What is differential abundance analysis?

Question

[vijinim]

I'm new to the field of metagenomics and I have been reading research work done on binning in metagenomics.

I have been reading this paper where the authors discuss about different metagenome binning approaches. The last approach is Differential abundance (DA). They explain the starting point of this method as differential coverage patterns across multiple samples where population changed in abundance over time. Can someone kindly explain to me what is meant by differential abundance? Is it the abundance of genomes in different samples?

Sorry if this is a naive question. I would really appreciate an explanation. :) Thank you!

Answer 1

[Noam Teyssier]

I believe what they're referring to is the relative change in genome abundances between samples where the genome distributions change relative to time. The pattern they're referring to would be the common distribution shift between samples, which would allow clustering of samples based on their common genome enrichment.

A toy example of this would be if there were 4 genomes sequenced across 100 samples and were uniform across all 4 at the start of the time series. At the end of the time series, if there were changes in abundances, it would be possible to use DA to group the samples that had the same enrichment in their genome fractions. If 25 of the samples all enriched for genome 1, they could be considered more similar than the remaining 75 which down selected genome 1.

I think in this reference though they are talking about contigs and not full genomes, but the idea is the same.

[vijinim]

Thank you very much for the explanation.