小柯机器人

利用人类肠道重建古微生物基因组
2021-05-16 15:43

美国Joslin糖尿病中心 Aleksandar D. Kostic课题组的研究利用人肠道重构了古代微生物的基因组。这一研究成果于2021年5月12日在线发表在国际学术期刊《自然》上。

在本研究中,研究人员进行了古细菌微生物基因组的大规模从头组装。从八份经过身份验证的人类古细菌样本(1,000-2,000年历史)中,研究人员重现了498个中等和高质量的微生物基因组,这些样本具有保存良好的美国西南部和墨西哥人DNA。在181个最古老与人类肠道起源相关的基因组中,有39%具有以前未知的物种基因组。这些结果为关键的人类共生史密斯甲烷短杆菌提供了多样化的时间表。与来自八个国家的789个当今人类肠道微生物组样本相比,古细菌样本与非工业化样本的肠道微生物群更相似。

palaeofaceces样本功能分析显示,古细菌抗生素抗性和粘蛋白降解基因的丰度显著降低,并且与工业化后的肠道微生物群相比,其流动性遗传元件的富集度更高。这项研究有助于从古代微生物群中发现和表征先前未知的肠道微生物,并通过古细菌的基因组重建来研究人类肠道微生物群的进化历史。

据悉,工业革命后人肠道微生物多样性的丧失与慢性病有关,这突出了研究肠道微生物组起源的重要性。但是,对工业革命以前肠道微生物组的组成知之甚少。

附:英文原文

Title: Reconstruction of ancient microbial genomes from the human gut

Author: Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Hbner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto Garca-Ortiz, Anglica Martnez-Hernndez, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Snje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar D. Kostic

Issue&Volume: 2021-05-12

Abstract: Loss of gut microbial diversity1,2,3,4,5,6 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.

DOI: 10.1038/s41586-021-03532-0

Source: https://www.nature.com/articles/s41586-021-03532-0

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:69.504
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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