Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.
Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA.
J Dent Res. 2020 Jun;99(6):685-694. doi: 10.1177/0022034520905792. Epub 2020 Feb 19.
Oral microbiome research has moved from asking "Who's there?" to "What are they doing?" Understanding what microbes "do" involves multiple approaches, including obtaining genomic information and examining the interspecies interactions. Recently we isolated a human oral Saccharibacteria (TM7) bacterium, HMT-952, strain TM7x, which is an ultrasmall parasite of the oral bacterium The host-parasite interactions, such as phage-bacterium or Saccharibacteria-host bacterium, are understudied areas with large potential for insight. The Saccharibacteria phylum is a member of Candidate Phyla Radiation, a large lineage previously devoid of cultivated members. However, expanding our understanding of Saccharibacteria-host interactions requires examining multiple phylogenetically distinct Saccharibacteria-host pairs. Here we report the isolation of 3 additional Saccharibacteria species from the human oral cavity in binary coculture with their bacterial hosts. They were obtained by filtering ultrasmall Saccharibacteria cells free of other larger bacteria and inoculating them into cultures of potential host bacteria. The binary cocultures obtained could be stably passaged and studied. Complete closed genomes were obtained and allowed full genome analyses. All have small genomes (<1 Mb) characteristic of parasitic species and dramatically limited de novo synthetic pathway capabilities but include either restriction modification or CRISPR-Cas systems as part of an innate defense against foreign DNA. High levels of gene synteny exist among Saccharibacteria species. Having isolates growing in coculture with their hosts allowed time course studies of growth and parasite-host interactions by phase contrast, fluorescence in situ hybridization, and scanning electron microscopy. The cells of the 4 oral Saccharibacteria species are ultrasmall and could be seen attached to their larger Actinobacteria hosts. Parasite attachment appears to lead to host cell death and lysis. The successful cultivation of Saccharibacteria species has significantly expanded our understanding of these ultrasmall Candidate Phyla Radiation bacteria.
口腔微生物组研究已经从“谁在那里？”转变为“它们在做什么？” 了解微生物“做什么”需要多种方法，包括获取基因组信息和检查种间相互作用。最近，我们分离出一种人类口腔拟杆菌（TM7）细菌 HMT-952 菌株 TM7x，它是口腔细菌的超小型寄生虫。宿主-寄生虫相互作用，如噬菌体-细菌或拟杆菌-宿主细菌，是研究较少但具有很大洞察力潜力的领域。拟杆菌门是候选门辐射的成员，候选门辐射是一个以前没有培养成员的大谱系。然而，扩大我们对拟杆菌-宿主相互作用的理解需要检查多个系统发育上不同的拟杆菌-宿主对。在这里，我们报告了从人类口腔中以二元共培养的方式分离出的另外 3 种拟杆菌物种，与它们的细菌宿主一起。通过过滤超小的拟杆菌细胞以去除其他较大的细菌并将其接种到潜在宿主细菌的培养物中获得了这些物种。获得的二元共培养物可以稳定传代和研究。获得了完整的闭合基因组，并允许进行全基因组分析。所有这些都具有寄生物种的小基因组（<1 Mb）和显著受限的从头合成途径能力，但都包括限制修饰或 CRISPR-Cas 系统，作为抵御外来 DNA 的先天防御的一部分。拟杆菌物种之间存在高水平的基因同线性。通过与宿主共培养进行分离培养，使我们能够通过相差、荧光原位杂交和扫描电子显微镜进行生长和寄生虫-宿主相互作用的时间过程研究。这 4 种口腔拟杆菌的细胞非常小，可以看到它们附着在较大的放线菌宿主上。寄生虫附着似乎导致宿主细胞死亡和裂解。拟杆菌物种的成功培养显著扩展了我们对这些超小型候选门辐射细菌的理解。
