How to start analysis with ASV data?

[Rishikesh12 (Rishikesh Dash)]

Hello Qiime2 community,
I have a doubt about how to start the analysis of ASV data. In our lab, we would like to do microbiome analysis at the species level. However, we are having problems because one species has occurred more than once. How can we proceed with species richness analysis, alpha diversity, and univariate analysis? Should we merge the ASVs or is it okay to proceed with more than one species?

Thank You
Rishikesh

[cherman2 (Chloe Herman)]

Hi @Rishikesh12,
This is not abnormal in my opinion. Each ASV are unique sequence but more than 1 unique sequences can be assigned to a species.

I would keep your asv separate for species richness analysis, alpha diversity, and univariate analysis steps. If you are interested in running ancom-bc, I would collapse to the species level for that analysis step if you are interested in the species level analysis.

Hope that helps

[Rishikesh12 (Rishikesh Dash)]

Actually I pulled out data from qiime to start analysis in R. ASV separate for all analysis, actually I didn't understand asv separate for species richnees and alpha diversity analysis? Is it possible to do analysis in qiime2 at species level ? Can you share me a any research paper where all analysis was done using ASV data ?

Thank you
Rishikesh

[cherman2 (Chloe Herman)]

Hi @Rishikesh12,

@Rishikesh12

actually I didn't understand asv separate for species richnees and alpha diversity analysis?

I was assuming that you were using qiime2 but I assumed when you were talking about species level analysis, you were running qiime taxa collapse at the species level and then running species richnees and alpha diversity analysis. I would recommend not grouping your asv into taxonomically labelled species before running diversity analysis.

It is possible to do species level analysis by running qiime taxa collapse.

@Rishikesh12

Can you share me a any research paper where all analysis was done using ASV data ?

There is a lot of papers that run asv analysis.
Here is one:
https://www.cell.com/cell/pdf/S0092-8674(21)00754-6.pdf

Also here is the link to all the papers that cite dada2 - I would say that most of these papers have all their diversity analysis at the asv level.
https://scholar.google.com/scholar?cites=1592655680316646386&as_sdt=805&sciodt=0,3&hl=en
Hope this helps!

[Rishikesh12 (Rishikesh Dash)]

Hey,

Thank You for information.
Can you please tell me the plugin or command for qiime taxa collapse for species level analysis?
I used phylogenetic tree for diversity calculation so for species level analysis can i use same or is there any different way?

[cherman2 (Chloe Herman)]

Hi @Rishikesh12,
Unfortunately there is now way to build a phylogenetic tree in qiime2 with a feature-table collasped to the species level. If you want to do diversity analysis at the species level, you will need to run core-metrics and skip core-metrics-phylogenetic.

Here is additional information that another moderator gave when a user asked a similar question but regarding genus level analysis.

Collapsing phylogenetic tree

Hello. I collapsed my feature table using plugin qiime taxa collapse to generate genus level (level 6) feature table. Now I am trying to do beta diversity UniFrac using the genus-level feature table. However, for doing that, I need a phylogenetic tree which each label matches ID in the table. Is there any method to generate or edit (collapse) a phylogenetic tree only to contain genus level information? Thank you in advance!

Hope that helps!