Qi Weihong, Vaughan Lloyd, Katharios Pantelis, Schlapbach Ralph, Seth-Smith Helena M B
Functional Genomics Center Zurich, University of Zurich, Switzerland.
Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich, Switzerland.
Genome Biol Evol. 2016 Jun 13;8(6):1672-89. doi: 10.1093/gbe/evw111.
Advances in single-cell and mini-metagenome sequencing have enabled important investigations into uncultured bacteria. In this study, we applied the mini-metagenome sequencing method to assemble genome drafts of the uncultured causative agents of epitheliocystis, an emerging infectious disease in the Mediterranean aquaculture species gilthead seabream. We sequenced multiple cyst samples and constructed 11 genome drafts from a novel beta-proteobacterial lineage, Candidatus Ichthyocystis. The draft genomes demonstrate features typical of pathogenic bacteria with an obligate intracellular lifestyle: a reduced genome of up to 2.6 Mb, reduced G + C content, and reduced metabolic capacity. Reconstruction of metabolic pathways reveals that Ca Ichthyocystis genomes lack all amino acid synthesis pathways, compelling them to scavenge from the fish host. All genomes encode type II, III, and IV secretion systems, a large repertoire of predicted effectors, and a type IV pilus. These are all considered to be virulence factors, required for adherence, invasion, and host manipulation. However, no evidence of lipopolysaccharide synthesis could be found. Beyond the core functions shared within the genus, alignments showed distinction into different species, characterized by alternative large gene families. These comprise up to a third of each genome, appear to have arisen through duplication and diversification, encode many effector proteins, and are seemingly critical for virulence. Thus, Ca Ichthyocystis represents a novel obligatory intracellular pathogenic beta-proteobacterial lineage. The methods used: mini-metagenome analysis and manual annotation, have generated important insights into the lifestyle and evolution of the novel, uncultured pathogens, elucidating many putative virulence factors including an unprecedented array of novel gene families.
单细胞和宏基因组测序技术的进步使得对未培养细菌的重要研究成为可能。在本研究中，我们应用宏基因组测序方法来组装上皮囊肿病（一种在地中海水产养殖物种金头鲷中出现的新兴传染病）未培养病原体的基因组草图。我们对多个囊肿样本进行了测序，并从一个新的β-变形菌谱系“候选鱼孢菌属”构建了11个基因组草图。这些基因组草图显示出具有专性细胞内生活方式的致病细菌的典型特征：基因组大小缩减至2.6 Mb，G + C含量降低，代谢能力减弱。代谢途径的重建表明，候选鱼孢菌属的基因组缺乏所有氨基酸合成途径，这迫使它们从鱼类宿主中获取营养。所有基因组都编码II型、III型和IV型分泌系统、大量预测的效应蛋白以及IV型菌毛。这些都被认为是毒力因子，是黏附、入侵和操纵宿主所必需的。然而，未发现脂多糖合成的证据。除了该属内共享的核心功能外，比对结果显示可分为不同的物种，其特征是存在不同的大基因家族。这些家族占每个基因组的三分之一，似乎是通过复制和多样化产生的，编码许多效应蛋白，并且似乎对毒力至关重要。因此，候选鱼孢菌属代表了一种新型的专性细胞内致病β-变形菌谱系。所使用的方法：宏基因组分析和人工注释，为这种新型未培养病原体的生活方式和进化提供了重要见解，阐明了许多假定的毒力因子，包括一系列前所未有的新基因家族。
