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Metadata and MAGs for "Global biosynthetic potential of Acidobacteriota" paper

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Autori principali:	Hrab, Pavlo, Zdouc, Mitja Maximilian, Terlouw, Barbara, Loureiro, Catarina, Schorn, Michelle A., de Ridder, Dick, Medema, Marnix H., Sipkema, Detmer
Natura:	Recurso digital
Pubblicazione:	Zenodo 2026
Soggetti:	Acidobacteria Acidobacteria/classification Acidobacteria/genetics Metagenome-assembled genomes
Accesso online:	Acceder al recurso
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_version_	1866901470538891264
author	Hrab, Pavlo Zdouc, Mitja Maximilian Terlouw, Barbara Loureiro, Catarina Schorn, Michelle A. de Ridder, Dick Medema, Marnix H. Sipkema, Detmer
author_facet	Hrab, Pavlo Zdouc, Mitja Maximilian Terlouw, Barbara Loureiro, Catarina Schorn, Michelle A. de Ridder, Dick Medema, Marnix H. Sipkema, Detmer
contents	<h1>Acidobacteriota MAGs and metadata</h1> <h2>Dataset contents</h2> <ul> <li><em>acido.mags.tar.gz</em> - 6,169 metagenome-assembled genomes (MAGs) of Acidobacteriota in FASTA format.</li> <li><em>metadata.tsv</em> - Tab-separated metadata table (6,169 rows, 54 columns) describing each MAG.</li> <li><em>environment_classification.png</em> - Environmental classification categories of the MAGs.</li> </ul> <h2>Column descriptions for metadata.tsv</h2> <h3>Genome identifier</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>record</code></td> <td>Unique genome identifier. Format depends on the source: NCBI Assembly accession (e.g., <code>GCA_000179915.2_ASM17991v2_genomic</code>), JGI taxon OID with bin number (e.g., <code>3300012889_2</code>), mOTUs-db genome name (e.g., <code>TARA_SAMEA2621099_MAG_00000082</code>), or sponge MAG label (e.g., <code>Aply16_bin.10.permissive</code>).</td> </tr> </tbody> </table> <h3>BGC annotations (antiSMASH)</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>bgc_category</code></td> <td>Semicolon-separated list of biosynthetic gene cluster (BGC) types detected by antiSMASH (e.g., <code>terpene;NRPS-like;T3PKS</code>).</td> </tr> <tr> <td><code>bgc_lengths</code></td> <td>Semicolon-separated list of BGC lengths in base pairs, in the same order as <code>bgc_category</code>.</td> </tr> <tr> <td><code>asmod_completeness</code></td> <td>Mean antiSMASH module completeness score across all detected BGCs (0–1).</td> </tr> <tr> <td><code>region_completeness</code></td> <td>Mean region completeness score across all detected BGC regions (0–1).</td> </tr> <tr> <td><code>candidate_completeness</code></td> <td>Mean candidate cluster completeness score (0–1).</td> </tr> <tr> <td><code>proto_cluster_completeness</code></td> <td>Mean proto-cluster completeness score (0–1).</td> </tr> <tr> <td><code>protocore_completeness</code></td> <td>Mean proto-core completeness score (0–1).</td> </tr> </tbody> </table> <h3>GTDB taxonomy</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>domain</code></td> <td>GTDB domain classification (all <code>d_Bacteria</code>).</td> </tr> <tr> <td><code>phylum</code></td> <td>GTDB phylum (all <code>p_Acidobacteriota</code>).</td> </tr> <tr> <td><code>class</code></td> <td>GTDB class (e.g., <code>c_Terriglobia</code>, <code>c_Vicinamibacteria</code>).</td> </tr> <tr> <td><code>order</code></td> <td>GTDB order (e.g., <code>o_Terriglobales</code>, <code>o_Bryobacterales</code>).</td> </tr> <tr> <td><code>family</code></td> <td>GTDB family (e.g., <code>f_Acidobacteriaceae</code>, <code>f_Koribacteraceae</code>).</td> </tr> <tr> <td><code>genus</code></td> <td>GTDB genus (e.g., <code>g_Edaphobacter</code>). Empty string if unclassified at this rank.