Supplementary dara for "Genome-inspired cultivation of bacteria from deep-sea sponge Geodia barretti"

Supplementary data accompanying the chapter "Targeted cultivation of Geodia barretti-associated bacteria informed by metagenomic predictions and host metabolomics". The deposit contains four .ods supplementary-table workbooks (33 sheets total) and five archives with the underlying sequence data, assemblies, and genome-scale metabolic models. Abstract Dominant bacterial symbionts of marine sponges encode rich biosynthetic potential but have resisted cultivation for decades. We mined 43 metagenome-assembled genomes (MAGs) from the deep-sea sponge Geodia barretti for degradation pathways of sponge tissue-accumulated metabolites and designed targeted oligotrophic media accordingly. Twelve months of cultivation at 4°C yielded 263 isolates spanning Actinomycetota, Bacteroidota, and Pseudomonadota; incubation time, rather than carbon source, drove isolation outcomes. Nine previously undescribed species were recovered, yet dominant symbiont lineages remained recalcitrant. Genome-scale metabolic modelling of a biosynthetically rich Acidobacteriota MAG (Marinacidobacterium sp.) indicated extensive auxotrophies in lysine, heme, and pyrimidine biosynthesis that carbon provision alone cannot rescue. Contents Supplementary tables (.ods) File Sup. Tables Scope metagenomics_g.barretti.ods 1–4 MAGs recovered from the G. barretti metagenome (43 MAGs): CheckM2 quality, antiSMASH BGC counts, GTDB-Tk taxonomy, Phydon predicted maximum growth. chapter3_data.ods 5–6 Cultivation outcome for the 263 isolates (genus-level 16S taxonomy, medium, time-point) and the full media-recipe table. 16_isolates_metadata.ods 7–20 Whole-genome data for the 16 sequenced isolates: read stats, assembly stats, CheckM/CheckM2/BUSCO quality, GTDB-Tk classification, and per-isolate dbCAN3 CAZyme annotations. Media_definitions_modelling.ods 21–33 COBRA medium definitions used for gap-filling, predicted growth rates, pFBA exchange fluxes, gap-filling statistics, pathway-enrichment results for Marinacidobacterium-unique essential reactions, and the gapseq transporter table for Marinacidobacterium sp. Data archives File Contents g.barretti_mags.zip Forty-three metagenome-assembled genomes from G. barretti (Gb6), with PGAP-style annotation outputs per MAG (.fna, .gbk, .gff, .ffn, .tsv, .sqn, log files). Used as input for taxonomy, growth-rate prediction, BGC mining, and metabolic modelling. 16_isolates_genomes.zip De novo Illumina assemblies (FASTA) of the 16 sequenced isolates listed in Table 4.1. Filenames correspond to working IDs in Sup. Table 7. models.zip Genome-scale metabolic models reconstructed with gapseq v1.4.0 for the 16 isolates and for Marinacidobacterium sp. on each substrate-specific medium (base / taurine / carnitine / creatinine / chitin / xylan). Each model is provided in SBML (.xml) and R serialised (.RDS) form, with the gapseq build log. Sanger_sequencing_ab1_files.zip Raw Sanger trace files (.ab1, 27F primer) for 16S rRNA gene amplicons of all 263 picked colonies underlying Sup. Table 5. picked_up_taurine_isolates_ab1.zip Raw Sanger traces (.ab1) for the parallel taurine-medium picks used to obtain representative isolates for WGS (see Isolate selection in Methods). Notes Each sheet in the .ods files maps to a Supplementary Table referenced in the main text; o MAG and isolate raw sequencing reads (Illumina, Nanopore) are deposited under the BioProject referenced in the main text; this Zenodo record provides the derived assemblies, annotations, and models. How to cite Please cite the associated chapter/manuscript alongside this Zenodo record. A BibTeX/RIS entry is available via the "Export" panel on this page.