how to select samples using stacked barplot

[Youngtae_Won]

Hello everyone,

As a beginner in microbiome research, I have a question for those of you with more experience in this field.

Before conducting shotgun sequencing, we aimed to determine which samples would be most suitable for analysis. To do this, we collected a variety of samples under different conditions (F, M, R) and volumes (1 mL, 15 mL, 30 mL), and evaluated their abundance profiles. We visualized these profiles using stacked bar plots, which yielded some interesting results.

Given this, how should we interpret the plots? Are there any recommended analysis methods or workflows that could help us better identify the optimal samples for shotgun sequencing?

Any advice or suggestions would be greatly appreciated.

[Youngtae_Won]

[colinbrislawn (Colin J Brislawn)]

Hello Youngtae Won,

Welcome to the forums!

Stacked bar plots are a great way to see major compositional shifts, like if one cohort is dominated by a single taxon compared to other groups.

"Optimal" can mean different things: highest alpha diversity, most representative of a group, or perhaps samples that show the clearest differences between your conditions or volumes.

Any 16S results that were surprising based on previously published papers?
What are you looking for with shotgun reads you can't get from 16S?