MetaPhlAn 4 was applied to synthetic metagenomes ( n = 70 samples) modeling different host and nonhost-associated environments and containing, on average, 47 genomes from both kSGBs and uSGBs (see Methods ). This evaluation directly on SGBs shows the reliability of MetaPhlAn 4 to quantify both known and unknown microbial species. Additional evaluation based on a mixture of new MAGs from samples not considered in the building of the genomic database (mixed evaluation, n = 5 samples) stresses its accuracy independently from the inclusion of the profiled data in the database. See Supplementary Tables 9 and 10 for more details (NHP = nonhuman primates, W = westernized, NW = nonwesternized). Box plots in a and b show the median (center), 25th/75th percentile (lower/upper hinges), 1.5 interquartile range (whiskers) and outliers (points).
