Red Sea Research Center, King Abdullah University of Science and Technologygrid.45672.32, Thuwal, Saudi Arabia.
Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
mSystems. 2022 Aug 30;7(4):e0036722. doi: 10.1128/msystems.00367-22. Epub 2022 Jul 5.
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
绝大多数的环境微生物尚未被培养，而关于珊瑚相关微生物 (CAMs) 的大部分知识都是通过扩增子测序和宏基因组学获得的。然而，探索培养的 CAMs 对于详细和全面地描述这些微生物在塑造珊瑚健康方面的作用至关重要，最终可以将它们用于生物技术，例如珊瑚益生菌和其他天然产物。在这里，介绍了用于获取培养的 CAMs 的策略和技术，同时讨论了每种策略的优缺点。我们强调了依赖培养的方法学中存在的差距和潜在改进，并指出了几种可能的替代方法（包括宏培养组学和扩散装置），这些方法可以用来获取 CAM 的“暗物质”（即目前尚未描述的 CAMs）。本研究提供了迄今为止对恢复培养珊瑚微生物组的方法学的最全面综合，并为下一代 CAM 宏培养组学的发展提出了建议。
