Pinevich Alexander V, Andronov Eugeny E, Pershina Elizaveta V, Pinevich Agnia A, Dmitrieva Helena Y
Saint Petersburg State University, Universitetskaya Quay, 7/9, P.O. Box 199034, St. Petersburg, Russia.
All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Russian Academy of Sciences, Podbelskogo Highway, 3, P.O. Box 196608, St. Petersburg-Pushkin, Russia.
Antonie Van Leeuwenhoek. 2018 Sep;111(9):1509-1521. doi: 10.1007/s10482-018-1054-4. Epub 2018 Feb 27.
Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer's personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by 'culturomics' will overcome this obstacle.
在微生物学作为一门学科刚起步时，就引入了对纯培养物的依赖，并且这种依赖一直很重要，尽管其适应性特性与混合培养物和环境菌群的特性本质上不同。纯培养物用于：（i）分类鉴定；（ii）病原体诊断；（iii）毒力和致病性研究；（iv）阐明代谢特性；（v）测试对抗生素的敏感性；（vi）全长基因组组装；（vii）在微生物保藏中心保藏菌株；以及（viii）描述新物种并进行名称验证。根据具体任务，对培养物纯度有不同要求，即满足传统标准或有必要进行更深入检测时。传统的验证方法（显微镜检查和平板培养对照）分辨率较低，且依赖观察者的个人判断。仅靠表型标准无法证明培养物的纯度，还应辅以基因组标准。我们考虑利用DNA高通量培养测序数据来定义仅针对一个基因型物种、无菌状态检测组和仅一个基因组的标准。其中第二和第三种方法更可取，尽管它们的分辨能力（深度）有限。因为即使进行深度测序，微量污染物也可能未被检测到，所以可靠的纯培养物应为从单个细胞或丝状体（多细胞细菌）衍生而来的克隆培养物。尽管这种类型的培养存在技术难题且无法大规模应用（转移到固体培养基上时相应接种物的生长机会可能较低），但人们希望“培养组学”引入的高通量培养方法能克服这一障碍。
