Antibiotics-induced monodominance of a novel gut bacterial order
Antibiotics-induced monodominance of a novel gut bacterial order
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DOI：
10.1136/gutjnl-2018-317715
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发表时间：
2019-10-01
期刊：
影响因子：
24.5
通讯作者：
Bork, Peer
中科院分区：
文献类型：
--
作者：
Hildebrand, Falk;Moitinho-Silva, Lucas;Bork, Peer
健康成人肠道微生物组的组成在长时间内相对稳定，并且已经培养和描述了最丰富和最流行的物种的代表。然而，微生物丰度可以改变扰动，如抗生素的摄入量，使识别和表征，否则低丰度species.Design分析肠道微生物的时间序列数据，我们使用鸟枪宏基因组学创建菌株水平的分类和功能概况。社区动态建模postintervention与关注条件罕见的类群和以前未知的bacteries.Results响应于一种常用的头孢菌素（ceftriaxone），我们观察到一个强有力的组成转变，在一个主题，其中一个以前未知的物种，（U）Borkfalki ceftriaxensis，被确定，开花到92%的相对丰度。基因组组装揭示，该物种（1）属于迄今未描述的厚壁菌门，（2）在至少三分之一的成年人中普遍存在，丰度低，（3）机会主义生长，在生态学上与典型的益生菌物种相似，（4）通过单核苷酸变异分析确定与健康宿主稳定相关。它是抗生素干预后的第一个定殖者，导致了持久的微生物群落转变和可能的9个细菌的永久性损失。ceftriaxensis和随后的Parabacteroides distasonis证明了肠道中存在单优势群落状态。我们的研究指出了人类肠道中低丰度但常见的未发现的财富，并呼吁进行更高分辨率的纵向研究，特别是对生态系统扰动的研究。
Objective The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.Design Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.Results In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, (U)Borkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.Conclusion The bloom of B-U. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.