[Coral-List] Call for SCTLD microbiome data

[Stephanie Rosales - NOAA Affiliate]

Hello Coral-List,



To more rapidly understand how the bacterial community is involved with the
Stony Coral Tissue Loss Disease (SCTLD) outbreak, the Pathogen
ID/Microbiome SubTeam of the Research Response Team is conducting a
meta-analysis with available datasets. The current contributions come from
studies that have already been published, are in review, or are still being
analyzed. In all, we have about nine datasets, which came from multiple
institutions (listed below).



We are making an open call to anyone who would like to share SCTLD
microbiome data to incorporate into this meta-analysis. If you have a 16S
rRNA gene V4 region dataset using the primers from 515F (Parada et al.,
2016) and 806R (Apprill et al., 2015), we kindly encourage you to consider
working with our group to include your data to further our understanding of
this ongoing outbreak. Our goal is to begin the first group of analyses by
the end of August. If you are in the process of generating 16S data but
will not be ready by August, we can discuss incorporating your data into a
subsequent iteration of the meta-analysis (Round 2) in the future.



We are also looking for White Plague (WP) II microbiome datasets that are
currently not on NCBI and that were generated with the same criteria
mentioned above. These datasets will be used to compare SCTLD to WP II.



If you would like to contribute, would like to join this group, and/or have
further questions please contact the SubTeam leads Stephanie Rosales
stephanie.rosales at noaa.gov and Chris Kellogg ckellogg at usgs.gov.



*Dataset contributors*

Abigail Clark and Erinn Muller (MOTE)

Amy Apprill (WHOI)

Bane Schill (USGS)

Jennifer Salnero (GMU)

Julia Stewart and Monica Medina (PSU)

Julie Meyer (UF)

Lindsay Huebner (FWC)

Anthony Bellantuono and Mauricio Rodriguez-Lanetty (FIU)





Thank you,



Stephanie and Chris



Apprill, A., McNally, S., Parsons, R., & Weber, L. (2015). Minor revision
to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11
bacterioplankton. Aquatic Microbial Ecology, 75(2), 129–137.
http://doi.org/10.3354/ame01753



Parada, A. E., Needham, D. M., & Fuhrman, J. A. (2016). Every base matters:
assessing small subunit rRNA primers for marine microbiomes with mock
communities, time series and global field samples. Environmental
Microbiology, 18(5), 1403–1414. http://doi.org/10.1111/1462-2920.13023

-- 
Stephanie Rosales, PhD
Senior Research Associate
NOAA/AOML, University of Miami/CIMAS
4301 Rickenbacker Causeway,
Key Biscayne, FL  33149, U.S.A
office: 305-361-4511