Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter

Junia Schultz, Flúvio Modolon, Alexandre S. Rosado, Christian R. Voolstra, Michael Sweet, Raquel S Peixoto

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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 in situ 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.
Original languageEnglish (US)
StatePublished - Jul 5 2022

Bibliographical note

KAUST Repository Item: Exported on 2022-09-14
Acknowledged KAUST grant number(s): BAS/1/1095-01-01, FCC/1/1973-51-01
Acknowledgements: This research paper was carried out in association with the ongoing R&D project registered as ANP 21005-4, “PROBIO-DEEP–Survey of potential impacts caused by oil and gas exploration on deep-sea marine holobionts and selection of potential bioindicators and bioremediation processes for these ecosystems” (UFRJ/Shell Brasil/ANP), sponsored by Shell Brasil under the ANP R&D levy as “Compromisso de Investimentos com Pesquisa e Desenvolvimento.” R.S.P. was supported through KAUST grant number BAS/1/1095-01-01 and KAUST Center Competitive Funding (CCF) FCC/1/1973-51-01). F.M. received support from the National Council for Scientific and Technological Development (CNPq) and the National Council for the Improvement of Higher Education (CAPES).


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