Université de Poitiers, UMR CNRS 7267, Ecologie et Biologie des Interactions (EBI), Poitiers, France; EAU DE PARIS, Direction de la Recherche & Développement et de la Qualité des eaux (DRDQE), Paris, France.
Water Res. 2013 Dec 1;47(19):6958-65. doi: 10.1016/j.watres.2013.07.047. Epub 2013 Oct 23.
Free-living amoebae (FLA) are protozoa that can be found in water networks where they prey on bacteria within biofilms. Most bacteria are digested rapidly by phagocytosis, however some are able to survive within amoebae and some are even able to multiply, as it is the case for Legionella pneumophila. These resisting bacteria are a potential health problem as they could also resist to macrophage phagocytosis. Several publications already reported intra-amoebal bacteria but the methods of identification did not allow metagenomic analysis and are partly based on co-culture with one selected amoebal strain. The aim of our study was to conduct a rRNA-targeted metagenomic analysis on amoebae and intra-amoebal bacteria found in drinking water network, to provide the first FLA microbiome in environmental strains. Three sites of a water network were sampled during four months. Culturable FLA were isolated and total DNA was prepared, allowing purification of both amoebal and bacterial DNA. Metagenomic studies were then conducted through 18S or 16S amplicons sequencing. Hartmannella was by far the most represented genus of FLA. Regarding intra-amoebal bacteria, 54 genera were identified, among which 21 were newly described intra-amoebal bacteria, underlying the power of our approach. There were high differences in bacterial diversity between the three sites. Several genera were highly represented and/or found at least in two sites, underlying that these bacteria could be able to multiply within FLA. Our method is therefore useful to identify FLA microbiome and could be applied to other networks to have a more comprehensive view of intra-amoebal diversity.
自由生活的阿米巴原虫（FLA）是一种原生动物，可在水网中找到，在那里它们以生物膜内的细菌为食。大多数细菌很快被吞噬作用消化，但有些细菌能够在阿米巴原虫内存活，有些甚至能够繁殖，例如嗜肺军团菌。这些具有抵抗力的细菌是一个潜在的健康问题，因为它们也可能抵抗巨噬细胞吞噬作用。已经有几篇文献报道了内阿米巴原虫内的细菌，但鉴定方法不允许进行宏基因组分析，并且部分方法基于与一种选定的阿米巴原虫菌株的共培养。我们的研究目的是对饮用水网络中发现的阿米巴原虫和内阿米巴原虫进行 rRNA 靶向宏基因组分析，提供环境菌株中第一个 FLA 微生物组。在四个月期间，从水网的三个地点进行采样。分离可培养的 FLA 并制备总 DNA，从而允许纯化阿米巴原虫和细菌 DNA。然后通过 18S 或 16S 扩增子测序进行宏基因组研究。到目前为止，哈特曼氏菌是 FLA 最具代表性的属。关于内阿米巴原虫，共鉴定出 54 个属，其中 21 个是新描述的内阿米巴原虫，这证明了我们方法的有效性。三个地点之间的细菌多样性存在很大差异。有几个属高度代表，并且/或至少在两个地点发现，这表明这些细菌能够在 FLA 内繁殖。因此，我们的方法可用于鉴定 FLA 微生物组，并可应用于其他网络，以更全面地了解内阿米巴原虫的多样性。
