MaAsLin2 rat fecal microbiome analysis

Hi, I am extremely new to using maaslin2. Currently, trying to check for significantly abundant species (or genera) between treatment groups. The experiment is looking at fecal microbiome transplantation in an animal model to treat Clostridiodes difficile infection. Some of the fundamental questions I am trying to answer using maaslin2 are listed below;

  1. Significant abundant species (or genera) in the transplant and non-transplant groups at the end of the experiment

  2. Significantly abundant species (or genera) before and after transplantation

  3. In the hybrid microbiome formed post transplantation, what species (or genera) belong to the host (rat) microbiome and to the transplanted microbiome

I have a metadata table for this (txt file), but I am bit confused about the data (features) file that is used as input for maaslin2. Is it just a taxonomy file with abundances downloaded as a csv file from the tax barplot produced in QIIME2?

Also, any help with what to put as analysis method, fixed effects, reference and transform would be very much appreciated, thank you :smiley: :smiley:

Hi @Kevin_Ketagoda,

The input would indeed be the abundances files. Generally MaAsLin2 works with TSV files and not CSV files. The difference being CSV’s use commas and TSV’s use tabs to separate fields.

As for what you want to include in your model. Based on your response it looks like you have a repeated measurements analysis and would want to include rat ID as a random effect. The fixed effects would then come down to what you are interested in asking (i.e. before or after transplant) and any other covariates you think are relevant and you might want to control for.

The default transformation and prevalence filters should do a good job on microbiome data so you can most likely stick with that.

Jacob Nearing