Fig. 2

Prevalence of unknown taxa in MetaPhlAn 4 profiling of the mouse gut microbiome. (A) Taxonomically unlabeled species-level genome bins (SGBs) are widely distributed though the dataset samples. SGBs are categorized into quartiles according to their prevalence across the samples included in the dataset, and the proportions of known and unknown SGBs (kSGBs and uSGBs, respectively) in each quartile are comparatively assessed. kSGBs prevail over uSGBs (test of equal proportions, statistical significance set at p-values < 0.05) exclusively in the fourth quartile, which includes SGBs with prevalence ranging from 75 to 100% of samples. Conversely, in the third quartile, uSGBs dominate over kSGBs. (B) At taxonomic levels higher than species, the fraction of the mouse gut microbiome that remains taxonomically uncharacterized is substantial. The panel depicts the fractions of known and unknown genome bins detected across the entire dataset for each taxonomic level: species, genus, family, order, and class. (C, D) Taxonomically annotated SGBs tend to display higher relative abundance compared to SGBs that currently lack taxonomic annotation. The relative abundance of each genome bin is averaged across either AD or WT samples collected at each time point, and these average relative abundances are then converted into ranks for each time point, with higher average values corresponding to higher ranks. The heatmaps show the ranks for SGBs (C) and family-level genome bins (FGBs, D) at each sampled time point. Color codes shown in legend help distinguish known from unknown genome bins, AD from WT samples, as well as sampling time points