Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.
IHU Méditerranée Infection, Marseille, France.
Clin Microbiol Rev. 2022 Sep 21;35(3):e0014021. doi: 10.1128/cmr.00140-21. Epub 2022 Jun 6.
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
候选门纲目放射(CPR)是人类微生物群中细菌域的一个新兴分支。这些微生物仍然知之甚少,它们于 1981 年首次在环境中被描述为“超微生物”,其细胞体积小于 0.1μm,并于 2007 年首次与人类口腔微生物群相关联。技术的发展对于研究人类微生物群中的 CPR 至关重要。事实上,尽管人们一直在努力,但由于这些超微生物仍然无法在无菌条件下培养,因此成像技术的进步使得能够对其进行观察和形态描述。尽管它们的基因组能力和分类学仍在研究中,但在分类学分类、生活方式方面已经取得了重大进展。此外,下一代测序技术的进步和生物信息学工具的不断发展,使得它们能够作为不同人类栖息地(包括口腔、胃肠道和生殖道)中的共生体被检测到,从而强调了 CPR 作为人类微生物群中不可忽视的一部分,对生理环境有影响。相反,几种病理表现出影响 CPR 水平的失调,包括炎症、粘膜和传染病。在对文献的全面综述中,我们提供了 CPR 研究的历史视角,概述了研究这些生物体的可用方法,并描述了它们的分类学和生活方式。此外,还介绍了它们在人类微生物组中的分布,包括在稳态和失调环境中的分布。未来的努力应集中于开发共培养物,如果可能的话,还应开发无菌培养物,以获得分离株,从而获得基因组,这将更好地理解这些超微生物,它们在人类微生物组中的重要性是不可否认的。