Metagenome-assembled genomes of 1,085 brown-alga-associated bacteria reveal high potential for polysaccharide degradation and indications of host-specificity in metabolic complementarities - Supplementary files

This dataset contains all the files that are too large to be included in the research article. 1085_bacterial_genomes.zip contains 1,085 bacterial genomes in Fasta format. The method used to collect and sequence these bacterial MAGs is described in the article currently in preparation, in the “Methods” section, under the heading “Genome processing.” These data were collected by a French team from the CEA. 1085_bacterial_padmet.zip contains 1,085 bacterial metabolic networks in PADMET format. The method used to reconstruct GSMNs of bacteria (genome-wide metabolic networks) is described in the article currently being written, in the “Methods” section, under the heading “Metabolic Network Analyses.” 1085_bacterial_sbml.zip contains 1,085 bacterial metabolic networks in SBML format. The method used to reconstruct GSMNs of bacteria (genome-wide metabolic networks) is described in the article currently being written, in the “Methods” section, under the heading “Metabolic Network Analyses.” 60_algal_padmet.zip contains 60 algal metabolic networks in PADMET format. Four of these species were excluded from the original Phaeoexplorer publication due to the poor quality of their genomes (Asterocladon rhodochortonoides, Nemoderma tingitanum, Fibrocapsa japonica, and Ectocarpus sp. 4), and there were thus excluded from these analyses too (Ascophyllum nodosum, Heterosigma akashiwo, and Sargassum natans), since no bacterial MAGs were sequenced from these samples. 60_algal_sbml.zip contains 60 algal metabolic networks in SBML format. Four of these species were excluded from the original Phaeoexplorer publication due to the poor quality of their genomes (Asterocladon rhodochortonoides, Nemoderma tingitanum, Fibrocapsa japonica, and Ectocarpus sp. 4), and there were thus excluded from these analyses too (Ascophyllum nodosum, Heterosigma akashiwo, and Sargassum natans), since no bacterial MAGs were sequenced from these samples. After_coevolution_steps_and_commands.pdf is a detailed report presenting all the statistical analyses conducted following the execution of the “coevolution” command in Holointeract, which identified bacteria with negative slopes among the 730 studied, as well as the compounds co-produced by these bacteria characterized by negative slopes. genome2representative.itol.txt Of the 1,085 bacterial MAGs, 589 were selected to reflect the taxonomic diversity of this bacterial dataset. In this file, you will find the 589 representative bacterial MAGs, each associated with an HTML color. genome2taxonomic_classification.itol.txt is the taxonomic classification of 1,085 bacterial genomes at the phylum and class levels, represented by different colors. Information on all taxonomic lineages is available at https://www.ncbi.nlm.nih.gov/datasets/taxonomy/. holointeract.sif is the Singularity image from the Holointeract program, which was used to study metabolic interactions between algae and bacteria. The Holointeract program is available on GitHub (https://github.com/AuReMe/HoloInteract/). In this study, the following commands are used: > holointeract metabolic_analysis --comm path_community --host path_hosts -o output_dir -s seeds.sbml -n test -m full –cpu=15 > holointeract coevolution --comm path_community --host path_hosts -o output_dir -s seeds.sbml -p hosts_tree.nwk -n test –cpu=15 matrix_artificial_holobiontes_39_algae_730_bacteria.csv is the matrix of producible compounds across all algal-bacterial pairings. 0=not producible, 1=producible only by the "holobiont", 2=producible by host alone; 3=producible by bacterium alone; 4 producible by host and bacterium. Cf Supplementary table S7 in the paper. Read this matrix using Python or R. metacyc 26.0.zip is the version 26.0 of the MetaCyc database (https://metacyc.org/) in PADMET and SBML format. It was used by Holointeract to reconstruct all the metabolic networks. MetaCyc is available under this license https://biocyc.org/download.shtml. ontosunbursts.zip is an archive which contains three “ontosunbursts.” Each “ontosunburst” consists of two files: a TSV file and an HTML file. They were created using https://github.com/AuReMe/Ontosunburst. ontosunburst_162_versus_1512_cpds.html is a dynamic HTML file. It is an enrichment analyses focusing on 162 metabolites that significantly contributed to the negative slopes. Please note that some compounds or classes of compounds have several parents and will therefore be displayed several times in the graph. ontosunburst_162_versus_1512_cpds.tsv is a matrix TSV file, used to generate the HTML file above. It is an enrichment analyses focusing on 162 metabolites that significantly contributed to the negative slopes. ontosunburst_heatmap_algae_cluster_6_versus_1512_compounds.html is a dynamic HTML file. It is an enrichment analyses show that within cluster 6 consists primarily in secondary metabolites that were co-produced by fewer than 100 bacteria. Cf figure 6D of paper. Please note that some compounds or classes of compounds have several parents and will therefore be displayed several times in the graph. ontosunburst_heatmap_algae_cluster_6_versus_1512_compounds.tsv is a matrix TSV file, used to generate the HTML file above. It is an enrichment analyses show that within cluster 6 consists primarily in secondary metabolites that were co-produced by fewer than 100 bacteria. Cf figure 6D of paper. ontosunburst_heatmap_algae_clusters_1_and_2_versus_1512_compounds.html is a dynamic HTML file. It is an enrichment analyses show that within clusters 1 and 2, acyl carrier proteins (ACPs) are particularly overrepresented. Cf figure 6B of paper. Please note that some compounds or classes of compounds have several parents and will therefore be displayed several times in the graph. ontosunburst_heatmap_algae_clusters_1_and_2_versus_1512_compounds.tsv is a matrix TSV file, used to generate the HTML file above. It is an enrichment analyses show that within clusters 1 and 2, acyl carrier proteins (ACPs) are particularly overrepresented. Cf figure 6B of paper. pathway-tools-26.0-linux-64-tier1-install is the Pathway Tools 26.0 Linux installer used to reconstruct the algal and bacterial metabolic networks. It took either a GenBank file or Fasta nucleotidic file and a GFF or a PF file. The PF format was developed in-house by the SRI (Stanford Research Institute). Pathway Tools is available under this license https://biocyc.org/download.shtml. phylogenetic_trees.zip is an archive which contains two phylogenetic trees in Newick format. all_mags_gtdbtk_bac120_msa_fasta_treefile.nwk is the phylogenetic tree of 1,085 bacterial MAGs, inferred from the maximum likelihood method. The maximum likelihood tree was constructed based on a concatenated alignment of 120 conserved bacterial marker proteins under an LG+F+I+G4 model of evolution and 1,000 ultrafast bootstrap replicates. Cf paper, Figure 2B. Phaeoexplorer_tree_24oct22_short_names.nwk is the phylogenetic tree of algae generated by Akita et al. (Mol Phylogenet Evol. 2022, https://doi.org/10.1016/j.ympev.2022.107408). All the algae in this phylogenetic tree were studied as part of Phaeoexplorer project (https://phaeoexplorer.sb-roscoff.fr/home/). Ribosomal_S11-t_class-MATRIX.csv is a matrix of relative abundances of bacterial classes across 68 algal microbiota based on ribosomal protein rpS11. This matrix was used to produce the Figure 2C, cf. Paper. The 68 algae come from the Phaeoexplorer project (https://phaeoexplorer.sb-roscoff.fr/home/).