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SPCMSC Scientist Publishes New Paper on Coral Microbiome Methods

SPCMSC Research Microbiologist Christina Kellogg and colleague Zoe Pratte publish a new paper, “Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes” in the journal Frontiers in Marine Science. 

A woman with gloves and safety glasses inserts a tray of tiny samples into a laboratory instrument
SPCMSC Research Microbiologist Christina Kellogg loading coral samples into an automated DNA extraction instrument for processing. (Credit: Chris Kellogg, USGS. Public domain.)

The study finds that it may be possible to compare more broadly across microbiome studies employing different methodologies than previously thought and underscores the importance of internal controls for data quality assurance. 

There is little agreement as to the best methodologies for preserving and extracting DNA from host-associated microbiomes that are vastly different from humans. This study examines methodology practices when working with challenging host-associated microbiomes, such as those associated with various coral species. In a field with very little consensus, Kellogg and Pratte discuss the feasibility and pitfalls of comparing samples across different methodologies. They suggest that samples that have been preserved with RNAlater, DNA/RNA Shield, or liquid nitrogen are similar enough to be compared across studies. Although small significant differences exist between extraction methods, those containing a bead-beating step are also similar enough to compare across studies, as long as researchers understand the caveat that small, subtle differences are likely to occur between methodologies. This finding is critical, as it will expand capacity for cross comparison of microbiomes preserved and extracted in different manners. 

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