which then provided their analysis and a FASTQ file. The raw data.
What is a FASTQ file (besides being megabytes big)? It is the DNA (technically the RNA) of the bacteria in the stool. It looks like this (using the 4 letters that DNA has):
The file that I am using as text would be around 16 megabytes. This data comes from a lab machine. The company then processes it through their software to match up sequences to bacteria.
In this post, I am using the FASTQ from uBiome and getting reports on the bacteria from:
- thryve inside
- sequentia biotech.
Naively, one would expect almost identical results. What I got is shown in detail below. At a high level we had the following taxa counts reported
- ubiome – 253
- thryve inside – 632
- biomesight – 558
- sequentia biotech 366
I did a more technical post on my other blog. From some providers, a taxonomy may be 40% on another 2% or even none… ugly!
Number One Issue: You cannot, repeat cannot, compare a taxonomy report from one lab with another. EVER!
- I have 8 uBiome reports and 2 Thryve reports. I can compare the uBiome to each other and the Thryve to each other. I can never mix their direct taxonomy reports !
Number Two Issue: If I wish to compare different lab reports, I MUST obtain the FastQ files from each lab and process them thru the same provider. The FastQ files are the raw data! For me, I prefer to push them through multiple providers which means that the 10 reports suddenly become 40 or 50 different reports in my site.
- This means a lot more work for the typical user. It also means that guidance, like that from Jason Hawrelak Criteria for Healthy Gut, would need to be revised to be provider specific!
I need to revise my site to show data by specific provider (while keeping the across all provider data still available). A lot of pages to revise and test.