BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.

中文翻译：

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对 15 世纪中期铁器时代中期班图语人古粪便样本的多代理分析阐明了“祖先”撒哈拉以南非洲肠道微生物组的结构。

背景古代人类粪便材料的考古发现为探索人类祖先肠道微生物组（IM）的分类组成和代谢能力提供了难得的机会。在这里，我们报告了对古代南非古粪便标本的鸟枪法宏基因组分析的结果。方法 在从南非林波波省布须曼岩石庇护所回收单个干燥古粪便样本后，我们对样本应用了多代理分析方案。从样本中提取古代 DNA 及其随后的鸟枪法宏基因组测序有助于对这种古代人类 IM 的分类学和代谢特征进行表征。结果 我们的结果表明，新石器时代“中铁器时代”（约公元 1460 年）讲班图语的个体的远端 IM 表现出的特征表明，其饮食很大程度上是混合的采集者-农牧民饮食。随后与蒂罗尔冰人 (Ötzi) 和当代哈扎狩猎采集者、马拉维农牧民和意大利人的 IM 进行比较表明，这种 IM 早于最近对“西方”饮食的适应，包括咖啡、茶、巧克力、柑橘和柑橘的消费。大豆、抗生素、止痛药的使用以及接触各种有毒环境污染物。结论 我们的分析揭示了当前人类 IM 可能对最近的饮食变化、处方药和环境污染物做出反应的一些原因和方式，为新石器时代出现后人类 IM 的进化提供了罕见的见解。一万二千年前。视频摘要。