</td> </tr> <tr> <td><code>species</code></td> <td>GTDB species (e.g., <code>s_Koribacter versatilis_A</code>). Empty string if unclassified at this rank.</td> </tr> </tbody> </table> <h3>Genome information</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>genome</code></td> <td>Genome FASTA filename within the archive (e.g., <code>637000001.fna</code>).</td> </tr> <tr> <td><code>secondary_cluster</code></td> <td>dRep secondary cluster assignment (e.g., <code>778_1</code>). Groups genomes at ~95% ANI.</td> </tr> <tr> <td><code>drep_cluster_size</code></td> <td>Number of genomes in the dRep secondary cluster.</td> </tr> <tr> <td><code>spec_met_ratio</code></td> <td>Specialized metabolite ratio: proportion of total CDS devoted to BGCs.</td> </tr> </tbody> </table> <h3>Genome quality metrics (CheckM2)</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>completeness</code></td> <td>CheckM2 estimated genome completeness (%).</td> </tr> <tr> <td><code>contamination</code></td> <td>CheckM2 estimated genome contamination (%).</td> </tr> <tr> <td><code>coding_density</code></td> <td>Fraction of the genome that is protein-coding.</td> </tr> <tr> <td><code>contig_n50</code></td> <td>Contig N50 in base pairs.</td> </tr> <tr> <td><code>avg_gene_length</code></td> <td>Average predicted gene length in base pairs.</td> </tr> <tr> <td><code>genome_size</code></td> <td>Total genome assembly size in base pairs.</td> </tr> <tr> <td><code>gc_content</code></td> <td>GC content as a proportion (0–1).</td> </tr> <tr> <td><code>total_cds</code></td> <td>Total number of predicted protein-coding sequences.</td> </tr> <tr> <td><code>total_contigs</code></td> <td>Total number of contigs in the assembly.</td> </tr> <tr> <td><code>max_contig_length</code></td> <td>Length of the longest contig in base pairs.</td> </tr> </tbody> </table> <h3>Environmental classification</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>broad_environment</code></td> <td>High-level environment: <code>terrestrial</code>, <code>aquatic</code>, or <code>Unknown</code>.</td> </tr> <tr> <td><code>narrow_environment</code></td> <td>Intermediate environment: <code>soil</code>, <code>freshwater</code>, <code>marine</code>, <code>plants</code>, <code>rhizosphere</code>, <code>other organisms</code>, or <code>Unknown</code>.</td> </tr> <tr> <td><code>specific_environment</code></td> <td>Detailed environment annotation where available (e.g., <code>wastewater</code>, <code>peatland</code>), or <code>Unknown</code>.</td> </tr> <tr> <td><code>host_associated</code></td> <td>Whether the genome is from a host-associated environment: <code>host-associated</code> or <code>Unknown</code>.</td> </tr> <tr> <td><code>sediment</code></td> <td>Whether the genome is from a sediment environment: <code>sediment</code> or <code>Unknown</code>.</td> </tr> </tbody> </table> <p><strong>For the environment classification, please see the environment_classification.png figure.</strong></p> <h3>BGC counts by type</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>bgc_count</code></td> <td>Total number of BGCs detected per genome.</td> </tr> <tr> <td><code>NRPS</code></td> <td>Number of non-ribosomal peptide synthetase (NRPS and NRPS-like) BGCs.</td> </tr> <tr> <td><code>terpene</code></td> <td>Number of terpene BGCs.</td> </tr> <tr> <td><code>PKS</code></td> <td>Number of polyketide synthase (PKS) BGCs (T1PKS, T3PKS, etc.).</td> </tr> <tr> <td><code>saccharide</code></td> <td>Number of saccharide BGCs.</td> </tr> <tr> <td><code>hybrid</code></td> <td>Number of hybrid BGCs.</td> </tr> <tr> <td><code>other</code></td> <td>Number of BGCs not classified into the above categories.