Supporting data for "Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals <i>Porites lutea</i> and <i>Isopora palifera</i>"

At present our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed towards the millimetre-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals <i>Porites lutea</i> and <i>Isopora palifera</i>, through a compendium of ~400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 microbial classes. Skeletal microbiomes harboured a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (<i>dsyB</i>) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22±15 genes in <i>P. lutea</i> and 28±23 in <i>I. palifera</i> with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulphate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.