An efficient pipeline for creating metagenomic-assembled genomes from ancient oral microbiomes

Metagenomic-assembled genomes (MAGs) are difficult to recover from ancient DNA (aDNA) due to substantial fragmentation, degradation, and multi-source contamination. These complexities associated with aDNA raise concerns about whether bioinformatic tools intended for interpreting modern DNA are suitable for reconstructing ancient MAGs. Using simulated modern and ancient data, we investigated: 1) how using binning tools designed for modern DNA affects our ability to effectively construct MAGs from ancient genomes; 2) the performance of three different binning tools for aDNA samples; and 3) whether a 'one size fits all' approach is suitable for ancient metagenomics. We established that binning tools for modern DNA performed efficiently on simulated modern and ancient DNA. When applied to 'real' archaeological DNA spanning 5000 years, we retrieve high-confidence MAGs in most cases.