Hi Justine,
thanks for your reply. I read the posts you suggest but my doubts still remain. In particular, a didn’t find some clear explanation about why should be not admissible to use a rarefacted table as a base for downstream analyzes like differential abundance testing or network construction. In the paper published by Swiis, it is only reported that rarefaction could lead to loss of sensitivity but not in an increased probability of false positive results. By searching the forum, I found a post (Filter Feature Table) in which @Nicholas_Bokulich strongly discourage to perform rarefaction before differential abundance testing but no reasons were provided. Furthermore, I performed my last analysis on both rarefacted and not rarefacted tables obtaining similar results. what do you think about?