The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains. We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach. Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.

中文翻译：

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使用受损DNA分子的选择性富集来挖掘古代微生物群。

源自死前和死后微生物定殖者的DNA之间不可避免的混合，使得从古代和历史样本中提取的微生物群中的真正微生物分类群的鉴定变得复杂。区分这些微生物DNA来源的一种可能性是查询是否存在古代DNA（aDNA）典型的与年龄相关的降解模式。由胞嘧啶脱氨引起的尿嘧啶的存在已在从各种来源回收的aDNA中被普遍检测到，并用作鉴定标准。在这里，我们采用文库制备方法，将携带尿嘧啶的分子与不携带尿嘧啶的分子分离，而该样本不包括尼安德特人的遗骸，标本室标本和考古植物的遗骸。我们显示，测序DNA库富集了携带尿嘧啶的分子，可有效放大与古代和历史起源的微生物混合物中与年龄相关的降解模式。在由于微生物混合物中较大的序列差异而难以检测到降解模式的情况下，这有助于发现真正的古代微生物分类群。另外，在尿嘧啶富集部分中的分类单元的相对富集可以帮助鉴定使用更具针对性的方法可能遗漏的真正的古代微生物分类单元。我们的实验表明，除了将其用于富集感兴趣生物的真实内源性DNA外，对受损DNA分子的选择性富集可以是发现古代微生物类群的宝贵工具。