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<p>DNA damage serves as a key indicator for authenticating ancient DNA. Accurate assessment of ancient DNA damage is crucial to preventing the introduction of contamination in subsequent genomic analyses, an important step in paleomicrobiological studies. However, current research on ancient DNA damage has mostly focused on human and animal samples, with microbial samples relatively underexplored. In this review, we summarize the characteristics of damage patterns in ancient microbial DNA. Current research indicates that the degree of damage in ancient microbial DNA differs from that observed in ancient human DNA in single-genome studies, while in metagenomic studies, damage patterns vary among different microbes within the same microbiota. Additionally, we discuss the potential impacts of ancient microbial DNA damage on downstream analyses and demonstrate the critical role of damage evaluation in molecular paleomicrobiology. Finally, this review compiles the available methods for identifying damage in ancient microbial DNA, thereby providing a reference to future studies in this area.</p>

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Features, impacts and identification of DNA damage in ancient microbes

  • 期刊论文

  • 发表日期：

    2026年5月20日

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  • Liwen Yang,
  • Kexin Li,
  • Yichen Liu,
  • Qiaomei Fu

摘要

DNA damage serves as a key indicator for authenticating ancient DNA. Accurate assessment of ancient DNA damage is crucial to preventing the introduction of contamination in subsequent genomic analyses, an important step in paleomicrobiological studies. However, current research on ancient DNA damage has mostly focused on human and animal samples, with microbial samples relatively underexplored. In this review, we summarize the characteristics of damage patterns in ancient microbial DNA. Current research indicates that the degree of damage in ancient microbial DNA differs from that observed in ancient human DNA in single-genome studies, while in metagenomic studies, damage patterns vary among different microbes within the same microbiota. Additionally, we discuss the potential impacts of ancient microbial DNA damage on downstream analyses and demonstrate the critical role of damage evaluation in molecular paleomicrobiology. Finally, this review compiles the available methods for identifying damage in ancient microbial DNA, thereby providing a reference to future studies in this area.