Advancing and refining archaeological dental calculus research using multiomic frameworks

Figures & data

Table 1. Key concepts and definitions in archaeological dental calculus analysis.

Key terms	Descriptions
Microbiome	A collection of microorganism genomes (e.g. bacteria, archaea, protists, fungi, and viruses) from an environmental context, such as dental calculus.
High-throughput sequencing	Technologies that sequence millions of DNA molecules in parallel. Unlike earlier methods such as Sanger sequencing, HTS can sequence multiple, whole genomes at once. Many software tools perform computational analyses for HTS data, with their own algorithms.
Metagenomics	The study of multiple genomes within a biological sample. Metagenomics relies on high-throughput sequencing technologies to study the DNA of microbes (and in some cases human) present within a sample.
Amplicon sequencing	A highly targeted sequencing approach that enables the analysis of genetic variation of genomic regions. The high-depth sequencing of PCR products (amplicons) provides an efficient method to identify and characterize microbial taxa present within a biological sample.
16S rRNA gene	A region of microbial genomes that has been widely studied for taxonomic profiling because it is conserved in most taxa.
Metaproteomics	The study of proteins within a single sample. The primary method of choice is mass spectrometry. Analytical techniques that rely on mass spectrometry measure the mass-to-charge ratio of ions. Such approaches can identify peptides and metabolites.
Host genomics	The study of all the DNA encoded on multiple chromosomes within a human cell. Methods used to obtain microbiome data can also be used to obtain host-genome data. The key difference between metagenomics and host genomics is reference mapping. Microbiome researchers will use a database containing microbial references while host geneticists will use human references.
Epigenomics	Analogous to genomics and proteomics, epigenomics refers to the study of epigenetic modifications of the genetic material within a biological sample. Epigenetic modifications can impact gene expression without altering the DNA sequence. Several methods can identify epigenetic modifications, including histone modification assays, ChIP-Chip and ChIP-Seq, DNA methylation assays, bisulfite sequencing, and chromatin accessibility assays.
Bioinformatics	The use of computer science, statistics, and mathematics to analyze and interpret biological and molecular data.

Figure 1. Schematic illustrating a multiomic framework for the study of archaeological dental calculus.