More complex Core Microbiome

[Yos.Dos (Yosef Avrahami)]

Dear Qiimers ,
Is there any feature in Qiime2 were i can analyze the Core microbiome more complexity? I mean, not to get only the regular chart (like the ‘core-features-filtered-table.qzv’ ), but also compare the results to other results, samples or data?
I know there is a workflow on qiime1 but … never touched it before…

Thank you all

[gregcaporaso]

Hi @Yos.Dos,
The core-features functionality in QIIME 2 more or less mirrors what was possible in QIIME 1 - the idea is to give you tools to do comparisons on your own, but we’re also interested in suggestions for use new analyses that could be added. Do you have specific comparisons in mind?

I’ll illustrate one way of exploring this data in more detail here. I’m starting with a few files from the Moving Pictures tutorial:

Gut-sample only feature table
Sample metadata
Taxonomy

What I’m doing here is computing the core features for the gut samples from Moving Pictures. I then open up the result (either with qiime tools view or using view.qiime2.org).

$ qiime feature-table core-features --i-table gut-table.qza --o-visualization gut-core-microbiome.qzv

$ qiime tools view gut-core-microbiome.qzv

In that visualization, I downloaded the core-features-1.000.tsv file (this will list the features that are in 100% of the samples), and then visualize that information with qiime metadata tabulate. I also use that file to filter the input feature table to only include the identified “core features”. (If we were to develop this further, we’d probably generate these for the user as part of the visualization - please let me know if you think that would be useful.)

$ qiime metadata tabulate --m-input-file core-features-1.000.tsv --o-visualization core-features-1.000.qzv

$ qiime feature-table filter-features --i-table gut-table.qza --o-filtered-table table-core-1.000.qza --m-metadata-file core-features-1.000.tsv

Finally I’m generating a taxonomy barchart that illustrates only the core features.

$ qiime taxa barplot --i-taxonomy taxonomy.qza --i-table table-core-1.000.qza --m-metadata-file sample-metadata.tsv --o-visualization barplot-core-1.000-only.qzv

You could, for example, generate these for several different body sites (gut, skin, mouth) to compare the composition of the core microbiomes across those sites. You can also do things like run qiime diversity alpha on this (and other) “core tables” to compare the size of the core microbiome across different sample groupings.

I hope this helps to get you started. If there are specific analyses that you’re interested in, please bring them up and we can discuss whether they’re already possible or whether they might be good feature requests.

[Yos.Dos (Yosef Avrahami)]

Hey @gregcaporaso,
Thank you very much for your specifically answer!.
This is what i wanted to get my analysis done.
I thought in another set of mind, but i don’t think there is a better way to do it.

Thank you!