Differential abundance
Differential abundance testing by diet and associations of species relative abundance with host metabolizable energy were carried out using the output of MetaPhlAn3 in the “MaAsLin2” R package (Version 1.12.0)For rigor and reproducibility, we repeated the differential abundance analyses with a different method using the same parameters as the original analyses. We validated our results related to differential abundance by diet with ANCOM-BC, an approach often used to evaluate differential abundance that has been found to produce results that frequently overlap with other approaches