DOI: 10.5061/dryad.jdfn2z3mk
title: Supplementary information from: An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

description: Archaeological dental calculus can provide detailed insights into the
 ancient human oral microbiome. We offer a multi-period, multi-site,
 ancient shotgun metagenomic dataset consisting of 174 samples obtained
 primarily from archaeological dental calculus derived from various
 skeletal collections in the United Kingdom. This article describes all the
 materials used, including the skeletons’ historical period and burial
 location, biological sex, and age determination, data accessibility, and
 additional details associated with environmental and laboratory controls.
 In addition, this article describes the laboratory and bioinformatic
 methods associated with the dataset development and discusses the
 technical validity of the data following quality assessments, damage
 evaluations, and decontamination procedures. Our approach to collecting,
 making accessible, and evaluating bioarchaeological metadata in advance of
 metagenomic analysis aims to further enable the exploration of
 archaeological science topics such as diet, disease, and antimicrobial
 resistance (AMR).
description: This dataset includes FastQC reports for raw data (Supplementary
 Material 1), FastQC reports for trimmed data (Supplementary Material 2),
 Fastp reports on the impact of data quality filtering (Supplementary
 Material 3), and mapDamage plots of the human DNA sequences recovered from
 the datasets (Supplementary Material 4). Detailed
 methods may be found in the associated publication. The dataset was
 collected from archaeological dental calculus and associated bone samples.
 DNA was extracted within dedicated biomolecular clean labs. After crushing
 to a powder, samples were pre-digested for 5 minutes with 1 mL of 0.5M
 EDTA to remove possible surface contamination. This pre-digestion
 supernatant was removed, and a further 1.1 mL of 0.5M EDTA was added and
 rotated at room temperature for seven days to fully demineralize. For the
 majority of samples, DNA was extracted from the dental calculus and bone
 samples using a protocol based on Dabney et al. (2013). All DNA extracts
 were quantified via Qubit® 2.0 Fluorometer using a High-Sensitivity DNA
 Assay. For each DNA extract, double-stranded whole genome shotgun Illumina
 libraries were prepared using a protocol based on Meyer and Kircher
 (2010). The dental calculus libraries were pooled in equimolar
 concentration and subjected to paired-end sequencing on multiple HiSeq2500
 lanes at the Wellcome Trust Sanger Institute (WTSI) or on a NextSeq
 platform, PE 150 + 150 bp Integrated Microbiome Resource (IMR) at
 Dalhousie. FastQC v0.11.9 was used to assess raw
 digital data quality. FastQC is a quality control tool for raw sequencing
 data that provides a modular collection of analyses used to gain insight
 into any flaws in the data before performing further analysis. The
 preprocessing programmer Fastp v0.23.2 was then utilised with default
 parameters. Fastp is a tool used to filter and trim poor-quality reads,
 cut adapters, repair mismatched base pairs, and produce overall quality.
 It also provides results that include both pre- and post-filtering data,
 allowing for a direct comparison of the filtering impact. Centrifuge
 v1.0.3 was used, with default parameters, to assign taxonomic labels by
 mapping sequences against the human genome, prokaryotic genomes, and viral
 genomes, including 106 SARS-CoV-2 complete genomes. Human reads from
 Centrifuge outputs were retained, and seqtk ‘subseq’ was used to convert
 them into fastq files that were then mapped to the human genome (hg38)
 (NCBI 2013) using BWA mem v0.7.17 . SAMtools v1.12  (-view -rmdup
 -flagstat -sort -index) was then utilised for alignment formatting and was
 sorted into BAM files that were run through mapDamage2 v2.2.2 with default
 parameters.
description: # Supplementary information from: An extensive archaeological dental
 calculus dataset spanning 5000 years for ancient human oral microbiome
 research
 [https://doi.org/10.5061/dryad.jdfn2z3mk](https://doi.org/10.5061/dryad.jdfn2z3mk) ## Description of the data and file structure Quality and authentication reports for metagenomic sequencing data associated with ancient dental calculus samples and associated controls. These include 174 samples (348 fastq files using paired end reads) from modern (n=10) and archaeological dental calculus (n=133) and tooth (n=2) samples, environmental controls (bone; n=7), and laboratory controls (extraction and library blanks; n=22). ### Files and variables #### File: Supplementary_Material_3_Fastp_reports_raw.zip **Description:** Results of Fastp analysis for metagenomic data obtained from ancient dental calculus, and associated bone and blank controls. The zip folder contains 174 html files with the Fastp report for each sample - the file name of begins with the sample name.  #### File: Supplementary_Material_1_FastQC_reports_raw.zip **Description:** Results of FastQC analysis for raw metagenomic data obtained from ancient dental calculus, and associated bone and blank controls. The zip folder contains 384 .html files with the FastQC report, with two files for each sample associate with forward (R1) and reverse paired-end sequencing data (R2). The file name of begins with the sample name.  #### File: Supplementary_Material_2_FastQC_reports_trimmed.zip **Description:** Results of FastQC analysis on quality filtered metagenomic data obtained from ancient dental calculus, and associated bone and blank controls following Fastp analysis. The zip folder contains 349 .html files with the FastQC report for the filtered data, with two files for each sample associate with forward (R1) and reverse paired-end sequencing data (R2). The file name of begins with the sample name.  #### File: Supplementary_Material_4_mapDamage.zip **Description:** Results of mapDamage analysis on human DNA sequences derived from filtered metagenomic data obtained from ancient dental calculus, and associated bone and blank controls. The zip folder contains 106 folders which contain the results for each analyzed sample - the folders are listed with the sample name (e.g., results_**C028**_S1_Human_pe_rmdup.sorted) and contain the output of the mapDamage software, including .txt, .csv, .log, and .pdf files. ## Code/software All bioinformatic coding scripts are available on GitHub ([https://github.com/DrATedder/dental_calculus_dataset/tree/main](https://github.com/DrATedder/dental_calculus_dataset/tree/main)) for all pre-processing (quality control, decontamination) and post-processing (mapDamage) protocols. ## Access information All raw sequencing data have been archived in the European Nucleotide Archive as fastq files in projects PRJEB1716, PRJEB12831, and PRJEB75938