Additional file 3 of Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Additional file 2: Supplementary Table S1. Number of sequence reads per quality control step across all metagenome samples using the MGnify metagenomics pipeline (EMBL-EBI), version 2.0 (project PRJEB13222). Supplementary Table S2. Basic information on the assembled metagenome dataset. Supplementary Table S3. Number of OTUs and sequence reads per prokaryote phylum across sample categories. Supplementary Table S4. (A) Taxonomic assignment and abundance of all prokaryotic OTUs of the dataset, according to the MGnify metagenomics pipeline (EMBL-EBI), version 2.0. (B) Similarity percentage (SIMPER) analyses indicating the contributions of specific operational taxonomic units (OTUs) to observed variation in the prokaryotic community structure between healthy and necrotic octocoral tissue. (C) “Indicspecies” analysis identifying “indicator” OTUs for the healthy and necrotic state of E. gazella tissue. Supplementary Table S5. General features of the assembled, “prokaryote-enriched” octocoral and seawater metagenomes according to the IMG/M annotation pipeline. Supplementary Table S6. Functional profiling of the assembled octocoral and seawater metagenomes (N = 17) according to Protein families (Pfam) annotations using the Integrated Microbial Genomes & Microbiomes (IMG/M) system from DOE-JGI. Supplementary Table S7. (A) Functional profiling and comparison of the assembled octocoral and seawater metagenomes (N=17) according to Clusters of Orthologous Groups of proteins (COGs) annotations using the Integrated Microbial Genomes & Microbiomes (IMG/M) system from DOE-JGI. (B) COG functions respectively enriched in the microbiomes of healthy octocoral tissue (green highlights) and recrotic octocoral tissue (orange highlights) and displayed in Figure 4. (C) Overview of functional features enriched either in the microbiomes of healthy (highlighted in green) or necrotic (highlighted in orange) octocoral tissue according to Clusters of Orthologous Groups of proteins (COGs) annotations using the Integrated Microbial Genomes & Microbiomes (IMG/M) system from DOE-JGI. Supplementary Table S8. (A) Secondary metabolite biosynthetic gene clusters (BGCs) predicted for each assembled metagenome (N = 17) using antiSMASH v. 5.0. (B) List of biosynthetic gene clusters with some level of homology to MIBiG database entries. (C) Closest taxonomic affiliation (Blastn searches) of biosynthetic gene clusters that shared some level of homology to MIBiG database entries. Supplementary Table S9. List of secondary metabolite-encoding biosynthetic gene cluster (BGC) families (GCFs) identified across the data by similarity network analysis using the BiG-SCAPE algorithm.