Linking biomass or DNA content to relative abundance


This probably sounds silly, but here’s a thought:

imagine a scenario where you have two treatments showing different chemical results. However, both treatments suggest relative abundance of a specific phyla to be higher than others. In that case, it becomes difficult to discuss variation in the treatments from a biological perspective (without relying on chemical data). I was wondering if there was a way QIIME2 could integrate the amount of DNA present in the different samples (because it is obvious that bacteria grew more in the latter scenario); hence correcting the relative abundance by the amount of DNA (or cellular biomass) might give a more absolute quantification of community composition? … maybe?

If it’s too silly, feel free to delete the question! :smiley: I actually have a similar scenario like that, so I was thinking how to solve this issue.

Hi @anirban.mcgill ,
Linking to biomass probably is not a good idea, as you would need to determine what amount is cellular, on-target, and correct for cell size for individual organisms, etc. Same with DNA content alone — you would need to correct for genome size, copy number, and determine how much is on-target. More tractable than biomass, but still makes too many assumptions.

On the other hand, integrating QPCR data to estimate absolute abundances from relative abundances has been done quite a few times in the literature, and other absolute quantitation methods exist (e.g., integrating flow cytometry, spike-ins, etc). No, QIIME 2 does not have any plugin to support integration of absolute counts (nor am I aware of other software that does) but it is a fairly straightforward multiplication. This has been on my mind to add to a QIIME 2 plugin for a while, e.g., to q2-feature-table. Maybe some day :rainbow: