Additional file 3 of Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae

Additional file 3: Description of supplementary tables. Table S1. Data associated with the 16S rRNA gene amplicon-based community profiling for all six sample sources analyzed in this study. Sequencing, assembly and binning statistics of the 23 metagenome datasets used in this study. These data include the time, season, geographical location, sample, environmental metadata for each sample and library information related to the amplicon sequencing. Furthermore included are summary analyses of the average relative abundances grouped by season and sample type at the genus and family levels, as well as statistical analyses of the proportions of core and dominant taxa in each sample. In addition, this file contains diversity indices, average relative abundances of domain, phylum, family, genus, OTU and ASV levels. Table S2. Data associated with the 16S rRNA gene-based community analyses of cultured bacterial strains, including information on sampling time, season, geographical location, source, culture conditions, 16S rRNA sequence information, new species attributes and taxonomic status information. Included are also summary analyses about average relative abundances at phylum, family, genus and OTU levels, as well as core taxa analyses results at the family and genus levels (matched to the 16S amplicon data). In addition, the file contains EZcloud and SILVA 138 sequence alignment results. Table S3. Summary data on the 1,619 MAGs and 965 draft genomes, including completeness, contamination, contig number, tRNA number, quality classification, size (Mbp), N50 value, species cluster ID in dRep, and the annotation results from GTDB SR202, EZcloud and SILVA 138 ordered according to their positions on the phylogenetic tree in Fig. 4. Table S4. Summary information about the four categories of PULs / PUL-like loci used in this study that were found with sliding window lengths from 1 and 10. The information includes: taxonomic affiliation, length (number of genes), number and type of comprised CAZyme genes, PUL composition (CAZyme genes, tonB, susCD, sulfatase genes), information on susCD genes in classical PULs and the density of CAZyme genes in each PUL. Table S5. Information on PULs from this study and published reference PULs, including descriptions of each PUL cluster in the SusC/D protein trees (single susCD PULs, hybrid susCD PULs, tandem-repeat susCD PULs, and tandem-repeat and hybrid susCD PULs). Also included is information about the source genome, the source genome type, its taxonomy and habitat as well as PUL ID, cluster number, number of CAZyme genes, composition (CAZymes gene, susCD, TonB and sulfatase genes) and genomes, possible substrate. For classical PULs, detailed information of the SusC/D protein tree is provided, including, gene ID, PUL ID, PUL type, PUL composition and potential substrates. Table S6. Details on the four categories of PULs and PUL-like loci used in this study in the 1,619 MAGs and 965 draft genomes, including gene composition. gene locus tags and gene annotations from multiple databases (KEGG, CAZy, EggNOG, COG, SignalP, MEROPS and Pfam). Table S7. Details on all BGCs predicted in the 1,619 MAGs and 965 draft genomes. This includes overall function predictions and gene function predictions according to KEGG, CAZy, EggNOG, COG, SignalP, MEROPS and Pfam searches. Table S8. Annotated putative PUL substrates based on dbCAN-PUL data (dbCAN-PUL is a database of experimentally characterized CAZyme gene clusters and their substrates), and substrate and enzyme cleavage information from the CAZy database ( http://www.cazy.org/ ). These substrates represent automatically derived similarity-based bioinformatic predictions and are thus not as accurate as biochemically characterizations of PUL functions would be.