Fig. 3

Genome-level taxonomic assignment of the brain bacterium. A Taxonomic assignment of the brain NTM contigs as assigned by searching against the NCBI-nt database, using BLASTn. The number of the assigned contigs is shown next the taxon names based on the lowest common ancestor (LCA) as determined by MEGAN (please refer to the “Methods” section for further details). B Unrooted phylogenetic tree of the family Mycobacteriaceae, including a single representative genome of each species, based on PhyloPhlAn marker genes. The background colors of the clades refer to: red, Mycobacterium spp.; yellow, Mycolicibacter spp.; green, Mycobacteroides spp.; and blue, Mycolicibacterium spp. C Heatmap-based on MASH distances of all characterized species’ genomes within the genus Mycolicibacterium including the genome of the brain bacterium (highlighted in bold red font). The heatmap annotations to the left of the heatmap refers to whether the microbe was isolated from a host or was reported as a human pathogen. For further details on the isolation sources, please refer to the Additional file 1: Table S6. D Damage plots of human DNA of different tissues as well as the brain NTM. The damage plots were generated considering the mapped reads of the indicated tissues different body tissues (i.e., tooth, intestinal tissues, skull, dura mater, and brain) against human genome (hg19) while the brain NTM was generated considering the brain metagenomic reads mapped against the brain NTM assembled genome. Ancient DNA damage represented by the terminal substitution of Cytosine to Thymine at the 5′ ends of the DNA fragments. The labels in parenthesis refer to sample ID and the mercury concentrations ± standard error. For further information on the read lengths distribution please refer to Additional file 2: Figure S3 [14, 15]. Note: The human DNA are showing variable levels of ancient DNA damages, despite of being of the same individual. The lowest levels of the human DNA damages are in the brain and dura mater samples, which goes with the abundance of the brain NTM and the mercury concentrations as well