Blanes Bay Microbial Observatory (BBMO) - Prokaryotic MAGs catalog v1

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Introduction
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This repository contains the first version (v1) of the prokaryotic metagenome-assembled genomes (MAGs) reconstructed from the Blanes Bay Microbial Observatory (BBMO) time series in the Northwestern Mediterranean Sea (http://bbmo.icm.csic.es). It includes genome (MAG) sequences, functional annotations, and abundance tables for MAGs recovered from 7 years of monthly metagenomic data (2009-2015), with abundances analyzed across 15 years (2008–2022, 175 monthly samples).

Briefly, seven years of metagenomic data were coassembled into four groups based on their genomic similarity (computed with Simka) with Megahit v.1.0. A total of 2311 MAGs were obtained by refining with MetaWRAP the MAGs produced during the binning of each coassembly with MetaBat2, Maxbin, and Concoct. A dereplicated set set consisting of 1,505 MAGs was obtained by dereplicating the previous MAGs using dRep at 99% identity (ANI).

The abundance of each MAG across the 15 years of metagenomic data was computed by a competitive mapping method with CoverM, only counting reads with at least 95% identity with the reference and 80% read coverage. Counts, RPKM, TPM, and number of covered bases are reported in the tables. 

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Location
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BBMO MAGs catalog versions will be available on the web only under the current ZENODO repository: 10.5281/zenodo.17159964

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Repository Structure and Format
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BBMO_MAGs_v1/
├── fasta/
│   └── [2311 individual MAG fasta files: bin.GX.YYY.fasta]
├── annotation/
│   ├── annotations_cazy/
│   ├── annotations_gff/
│   ├── annotations_ko/
│   ├── annotations_pfam/
│   ├── genome_genes/
│   ├── genome_proteins/
│   ├── ko_classify/
│   ├── cazy_frequency_table.tsv
│   ├── ko_frequency_table.tsv
│   └── pfam_frequency_table.tsv
├── abundance_tables/
│   ├── ReadCounts.1505MAGs.95id.80rcov.tsv
│   ├── RPKM.1505MAGs.95id.80rcov.tsv
│   ├── TPM.1505MAGs.95id.80rcov.tsv
│   └── CoveredBases.1505MAGs.95id.80rcov.tsv
│   ├── ReadCounts.2311MAGs.95id.80rcov.tsv
│   ├── RPKM.2311MAGs.95id.80rcov.tsv
│   ├── TPM.2311MAGs.95id.80rcov.tsv
│   └── CoveredBases.2311MAGs.95id.80rcov.tsv
├── final_genomes_nondereplicated_list.2311MAGs.txt
└── final_genomes_dereplicated_list.1505MAGs.txt

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Directory Descriptions
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1. fasta/
   - Contains the 2311 original high-quality MAGs in FASTA format (not dereplicated, > 50% completeness, < 10% contamination).
   - Filenames follow: bin.GX.YYY
     - GX = co-assembly group (G1 to G4)
     - YYY = unique numeric identifier within each co-assembly group

2. annotation/
   - Functional annotations generated using EnrichM for the 2311 MAGs.
   - Includes:
     - Gene predictions (GFF, nucleotide sequences, protein sequences)
     - Functional annotations (CAZy, KO, Pfam)
     - Frequency tables per function (e.g., KO, CAZy, Pfam)
   - Note: MAG identifiers in this directory follow the format gX.bin.YYY, but correspond to the same MAGs.
     - gX = co-assembly group (g1 to g4)
     - YYY = unique numeric identifier within each co-assembly group

3. abundance_tables/
   - Abundance data across 175 monthly BBMO samples (15 years) for both sets (non- and dereplicated MAGs).
   - Tables include:
     - `ReadCounts.*MAGs.95id.80rcov.tsv`: raw read counts per MAG
     - `RPKM.*MAGs.95id.80rcov.tsv`: reads per kilobase of genome per million of mapped reads
     - `TPM.*MAGs.95id.80rcov.tsv`: transcripts per million
     - `CoveredBases.*MAGs.95id.80rcov.tsv`: number of bases covered per MAG and sample

4. final_genomes_dereplicated_list.*MAGs.txt
   - Metadata table of the 1505 dereplicated MAGs (99% ANI), including:
     - Completeness
     - Contamination
     - Genome size
     - N50
     - GC content
     - Taxonomic classification (GTDBtk release202)
   - Metadata table of the 2311 non-dereplicated MAGs, including:
     - Completeness
     - Contamination
     - Genome size
     - GC content
     - N50
     - Taxonomic classification (GTDBtk release 202)

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Future format changes
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No major changes are expected for the current MAG catalog version. New versions should include updated versions of annotations or new set of MAGs with additional genomes, numbered as new catalog versions. 

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Contact information
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For any questions, please get in touch with Dr. Francisco Latorre `latorre@icm.csic.es` or Dr. Ramiro Logares `ramiro.logares@icm.csic.es`

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Acknowledgements
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This work is an effort of the Ecology of Marine Microbes (EMM) group at the Institut de Ciències del Mar, Barcelona, Spain (ICM - CSIC). All the bioinformatics analyses were performed at the Marine Bioinformatics Core Service ICM - CSIC (MARBITS).

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Copyright notice
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Blanes Bay Microbial Observatory (BBMO) - Prokaryotic MAGs catalog Copyright (C) 2025.

This catalog is provided “as is” and without any warranty of any kind, of openly available for non-commercial purposes. You can redistribute and/or modify it as you wish, under the terms of the Creative Commons Attribution Share Alike 4.0 International license. 

For commercial purposes, please contact us.