Atlas Biomed

Atlas Biomed provides microbiome tests in the UK, Austria, Denmark, Canada, Belgium and Germany. You may upload them here (after reading this post).

Perceived Issues with them

I have been informed of the following by their users:

  • They do not provide a download link for CSV files. Users have had to email support. They received an Excel file (which can then be saved as a Tab-limited text file which may be uploaded).
  • The FastQ files from them are atypical and at present cannot be used for alternative-analysis thru BiomeSight or Thryve.
  • They do not provide NCBI Taxon numbers, only names (which cannot all be matched to NCBI names).
  • They do not provide rollup numbers to higher level of taxonomy ranks. In fact, their numbers total 100% identification. This is misleading because there are bacteria that still cannot be identified and other processors often report 5-10% unknown bacteria.

In examining some sample files, I also found that the bacteria count appears to be 50% or less of those reported by BiomeSight or Thryve.

Qualified Import

Thanks to an open source project, I managed to get over 99% reliable matching to NCBI Taxon numbers on test samples. I also generate rollups to higher taxonomy rank from their “bottom” level numbers using the NCBI hierarchy.

I prefer the lab to own both the NCBI taxonomy numbers and the rollups — they can be gotchas with appropriate interpretations and they are the people that should know best.

Bottom Line

Imports are now supported. I have emailed them to see if they will add an automatic transfer of data to similar to what BiomeSight has implemented.

At present, for your next microbiome sample, I would suggest BiomeSight [Discount Code: Micro] or Thryve for more data for the cost.