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Sci Rep:在古人类样本中识别细菌“罪魁祸首”

来源:Nature中文网 2014-03-14 21:41

本期Scientific Reports杂志报告了对古人类样本进行筛查来寻找传染病的一个新方法。这项原理证明研究利用一个微生物检测阵列在两个古人类样本中正确识别出了以前被确认的细菌病原体的DNA。该方法也许为跨越时间和空间进行健康研究提供了一个高效的、廉价的古病理学工具。

研究传染病起源和人口健康问题所面临的挑战之一是,古人类遗留物一般含有高度降解的DNA,在其中能够感染的部分经常只是少数。这会使得基于序列的元基因组分析成本高昂、耗费时间。Hendrik Poinar及同事提出,微阵列(它们的多功能性对现代临床样本已得到充分证明)也许能够为复杂样本中的微生物多样性提供一个快速的、但又全面的快照,而不需要进行冗长的分析,也不会产生高吞吐量筛选所涉及的高成本。

本文作者利用“劳伦斯·利弗莫尔微生物检测阵列”(LLMDA)成功识别出了以前确认的人类细菌病原体,其中包括在来自公元1849年的一个小肠样本中识别出了霍乱弧菌(造成霍乱)和在来自公元1348年的一颗牙齿中识别出了鼠疫耶尔森氏菌(造成“黑死病”瘟疫)。这些发现表明,LLMDA能在古样本中识别出原始的和/或共感染的细菌病原体。该研究显示了微阵列成为考古样本的一个有用筛选工具的潜力,利用它们可以对微生物特征进行快速、廉价和准确的重建。(生物谷Bioon.com)

生物谷推荐的英文摘要

Scientific Reports                doi:10.1038/srep04245

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array

Alison M. Devault,  Kevin McLoughlin,  Crystal Jaing,  Shea Gardner,  Teresita M. Porter, Jacob M. Enk,  James Thissen,  Jonathan Allen,  Monica Borucki,  Sharon N. DeWitte,  Anna N. Dhody  & Hendrik N. Poinar

Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.

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