Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
Gut. 2019 Oct;68(10):1781-1790. doi: 10.1136/gutjnl-2018-317715. Epub 2019 Jan 18.
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.
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.
In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, , 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.
The bloom of and a subsequent one of 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.
健康成年人肠道微生物组的组成在很长一段时间内相对稳定，并且已经培养和描述了最丰富和最普遍的物种代表。然而，微生物丰度会因干扰而发生变化，例如抗生素摄入，从而能够识别和表征否则丰度较低的物种。
我们分析了肠道微生物时间序列数据，使用 shotgun 宏基因组学创建了菌株水平的分类和功能图谱。在干预后，我们重点对条件稀有分类群和以前未知的细菌进行了群落动态建模。
在对一种常用的头孢菌素（头孢曲松）的反应中，我们观察到一个个体的组成发生了强烈变化，其中鉴定出一种以前未知的物种 ，其相对丰度达到 92%。基因组组装表明，该物种（1）属于厚壁菌门（Firmicutes）中一个迄今尚未描述的目，（2）至少在三分之一的成年人中普遍以低丰度存在，（3）是机会性生长的，在生态上类似于典型的益生菌物种，（4）通过单核苷酸变异分析被确定为与健康宿主稳定相关。它是抗生素干预后的第一个定植者，导致了持久的微生物群落变化，并可能导致九种共生菌永久丧失。
的爆发和随后 的爆发表明在肠道中存在单优势群落状态。我们的研究表明，人类肠道中存在大量未被发现的低丰度但常见的分类群，并呼吁进行更具分辨率的纵向研究，特别是在生态系统干扰方面。
