The files in this data release are the raw DNA sequence files referenced in the journal article by Goldsmith and others (2018) entitled "Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype". They represent a 16S rRNA gene amplicon survey of the corals' microbiome completed using Roche 454 pyrosequencing with titanium reagents. The raw data files of 454 sequences associated with this study have also been submitted to the NCBI Sequence Read Archive under Bioproject number PRJNA348705. For more information, you may contact Christina Kellogg at the USGS St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33710; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov. The folder labeled "Primnoa_raw_data" contains the original SFF sequence files received from the sequencing vendor as well as two mapping files. The samples were sequenced on two different pyrosequencing runs, so there are four SFF files (two for each run). The folder also contains .qual and .fna files corresponding to each SFF file. To perform initial splitting of the samples from these runs (which also contain other sequences from different studies), it is necessary to have a mapping file that corresponds to each run. The file titled "Primnoa3008_map.txt" is the mapping file that goes with sequencing files ID2UZ7K01.sff and ID2UZ7K02.sff from the first run. The file titled "Primnoaprim1_map.txt" is the mapping file that goes with sequencing files H8MF54001.sff and H8MF54002.sff from the second run. The column headers in the mapping files are as follows: SampleID: a unique identifier for each sample BarcodeSequence: multiplex identifier; arbitrary short DNA sequence used to identify the sequences from this particular sample out of the pool of samples included on a multiplexed run LinkerPrimerSequence: sequence of the forward primer used in polymerase chain reaction to amplify the DNA extracted from the sample ReversePrimer: sequence of the reverse primer used in polymerase chain reaction to amplify the DNA extracted from the sample Plate: identifier for sequencing plate on which DNA extracted from the sample was sequenced Name: complete name of sample Species: coral species sampled OceanBasin: ocean basin in which the sample was collected Location: geographic location name for where the sample were collected Temperature: water temperature at which coral sample was collected; units are degrees Celsius Depth: water depth at which coral sample was collected; units are meters Salinity: salinity at which coral sample was collected; units are psu (practical salinity units) Latitude: latitude at which the sample was collected; units are decimal degrees Longitude: longitude at which the sample was collected; units are decimal degrees Month: month in which the sample was collected Year: year in which the sample was collected Description: may contain notes regarding sample collection or processing In order to confirm the presence of members of the Chlamydiales order in the bacterial communities of Alaskan Primnoa corals (Primnoa pacifica), bacterial DNA extracted from those corals was amplified using primers targeting the 23S rRNA gene in Chlamydiales (Everett and others (1999), Journal of Clinical Microbiology 37(3):575-580). Amplicons were cloned and screened, then sequenced using Sanger sequencing. Two variant sequences were obtained (607 bp each) and are contained in the file titled "Chlamydiales_23S.txt". The 23S sequences have been submitted to NCBI (GenBank) under accession numbers KY010287 and KY010288. The text document titled "Primnoa_workflow.txt" details the scripts run in the bioinformatic package QIIME version 1.9.1 (Caporaso and others (2010), Nature Methods 7:335-336, doi:10.1038/nmeth.f.303), default or chosen settings used for each script, and the names of the input/output files associated with each script. The file labeled "Primnoa_metadata.txt" is MIMARKS (minimum information about a marker gene) compliant metadata, based on standards developed by the Genomic Standards Consortium for reporting marker gene sequences (Yilmaz and others, 2011, Nature Biotechnology 29:415-420, doi:10.1038/nbt.1823). The column headers are defined as follows: project_name: a description of the project's contents sample_name: a unique identifier for each sample bioproject_id: a unique accession number under which the raw data files have been submitted to the NCBI Sequence Read Archive (SRA) sample_title: a more detailed version of sample_name organism: what is being sequenced; in this case, a coral metagenome. Metagenome is defined as a collection of genetic material (genomes) from a mixed community of organisms. host: organism with which the microbial community being sequenced is associated collection_date: the date upon which the samples were collected; format is year geo_loc_name: geographic location name for where the samples were collected lat_lon: the latitude and longitude where the samples were collected; units are decimal degrees samp_collect_device: sample collection device that was used to obtain these samples samp_mat_process: sample material process; specifically how were the samples preserved in the field for later study source_material_id: identification of the source material that the sequenced samples were derived from (more specific than host; for example, what part of the host) samp_size: sample size; what amount of sample was used to extract DNA for sequencing nucl_acid_ext: nucleic acid extraction; DOI is provided for the paper which describes the specific extraction method employed for these samples nucl_acid_amp: nucleic acid amplification; DOI is provided for the paper which describes the specific primers and amplification methods employed for these samples lib_size: library size; how many sequences were present in each sample at the beginning of analysis target_gene: which marker gene was targeted by the chosen primers; 16S ribosomal RNA Gene target_subfragment: what portion of the marker gene was targeted by the chosen primers; variable regions V4-V5 of the 16S rRNA Gene pcr_primers: sequences of the forward and reverse primers used in polymerase chain reaction to amplify the DNA mid: multiplex identifiers; arbitrary short DNA sequence used to identify the sequences from this particular sample out of the pool of samples included on a multiplexed run seq_meth: sequence method; what sequencing technology was used to produce these data depth: water depth at which coral samples were collected; units are meters temp: water temperature at which coral samples were collected; units are degrees Celsius samp_store_temp: sample storage temperature between field collection and laboratory processing; -20 degrees Celsius salinity: salinity at which coral samples were collected; psu = practical salinity units contact_name: contact person for data contact_email: email of contact person for data