Feature table and representative sequences for downstream analyses

General Discussion
1

Hello Users,

I've been using QIIME2 for some time now in my research, where I’m investigating the effects of maternal interventions in mice on the gut microbiome of their offspring. For each dam (mouse mom), I have multiple offspring samples.

I'm considering averaging the feature counts across offspring from the same dam, as my primary interest lies in assessing the maternal-level effects. However, I’m concerned that this approach might introduce complications in downstream analyses such as alpha and beta diversity, taxonomic profiling, etc.

I’d really appreciate any insights or suggestions you might have on this—particularly regarding whether averaging is appropriate in this context, or if there are better alternatives.

Thank you!
Anandi

2

Hi @Anandi_Batabyal ,

Sounds like an interesting study!

I would recommend against merging results from the different offspring. These serve as biological replicates, which will be important for downstream statistical testing. Merging these will reduce your ability to detect robust differences between your treatment groups. So exactly as you put it yourself:

I hope that helps!

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