</td> </tr> <tr> <td><code>RiPP</code></td> <td>Number of ribosomally synthesized and post-translationally modified peptide (RiPP) BGCs.</td> </tr> <tr> <td><code>halogenated</code></td> <td>Number of halogenated BGCs.</td> </tr> </tbody> </table> <h3>BGC ratios by type</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>RiPP_ratio</code></td> <td>Fraction of total BGCs that are RiPPs.</td> </tr> <tr> <td><code>halogenated_ratio</code></td> <td>Fraction of total BGCs that are halogenated.</td> </tr> <tr> <td><code>NRPS_ratio</code></td> <td>Fraction of total BGCs that are NRPS/NRPS-like.</td> </tr> <tr> <td><code>terpene_ratio</code></td> <td>Fraction of total BGCs that are terpenes.</td> </tr> <tr> <td><code>PKS_ratio</code></td> <td>Fraction of total BGCs that are PKS.</td> </tr> <tr> <td><code>saccharide_ratio</code></td> <td>Fraction of total BGCs that are saccharides.</td> </tr> <tr> <td><code>hybrid_ratio</code></td> <td>Fraction of total BGCs that are hybrids.</td> </tr> <tr> <td><code>other_ratio</code></td> <td>Fraction of total BGCs in the "other" category.</td> </tr> </tbody> </table> <h3>Source provenance</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>source</code></td> <td>Metadata origin for the genome: <code>JGI</code> (3,132 genomes from IMG/M), <code>NCBI</code> (1,638 genomes from NCBI Assembly), <code>mOTUs-db</code> (1,278 genomes from the mOTUs database), or <code>Sponge</code> (121 genomes from a local sponge metagenome collection).</td> </tr> <tr> <td><code>project</code></td> <td>Project or study identifier. Contains BioProject accession for NCBI genomes (e.g., <code>PRJNA48971</code>), IMG taxon OID for JGI genomes (e.g., <code>3300012889</code>), or publication URL for mOTUs-db genomes. Empty for Sponge genomes.</td> </tr> <tr> <td><code>sample</code></td> <td>BioSample accession for NCBI genomes (e.g., <code>SAMN00100755</code>). Empty for all other sources.</td> </tr> </tbody> </table>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_18936217
institution	Zenodo
language
publishDate	2026
publisher	Zenodo
record_format	zenodo
spellingShingle	Metadata and MAGs for "Global biosynthetic potential of Acidobacteriota" paper Hrab, Pavlo Zdouc, Mitja Maximilian Terlouw, Barbara Loureiro, Catarina Schorn, Michelle A. de Ridder, Dick Medema, Marnix H. Sipkema, Detmer Acidobacteria Acidobacteria/classification Acidobacteria/genetics Metagenome-assembled genomes <h1>Acidobacteriota MAGs and metadata</h1> <h2>Dataset contents</h2> <ul> <li><em>acido.mags.tar.gz</em> - 6,169 metagenome-assembled genomes (MAGs) of Acidobacteriota in FASTA format.</li> <li><em>metadata.tsv</em> - Tab-separated metadata table (6,169 rows, 54 columns) describing each MAG.</li> <li><em>environment_classification.png</em> - Environmental classification categories of the MAGs.</li> </ul> <h2>Column descriptions for metadata.tsv</h2> <h3>Genome identifier</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>record</code></td> <td>Unique genome identifier. Format depends on the source: NCBI Assembly accession (e.g., <code>GCA_000179915.2_ASM17991v2_genomic</code>), JGI taxon OID with bin number (e.g., <code>3300012889_2</code>), mOTUs-db genome name (e.g., <code>TARA_SAMEA2621099_MAG_00000082</code>), or sponge MAG label (e.g., <code>Aply16_bin.10.permissive</code>).</td> </tr> </tbody> </table> <h3>BGC annotations (antiSMASH)</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>bgc_category</code></td> <td>Semicolon-separated list of biosynthetic gene cluster (BGC) types detected by antiSMASH (e.g., <code>terpene;NRPS-like;T3PKS</code>).</td> </tr> <tr> <td><code>bgc_lengths</code></td> <td>Semicolon-separated list of BGC lengths in base pairs, in the same order as <code>bgc_category</code>.