The files in this data release are the raw DNA metagenome sequence files referenced in Chapter 2 of the Bureau of Ocean Energy Management Environmental Studies Program Report entitled "Multidisciplinary Assessment of Deep-Water Coral Ecosystems: Tools to Detect Impacts of Sub-lethal Stress." Chapter 2, written by Christina A. Kellogg, is entitled "Deep-Sea Coral Metagenomes." The files represent a shotgun metagenome dataset from ten unique colonies of the cold-water coral Lophelia pertusa sampled in the Gulf of Mexico and western Atlantic Ocean to examine their microbial metagenomes. Samples from the Gulf of Mexico were collected in 2009 and 2010. Samples from the Atlantic Ocean were collected in 2009. The sequences were produced by random shearing of the DNA, construction of a TruSeq library, and sequencing by Argonne National Laboratory on an Illumina HiSeq 2000 sequencing system. The raw data files associated with this study have also been submitted to the NCBI Sequence Read Archive under Bioproject number PRJNA471489. For more information, please see the README file.