Core Microbiome

[thinesh (Thinesh Thangadurai)]

Dear Team,

I have analyzed my 16s samples and got my ASV table, which I imported to R.

Now I wanted to do a core microbiome analysis for my samples. Do we have the core microbiome analysis option available in QIIME?

Kindly guide me for the same.

[cherman2 (Chloe Herman)]

Hey @thinesh,
I would recommend the Moving Pictures Tutorial. Its a pretty good place to start for common basic analysis of the microbiome.

[SoilRotifer (Mike Robeson)]

There is the q2-coremicrobiome plugin. Though I am not sure if it will work with the most recent versions of . But you can always install an older version of (e.g. 2020.8) as a separate conda environment and install and run the plugin there.

[thinesh (Thinesh Thangadurai)]

Hi Have read that. Actually, I followed Parkinson's tutorial and got the ASV table.

Now wanted to do further analysis like core microbiome and Network analysis.

Thanks.

[thinesh (Thinesh Thangadurai)]

Thank you, Mike. Will try that way in the coming days and update you.

I have one more query,

1. Can I analyze my samples with genus level in QIIME?

2. Does Network analysis is available now in Qiime?

regards.

[SoilRotifer (Mike Robeson)]

@thinesh

• Can I analyze my samples with genus level in QIIME?

Yep. You can try approaches like collapse-taxonomy. If you are using a standard 7-rank taxonomy you'd set --p-level 6 to collapse all of your features to genus level.

@thinesh

Does Network analysis is available now in Qiime?

There is q2-scnic. But I am unsure if it works with the current QIIME 2 release. Perhaps others on the forum may know?

[cherman2 (Chloe Herman)]

Hi,
Sorry @thinesh, I think I misunderstood your question but I am glad @SoilRotifer was able to help. As for Q2-scnic, it doesn't work on the current release but I have had success by using it in the 2021.4 release.

[thinesh (Thinesh Thangadurai)]

Thanks, Chloe, Will check and update how it goes.

[thinesh (Thinesh Thangadurai)]

Yep. You can try approaches like collapse-taxonomy. If you are using a standard 7-rank taxonomy you'd set --p-level 6 to collapse all of your features to genus level.

Thanks. But, In qiime 2 when we do the core matrix analysis that takes only the data compiled from the Species level. Is there any other way though?

Regards.

Regards.

[SoilRotifer (Mike Robeson)]

@thinesh

Thanks. But, In qiime 2 when we do the core matrix analysis that takes only the data compiled from the Species level. Is there any other way though?

I am unsure of what you're asking. Why not just analyze the data as ASVs? You'll likely find patterns that won't revel themselves when focusing on taxonomy. For example, see Debelius et al..

It'd probably be best for you to clarify your goals. What questions are you trying to address that you can't with ASVs, regardless of the taxonomy?