Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Project Information
• Funding

A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources. These data are described in Huggett and Apprill (in press).

Metadata for the database is available by clicking the "Get Data" button on this project page.  The database is available for download as the following ARB file: ​coralmicrobiome_database.arb (37 MB)

ARB software (version arb-6.06) is available from http://www.arb-home.de/downloads.html

The coral-microbial database was built over time using the ARB software (Ludwig et al., 2004). Initially, the All-Species Living Tree Project (LTP) s95 database containing SSU rRNA gene sequences for type strains of bacteria, archaea and eukarya was used as the database backbone (Yarza et al., 2008). In 2009, we used the search criteria ‘coral + bacteria’ and ‘coral + archaea’ within BLAST (Altschul et al., 1990) to obtain coral-associated SSU rRNA gene sequences from studies that applied cultivation-dependent or independent approaches from the GenBank database (Benson et al., 2008). These sequences were aligned using SINA (Pruesse et al., 2007) and imported into ARB. This database was then revised by first searching for all sequences coded as ‘coral*’ in any field. From these, sequences that matched ‘eukaryot*’ in the field tax_slv were removed, and all others were marked. An initial search of these marked sequences for those that had *coral* in the field isolation_source was done and these were manually checked. For those that were isolated from a coral (soft or hard, tropical or deep sea, etc.) were assigned ‘coral’ in the remark field. For those that were not isolated from a coral all were assigned ‘checked’ in the remark field. At this stage, there were 1333 sequences remaining with the term *coral* in any field. These were manually checked for their description and isolation details and marked either ‘coral’ or ‘checked’ in the remark field. From these, a database was created that contained just the sequences marked ‘coral’ from our in-house (2009) database. This small curated database was then merged with the SSU_Ref111_SILVA_NR (Pruesse et al., 2007) database (released 19 July 2012) which created new names for the living tree sequences. All sequences that were brought in from the small living tree database were marked with an identifier and the SSU_Ref database was searched as above to locate sequences in the SSU_Ref database that were bacteria or archaea sequences derived from corals. Information was added to these sequences in the location, author, journal and host species fields and all were given the term ‘coral’ in the remark field.

Next, the ISI web of science electronic database was searched for any publications that contained the search term 'coral*' and 'bacteria*' or ‘coral*’ and ‘archaea* in ‘topic’ from 2010 to present. From these, the publications were manually checked and any manuscript that mentioned sequence data or appeared likely to contain Sanger sequence data was obtained. If sequence data was associated with a manuscript, the corresponding sequences were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) in fasta format, aligned using the online SINA aligner (Pruesse et al., 2007) and imported into arb. If replicates were located they were removed from arb. Newly imported sequences were manually curated to include as much metadata as possible. These included the location (in country field), host (in host field), author names (in author field) and any other accessible data (e.g. Journal).

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as "nd" for "no data."  nd is the default missing data identifier in the BCO-DMO system.
* converted non-delimiter commas to semicolons to support export as csv
* removed duplicate column of lengths
* data version 2: 2018-08-06 is an update of data version 1: 2018-05-11 with the following change. In the file coralmicrobiome_database.arb, phylogenetic trees were updated to include those available in Huggett and Apprill (in press) which describes this dataset.

Dataset version 2 (2021-06-10) replaces version 1(2018-08-06):
* Converted file to UTF-8

Description from NSF award abstract:
Reef-building corals are in decline worldwide due in part to climate change and other human activities, and it is becoming increasingly important to understand what aspects of coral biology are degraded by environmental stress which then leads to coral mortality. It is now widely known that corals harbor communities of bacteria and archaea that are believed to play important roles in maintaining the health of their hosts, but we lack any appreciable understanding about the identity of the microbial associates regularly residing within healthy, reef-building corals. This project asks the central question: do reef-building corals harbor fundamental or persistent microbial associates that are symbiotic within their tissues? In order to address this hypothesis, the investigator will assess the identity of the bacterial and archaeal microbes using a variety of molecular and microscopy approaches that includes the identification and localization of a widespread group of coral bacterial associates belonging to the genus Endozoicomonas. The results of this study will then be used to develop additional questions about the role of these microbial associates in nutrient cycling and how they contribute to the health and survival of corals.