Relative_Ancom_analysis

Dear all,
I have a gut microbiome dataset from a clinical trial. It is a pre-post trial with 2 groups: placebo, synbiotic.
I would like to find the compare the change in the taxonomy of the two groups. I understand that ancom analyzing does it but it does it only for a single group[placebo or synbiotic]. I wish to do ancom analysis to find a relative change in the synbiotic group with respect to the placebo group.
I was not able to do it using paired differences. Is there any other method/plugins which I can use? I tried to find it in the forum but could not find it.
Thank you

  • Aakash

Hi, @Aakash_Mantri :wave:

I think you might find The Parkinson’s Mouse Tutorial helpful. It demonstrates a workflow where ANCOM is run separately on two different groups. Please see the ANCOM section and the sections that follow it:

https://docs.qiime2.org/2020.8/tutorials/pd-mice/#differential-abundance-with-ancom

Hi Andrew,

Thank you for your reply. So if I understand right, the ancom does the analysis on the different groups separately. How do I do a relative analysis of the group? in my case, a relative change in the abundance of bacteria of symbiotic[treatment] group with respect to the change in the bacteria of the placebo.
I am also interested in 5 strains of bacteria.
Thanks

Hello @Aakash_Mantri
Sorry for the late response
Andrew is out of the office this week and will be back soon!
Thank you for your patience

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Hi, @Aakash_Mantri! Thanks for your patience.

My apologies if I am missing something, but it seems to me that your situation mirrors what is demonstrated in the tutorial I linked to above. Can you please clarify what questions you have about your situation that are not made clear in the Parkinson’s Mouse tutorial?

Thanks,
Andrew

Hi, @andrewsanchez
If I understand correctly, the tutorial does ancom analysis for donor and genotype separately,
My clinical trial looks like this:

I wish to check whether the change in the abundance of 'actinobacteria' [example] between the sessions for the symbiotic group, relative to the change in the abundance of 'actinobacteria' between sessions for the placebo group is significant or not?

Thank you

  • Aakash

Hi, @Aakash_Mantri,

It sounds to me like there may be some confusion about the purpose ANCOM serves in your analysis. Please review the ANCOM paper to understand why you must run ANCOM on these groups separately. Please also see the notes about ANCOM here.

That is correct. These steps must be done separately. ANCOM assumes that few (less than about 25%) of the features are changing between groups. As demonstrated in the tutorial I linked to, the workflow is to run ANCOM separately on each group you wish to compare. The next step is to compare the two resulting visualizations which are output by qiime composition ancom . ANCOM doesn’t do this step for you - you need to do evaluate the difference in relative abundance by interpreting the two visualizations side by side. In other words, ANCOM doesn’t do the analysis for you - it provides you the data and visualizations which you then need to analyze.

Please see the green question box towards the end of the ANCOM section for further clarification.

The next section in the Parkisons Mice tutorial shows how to do this. Please see https://docs.qiime2.org/2020.8/tutorials/pd-mice/#taxonomic-classification-again and let me know if you have any questions on this step. :mouse:

I hope this helps, @Aakash_Mantri! Please let me know if you have any more questions.

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