I am relatively new to microbiome data analysis and I was wondering if someone with more experience could provide some advice.
I am collaborating with another research group who has been collecting 16S data on children at multiple ages. They have sent me a phylogenetic tree, an OTU table, and a metadata file for a dataset which includes samples at Age 1 and samples at Age 2.
My question is, if I am interested in analyzing data from these two ages separately, will having them in one dataset which combines the two ages and one phylogenetic tree produce different diversity results than if I were to separately generate phylogenetic trees and then diversity metrics for the sample at each age?
Thank you in advance for any insight you can provide!