Extended Data Fig. 6: De novo genome reconstruction from palaeofaeces recovers 181 authenticated ancient gut microbial genomes, 39% of which are novel SGBs.
From: Reconstruction of ancient microbial genomes from the human gut
Related to Fig. 2. a–d, CheckM79 quality estimation for de novo reconstructed microbial genomes for the 209 filtered bins (low-quality bins, n = 285; medium-quality bins, n = 175; high-quality bins, n = 34). Genomes were classified as low quality (LQ; completeness ≤ 50% or contamination > 5%), medium quality (MQ; 90% ≥ completeness > 50%, contamination < 5%) or high quality (HQ; completeness > 90% and contamination < 5%). a, Filtering steps, number of bins that belong to each of the quality categories and classification of novel SGBs. b, Contamination and completeness distribution for the filtered bins. c, Distribution of the number of contigs for each of the quality categories. d, Distribution of contig N50 values for each of the quality categories. e, Damage levels, specifically C-to-T substitutions at the 5′ end and G-to-A substitutions at the 3′ end of the reads, for each ancient bin as estimated by DamageProfiler88 (medium-quality bins, n = 175; high-quality bins, n = 34). f, GTDB-Tk23 species assignment for the known species. In c–e, data are presented as box plots (middle line, median; lower hinge, first quartile; upper hinge, third quartile; upper whisker extends from the hinge to the largest value no further than 1.5× the interquartile range from the hinge; lower whisker extends from the hinge to the smallest value at most 1.5× the interquartile range from the hinge; data beyond the end of the whiskers are individually plotted outlying points).
