A simple and effective method to enrich endogenous DNA from mammalian faeces.

Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over bacteria by using sodium dodecyl sulphate so as to discharge endogenous DNA into liquid phase before bacterial DNA. By brief centrifugation, total DNA with enriched endogenous fraction can be extracted from the supernatant using routine methods. Our assessments showed that the endogenous DNA extracted by PEERS was significantly enriched for various types of faeces from different species, preservation time and conditions. It significantly improves the genotyping correctness and efficiency of genome resequencing with the total additional cost of $ 0.1 and a short incubation step to treat a faecal sample. We also provide methods to assess the enrichment efficiency of mitochondrial and nuclear DNA and models to predict the usability of faecal DNA for genotyping of short tandem repeat, single-nucleotide polymorphism and whole-genome resequencing. © 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

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Liang Yu Cui, Bo Yang Liu, Hai Meng Li, Yi Xin Zhu, Yong Heng Zhou, Chang Su, Yin Ping Tian, Hai Tao Xu, Dan Liu, Xiao Ping Li, Yue Ma, Guang Shun Jiang, Huan Liu, Shu Hui Yang, Tian Ming Lan, Yan Chun Xu. A simple and effective method to enrich endogenous DNA from mammalian faeces. Molecular ecology resources. 2024 May;24(4):e13939

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PMID: 38372463

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