At the time of writing this article, we're commonly seeing the following 2 species in uploads from Ombrelab that are not included in the Ombrelab results or csv.
Bilophila wadsworthia
Bifidobacterium longum
Users are also seeing lower relative abundances of these after uploading from Ombrelab:
Alistipes (these Biomesight Greengenes include in Bacteroides). Please run a RDP analysis if you wish to see Alistipes.
Eubacterium
Ombrelab also includes Lactobacillus Rogosae under Lactobacillus, even though this is no longer considered as part of the Lactobacillus genus.
The differences we are seeing are due to:
1. Different classifiers (the machine learning algorithm that performs the classification). Biomesight uses a Bayesian classifier .
2. Different gene sequence databases. Biomesight uses the Greengenes gene sequence database. RDP is available as a CSV only analysis.
There is currently no consensus in the scientific community on a preferred sequence database or classification algorithm and parameters, so these analyses differences are common when re-analyzing the same sample. These differences are one of the main reasons users upload their Ombrelab results to Biomesight.