UMR-S 722, INSERM, Paris, France.
Appl Environ Microbiol. 2013 Aug;79(16):5005-12. doi: 10.1128/AEM.01423-13. Epub 2013 Jun 14.
Escherichia coli is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of E. coli in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the E. coli population, i.e., 10(5) CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the E. coli microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains.
大肠杆菌可分为四个主要的系统发育群，每个群都表现出生态特化现象。为了了解大肠杆菌在其主要栖息地的种群结构，我们使用一种新的实时 PCR 方法，直接从 100 名健康人体的粪便中评估这些系统发育群的相对比例，这种方法可以研究大量的样本。我们的技术检测下限为大肠杆菌种群的 0.1%，即粪便中 10(5)CFU/g；在基于单个菌落分析的其他方法中，检测下限为 10%。在 21%、48%、21%和 8%的受试者中，分别同时发现了一个、两个、三个或四个系统发育群。在 40%的受试者中发现了丰度低于种群的 10%的系统发育群，揭示了个体内高度的多样性。系统发育群 A 和 B2 分别在 74%和 70%的受试者中被检测到，系统发育群 B1 和 D 分别在 36%和 32%的受试者中被检测到。当系统发育群 B2 占主导地位时，它往往不会与其他系统发育群共同存在。相比之下，当系统发育群 A 占主导地位时，其他系统发育群则存在。这些数据表明，在人类肠道中，单一物种的成员之间存在着复杂的相互作用模式，并确定了一个以低频率存在的克隆库。这些少量克隆的存在可以解释单个个体中大肠杆菌微生物组组成随时间波动的原因。它们也可能构成毒力和/或耐药菌株的储存库。