</td> </tr> <tr> <td><code>asmod_completeness</code></td> <td>Mean antiSMASH module completeness score across all detected BGCs (0–1).</td> </tr> <tr> <td><code>region_completeness</code></td> <td>Mean region completeness score across all detected BGC regions (0–1).</td> </tr> <tr> <td><code>candidate_completeness</code></td> <td>Mean candidate cluster completeness score (0–1).</td> </tr> <tr> <td><code>proto_cluster_completeness</code></td> <td>Mean proto-cluster completeness score (0–1).</td> </tr> <tr> <td><code>protocore_completeness</code></td> <td>Mean proto-core completeness score (0–1).</td> </tr> </tbody> </table> <h3>GTDB taxonomy</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>domain</code></td> <td>GTDB domain classification (all <code>d_Bacteria</code>).</td> </tr> <tr> <td><code>phylum</code></td> <td>GTDB phylum (all <code>p_Acidobacteriota</code>).</td> </tr> <tr> <td><code>class</code></td> <td>GTDB class (e.g., <code>c_Terriglobia</code>, <code>c_Vicinamibacteria</code>).</td> </tr> <tr> <td><code>order</code></td> <td>GTDB order (e.g., <code>o_Terriglobales</code>, <code>o_Bryobacterales</code>).</td> </tr> <tr> <td><code>family</code></td> <td>GTDB family (e.g., <code>f_Acidobacteriaceae</code>, <code>f_Koribacteraceae</code>).</td> </tr> <tr> <td><code>genus</code></td> <td>GTDB genus (e.g., <code>g_Edaphobacter</code>). Empty string if unclassified at this rank.</td> </tr> <tr> <td><code>species</code></td> <td>GTDB species (e.g., <code>s_Koribacter versatilis_A</code>). Empty string if unclassified at this rank.</td> </tr> </tbody> </table> <h3>Genome information</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>genome</code></td> <td>Genome FASTA filename within the archive (e.g., <code>637000001.fna</code>).</td> </tr> <tr> <td><code>secondary_cluster</code></td> <td>dRep secondary cluster assignment (e.g., <code>778_1</code>). Groups genomes at ~95% ANI.</td> </tr> <tr> <td><code>drep_cluster_size</code></td> <td>Number of genomes in the dRep secondary cluster.</td> </tr> <tr> <td><code>spec_met_ratio</code></td> <td>Specialized metabolite ratio: proportion of total CDS devoted to BGCs.</td> </tr> </tbody> </table> <h3>Genome quality metrics (CheckM2)</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>completeness</code></td> <td>CheckM2 estimated genome completeness (%).</td> </tr> <tr> <td><code>contamination</code></td> <td>CheckM2 estimated genome contamination (%).</td> </tr> <tr> <td><code>coding_density</code></td> <td>Fraction of the genome that is protein-coding.</td> </tr> <tr> <td><code>contig_n50</code></td> <td>Contig N50 in base pairs.</td> </tr> <tr> <td><code>avg_gene_length</code></td> <td>Average predicted gene length in base pairs.</td> </tr> <tr> <td><code>genome_size</code></td> <td>Total genome assembly size in base pairs.</td> </tr> <tr> <td><code>gc_content</code></td> <td>GC content as a proportion (0–1).</td> </tr> <tr> <td><code>total_cds</code></td> <td>Total number of predicted protein-coding sequences.</td> </tr> <tr> <td><code>total_contigs</code></td> <td>Total number of contigs in the assembly.</td> </tr> <tr> <td><code>max_contig_length</code></td> <td>Length of the longest contig in base pairs.</td> </tr> </tbody> </table> <h3>Environmental classification</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>broad_environment</code></td> <td>High-level environment: <code>terrestrial</code>, <code>aquatic</code>, or <code>Unknown</code>.</td> </tr> <tr> <td><code>narrow_environment</code></td> <td>Intermediate environment: <code>soil</code>, <code>freshwater</code>, <code>marine</code>, <code>plants</code>, <code>rhizosphere</code>, <code>other organisms</code>, or <code>Unknown</code>.