A targeted approach to enrich host-associated bacteria for metagenomic sequencing.

Autor:	Dungan AM; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia., Tandon K; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia., Jameson V; Melbourne Cytometry Platform, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC 3010, Australia., Gotze CR; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.; Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia., Blackall LL; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia., van Oppen MJH; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.; Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia.
Jazyk:	angličtina
Zdroj:	FEMS microbes [FEMS Microbes] 2023 Nov 28; Vol. 5, pp. xtad021. Date of Electronic Publication: 2023 Nov 28 (Print Publication: 2024).
DOI:	10.1093/femsmc/xtad021
Abstrakt:	Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes , targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the ' Endozoicomonas ' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities. Competing Interests: The authors declare no conflicts of interest. (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)
Databáze:	MEDLINE
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