Is MaAsLin appropriate for a crossover study design?

Hi all,

I’m wondering if you have any thoughts on whether maaslin2 is appropriate for a 3x3 (or k x k) cross-over study design. While technically the design has repeated measurements of the microbiome where a mixed model might be appropriate, it doesn’t seem like we can account for sequence or period with this model. Would you agree? I wonder if there is a method that is more suited to the crossover design than a straightforward longitudinal design.

Interested in your thoughts.


Hi @Lyoon6 - you might be able to run MaAsLin2’s mixed-effects model if you can prepare your crossover data in the desired format (see e.g. As you have speculated, this is not straightforward using the default MaAsLin2 pipeline, but it seems to be possible based on the description here: Hope this helps!

Thanks! I’ll look into these possibility. I’m new to the microbiome field and was hoping these was straightforward method for a crossover design with microbiome data but I guess it’s not done often enough to warrant a separate package.