</td> </tr> <tr> <td><code>specific_environment</code></td> <td>Detailed environment annotation where available (e.g., <code>wastewater</code>, <code>peatland</code>), or <code>Unknown</code>.</td> </tr> <tr> <td><code>host_associated</code></td> <td>Whether the genome is from a host-associated environment: <code>host-associated</code> or <code>Unknown</code>.</td> </tr> <tr> <td><code>sediment</code></td> <td>Whether the genome is from a sediment environment: <code>sediment</code> or <code>Unknown</code>.</td> </tr> </tbody> </table> <p><strong>For the environment classification, please see the environment_classification.png figure.</strong></p> <h3>BGC counts by type</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>bgc_count</code></td> <td>Total number of BGCs detected per genome.</td> </tr> <tr> <td><code>NRPS</code></td> <td>Number of non-ribosomal peptide synthetase (NRPS and NRPS-like) BGCs.</td> </tr> <tr> <td><code>terpene</code></td> <td>Number of terpene BGCs.</td> </tr> <tr> <td><code>PKS</code></td> <td>Number of polyketide synthase (PKS) BGCs (T1PKS, T3PKS, etc.).</td> </tr> <tr> <td><code>saccharide</code></td> <td>Number of saccharide BGCs.</td> </tr> <tr> <td><code>hybrid</code></td> <td>Number of hybrid BGCs.</td> </tr> <tr> <td><code>other</code></td> <td>Number of BGCs not classified into the above categories.</td> </tr> <tr> <td><code>RiPP</code></td> <td>Number of ribosomally synthesized and post-translationally modified peptide (RiPP) BGCs.</td> </tr> <tr> <td><code>halogenated</code></td> <td>Number of halogenated BGCs.</td> </tr> </tbody> </table> <h3>BGC ratios by type</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>RiPP_ratio</code></td> <td>Fraction of total BGCs that are RiPPs.</td> </tr> <tr> <td><code>halogenated_ratio</code></td> <td>Fraction of total BGCs that are halogenated.</td> </tr> <tr> <td><code>NRPS_ratio</code></td> <td>Fraction of total BGCs that are NRPS/NRPS-like.</td> </tr> <tr> <td><code>terpene_ratio</code></td> <td>Fraction of total BGCs that are terpenes.</td> </tr> <tr> <td><code>PKS_ratio</code></td> <td>Fraction of total BGCs that are PKS.</td> </tr> <tr> <td><code>saccharide_ratio</code></td> <td>Fraction of total BGCs that are saccharides.</td> </tr> <tr> <td><code>hybrid_ratio</code></td> <td>Fraction of total BGCs that are hybrids.</td> </tr> <tr> <td><code>other_ratio</code></td> <td>Fraction of total BGCs in the "other" category.</td> </tr> </tbody> </table> <h3>Source provenance</h3> <table> <tbody> <tr> <th>Column</th> <th>Description</th> </tr> <tr> <td><code>source</code></td> <td>Metadata origin for the genome: <code>JGI</code> (3,132 genomes from IMG/M), <code>NCBI</code> (1,638 genomes from NCBI Assembly), <code>mOTUs-db</code> (1,278 genomes from the mOTUs database), or <code>Sponge</code> (121 genomes from a local sponge metagenome collection).</td> </tr> <tr> <td><code>project</code></td> <td>Project or study identifier. Contains BioProject accession for NCBI genomes (e.g., <code>PRJNA48971</code>), IMG taxon OID for JGI genomes (e.g., <code>3300012889</code>), or publication URL for mOTUs-db genomes. Empty for Sponge genomes.</td> </tr> <tr> <td><code>sample</code></td> <td>BioSample accession for NCBI genomes (e.g., <code>SAMN00100755</code>). Empty for all other sources.</td> </tr> </tbody> </table>
title	Metadata and MAGs for "Global biosynthetic potential of Acidobacteriota" paper
topic	Acidobacteria Acidobacteria/classification Acidobacteria/genetics Metagenome-assembled genomes
url	https://doi.org/10.5281/zenodo.18936217