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Comprehensive analysis of microorganisms accompanying human archaeologicalremains

机译：对人类考古学伴随微生物的综合分析遗迹

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Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompaniedthe individual before death. Our study showed that the microbiome observed in anindividual sample is not reliant on the method or duration of sample storage. Moreover,shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformaticsanalysis allowed both the identification of ancient microbial species, including potentialpathogens, and their differentiation from contemporary species that colonized humanremains more recently.
机译：元基因组分析已成为有关微生物群落的普遍信息来源，这些微生物群落占据着众多生态位，包括考古标本。已经表明，从古代样品中提取的绝大多数DNA来自细菌（可能是现代污染物）。然而，从未对广泛范围的不同样品进行系统的表征人类遗体的微生物DNA的研究。我们使用宏基因组学方法对161个考古人类遗骸中存在的微生物群落进行了比较分析。从人类骨骼的牙齿中分离出DNA样品，其日期为100 AD至1200 AD。这些骨骼是从中欧的7个考古现场收集的，并在不同条件下保存。大多数已鉴定的微生物是普遍存在的环境细菌，不久前很可能已污染了宿主。我们观察到，微生物群落的组成是特定于样品的，并且与其时间或地理起源无关。此外，在三分之二的样本中还发现了人类口腔/肠道菌群典型的细菌和古细菌痕迹以及潜在的病原体。与人类相关物种的遗传物质相比，占大多数已鉴定细菌的环境物种相反，其DNA损伤模式可与内源性人类古代DNA相提并论，这表明这些微生物可能伴随着死亡前的个人。我们的研究表明，在单个样本不依赖于样本存储的方法或持续时间。此外，从古代标本中提取的DNA的浅层测序以及随后的生物信息学分析允许鉴定古代微生物物种，包括潜在微生物病原体及其与殖民人类的当代物种的区分仍然是最近的。

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