Genome-scale community modelling reveals key metabolic cross-feedings in epipelagic bacterioplankton communities (Supplementary Materials)

A comprehensive catalog of 19,791 marine prokaryotic isolates (WGS), single-amplified genomes (SAGs) and metagenomic-assembled genomes (MAGs) compiled from MarRef v4.0 (N=943, mostly high-quality WGS), MarDB v4.0 (N=12,963), and the aquatic representative genomes from the ProGenomes database v1.0 (N=566). This collection of well-documented genomes was complemented by 5,319 MAGs assembled from four distinct studies, namely: Parks et al. 2017 (DOI; N=1,765; downloaded from EBI), Tully et al. 2017/2018 (DOI and DOI; N=2,597; downloaded from EBI), and Delmont et al. 2018 (DOI; N=957; downloaded from FIGSHARE). The Parks et al. study contained genomes reconstructed from non-marine biomes. Thus, a selection of 1,765 genomes was extracted by searching for specific keywords: “tara|marine|sea|ocean|mediterranean” (case insensitive). Note that depending on their study of origin, included MAGs may have been reconstructed using different assembling and binning methods.

The archive includes:

• a metadata file describing the quality and redundancy of the genomes named `EcoSysMic_metadata.tsv`
• sequences of the 19,791 (redundant) genomes in `All/WGS`
• companion files in `All/Data` and `dRep95/Data` (see Methods in the associated paper), including
  • predicted CDS and EggNOG functional annotations
  • predicted GTDB taxonomy
  • CarveMe reconstructed metabolic models and their MEMOTE quality

The 7,658 non-redundant species-level genomes (delineated by a 95% ANI threshold over 60% of genome length) that were used in the associated paper are defined by the column `is_drep95` in the metadata file.