Searching metagenomic datasets for a specific species

Question

[Sarah]

Hi,

There are a vast number of metagenomic datasets available from microbiomes in different environments, such as marine, terrestrial, human, etc. These datasets seem to capture a massive amount of data relating to community composition. As such, I am wondering if there is a way to systematically search metagenomic datasets for a specific species.

In other words, given a species X, is there a method to identify all such metagenomes Y that contain X?

Thank you!

Answer 1

[Mensur Dlakic]

I don't know of a simple way to do this. It requires building profiles of some kind for all metagenomes out there, which I don't think has been done systematically. However, if you are willing to do some work, it can be done.

• https://github.com/MrOlm/inStrain
• https://bitbucket.org/berkeleylab/jgi-genomeconstellation/src/master/

[Sarah]

Thank you for your help!

Answer 2

[Sej Modha]

It depends on what you are after.

A lot of metagenomic datasets have their own taxonomy identifiers on NCBI taxonomy and are available under organismal metagenomes

e.g. human gut metagenome.

You could access them through SRA-toolkit or something equivalent once you have identified the dataset of interests?