Loss of gut microbial diversity^1,2,3,4,5,6 in industrial populations is associated with chronic diseases⁷, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

工业人群肠道微生物多样性的丧失^1,2,3,4,5,6与慢性病有关⁷，强调研究我们祖先的肠道微生物组的重要性。然而，关于工业化前肠道微生物组的组成知之甚少。在这里，我们对古粪便中的微生物基因组进行了大规模的从头组装。我们从美国西南部和墨西哥保存完好的 8 个经过验证的人类古粪便样本（1000-2000 年历史）中重建了 498 个中等质量和高质量的微生物基因组。在 181 个基因组中，有最强有力的证据表明它们是古老的和人类肠道起源的，其中 39% 代表了以前未描述的物种水平基因组箱。提示约会表明关键的人类共生体Methanobrevibacter smithii的大致多样化时间表. 与来自 8 个国家的 789 个当今人类肠道微生物组样本相比，古粪便样本更类似于非工业化人类肠道微生物组而不是工业化人类肠道微生物组。古粪便样本的功能分析显示，抗生素抗性和粘蛋白降解基因的丰度显着降低，以及相对于工业肠道微生物组的移动遗传元件的富集。这项研究有助于从古代微生物组中发现和表征以前未描述的肠道微生物，并通过古粪便的基因组重建研究人类肠道微生物群的进化历史。