Abstract
Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
Highlights
We offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record
Mineralized dental plaque from the archaeological record is a rich reservoir of ancient biomolecules [1], containing endogenous oral microbiota, opportunistic pathogens and food particles [2,3]
We provide a comparison of M. leprae DNA preservation in both dental calculus and tooth-root dentine
Summary
Mineralized dental plaque (calculus) from the archaeological record is a rich reservoir of ancient biomolecules [1], containing endogenous oral microbiota, opportunistic pathogens and food particles [2,3]. All previously published ancient genomes were UDG-treated (deaminated bases removed), higher stringency parameters (−n 0.2, −l 32) were applied to the whole dataset (modern and ancient) when mapping with bwa-aln This was done for all genomes with the exception of samples I30_W-09, NHDP-55, NHDP-63, NHDP-98, Thai-53 and 2936 that had an average read length below 50 bp (electronic supplementary material, table S3). Picard tools was used to convert to fastq files and SeqKit [56] was used to extract 4000 mapping reads from the M. leprae alignment and 100 000 reads from the human genome alignments for SK92 calculus and dentine, respectively, with mapDamage2.0 [37] used to quantify post-mortem DNA damage for each subset. The recovered peptides diagnostic for species identification are found in electronic supplementary material, table S7
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