I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup. For this, it would be useful to be able to distinguish whether a specific organism is a microbe or not, as it allows:
- to detect potentially false findings,
- to avoid an unnecessary inflation of the metagenomic database.
For animals and plants, this is straightforward, as they are never microbes. However, for fungi (and some other clades) it gets complicated. At the very least, I failed to find a simple list of microbial or non-microbial clades.
Ideally, I would like to have a function that maps a taxonomic ID to a boolean stating whether this organism is microbial. I acknowledge that this is utopic since microbe is not that well defined, there are facultatively multicellular organisms, and for some cases it may simply not be known. I am therefore happy with any reasonable approximation such as unicellularity. In particular, given my application, a small chance of falsely identifying an organism as microbial is not an issue.
I am currently working with the NCBI database accessed via the ETE 3 module for Python, but I am open to use other databases and tools.