Mining ancient microbiomes using selective enrichment of damaged DNA molecules

Area of Science:

• Ancient DNA (aDNA) research
• Microbiome analysis
• Molecular biology techniques

Background:

• Distinguishing ancient microbial DNA from modern contaminants is challenging due to mixed DNA sources.
• Ancient DNA (aDNA) exhibits characteristic degradation patterns, such as uracil formation from cytosine deamination, serving as an authentication marker.
• Previous methods struggled to identify authentic ancient microbes in complex mixtures with high sequence divergence.

Purpose of the Study:

• To develop and validate a library preparation method for enriching ancient microbial DNA based on uracil content.
• To improve the identification and authentication of bona fide microbial taxa in ancient and historical samples.
• To assess the utility of selective enrichment of damaged DNA for discovering ancient microbial communities.

Main Methods:

• Utilized a library preparation technique to separate DNA molecules based on the presence or absence of uracils.
• Applied this method to diverse ancient samples, including Neandertal remains, herbarium specimens, and archaeological plant materials.
• Sequenced DNA libraries enriched for uracil-containing molecules to amplify age-associated degradation patterns.

Main Results:

• Sequencing uracil-enriched DNA libraries effectively amplified age-associated degradation patterns in microbial DNA mixtures.
• This enrichment facilitated the discovery of authentic ancient microbial taxa, especially in samples with difficult-to-detect degradation patterns.
• Relative enrichment of taxa in the uracil-rich fraction aided in identifying genuine ancient microbial taxa that might otherwise be overlooked.

Conclusions:

• Selective enrichment of damaged DNA molecules, characterized by uracil presence, is a valuable tool for discovering ancient microbial taxa.
• This approach complements existing methods for enriching endogenous DNA and enhances the identification of authentic ancient microbes.
• The findings provide a novel strategy for microbiome research on ancient and historical samples.