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

Standeven, F. J.; Dahlquist-Axe, G.; Speller, C. F.; Meehan, C. J.; Tedder, A.

2024-09-18 microbiology
10.1101/2024.09.18.613623 bioRxiv
Show abstract

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.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.