{ "type": "genome", "identifier": "GCA_019118545.1", "organism": "Candidatus Mediterraneibacter merdavium", "title": "Candidatus Mediterraneibacter merdavium", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Quadram Institutte", "publication": [ {} ], "properties": { "assembly_accession": "GCA_019118545.1", "bioproject": "PRJNA543206", "biosample": "SAMN15816660", "wgs_master": "DWYT00000000.1", "refseq_category": "na", "taxid": "2838676", "species_taxid": "2838676", "organism_name": "Candidatus Mediterraneibacter merdavium", "infraspecific_name": "", "isolate": "ChiBcolR7-8672", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/05", "asm_name": "ASM1911854v1", "submitter": "Quadram Institutte", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/118/545/GCA_019118545.1_ASM1911854v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-05", "dateModified": "2021-07-05", "datePublished": "2021-07-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Candidatus Mediterraneibacter merdavium" ], "sample_taxid": [ "2838676" ], "sample_host_organism": [ "Gallus gallus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "0.794 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 77.08, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2770301", "Number of Sequences": "168", "Longest Sequences (bp)": "107344", "N50 (bp)": "20714", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.6", "Number of CDSs": "2404", "Average Protein Length": "327.7", "Coding Ratio (%)": "85.3", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mediterraneibacter catenae", "strain": "strain=SW178", "accession": "GCA_008691045.1", "taxid": 2594882, "species_taxid": 2594882, "relation_to_type": "type", "validated": true, "ani": 78.6425, "matched_fragments": 241, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] torques", "strain": "strain=ATCC 27756", "accession": "GCA_000153925.1", "taxid": 33039, "species_taxid": 33039, "relation_to_type": "type", "validated": true, "ani": 77.7094, "matched_fragments": 149, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] lactaris", "strain": "strain=ATCC 29176", "accession": "GCA_025152405.1", "taxid": 46228, "species_taxid": 46228, "relation_to_type": "type", "validated": true, "ani": 77.6193, "matched_fragments": 123, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] lactaris", "strain": "strain=ATCC 29176", "accession": "GCA_000155205.1", "taxid": 46228, "species_taxid": 46228, "relation_to_type": "type", "validated": true, "ani": 77.6023, "matched_fragments": 123, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mediterraneibacter massiliensis", "strain": "strain=Marseille-P2086", "accession": "GCA_001487105.1", "taxid": 1720300, "species_taxid": 1720300, "relation_to_type": "type", "validated": true, "ani": 77.258, "matched_fragments": 109, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilistercora timonensis", "strain": "strain=Marseille-P3756", "accession": "GCA_900312975.1", "taxid": 2086584, "species_taxid": 2086584, "relation_to_type": "type", "validated": true, "ani": 77.1632, "matched_fragments": 98, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schaedlerella arabinosiphila", "strain": "strain=DSM 106076", "accession": "GCA_003885045.1", "taxid": 2044587, "species_taxid": 2044587, "relation_to_type": "type", "validated": true, "ani": 77.0553, "matched_fragments": 153, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea longicatena", "strain": "strain=DSM 13814", "accession": "GCA_025150085.1", "taxid": 88431, "species_taxid": 88431, "relation_to_type": "type", "validated": true, "ani": 76.9372, "matched_fragments": 63, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=JCM6515", "accession": "GCA_008121495.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8809, "matched_fragments": 130, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=ATCC 29149", "accession": "GCA_000169475.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8628, "matched_fragments": 131, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=ATCC 29149", "accession": "GCA_025152275.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "type", "validated": true, "ani": 76.8585, "matched_fragments": 135, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=ATCC 29149", "accession": "GCA_009831375.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8106, "matched_fragments": 133, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=ATCC 29149", "accession": "GCA_002959615.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8093, "matched_fragments": 131, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Muricomes intestini", "strain": "strain=DSM 29489", "accession": "GCA_004346165.1", "taxid": 1796634, "species_taxid": 1796634, "relation_to_type": "type", "validated": true, "ani": 76.6643, "matched_fragments": 66, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marvinbryantia formatexigens", "strain": "strain=I-52", "accession": "GCA_900102475.1", "taxid": 168384, "species_taxid": 168384, "relation_to_type": "type", "validated": true, "ani": 76.2048, "matched_fragments": 61, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marvinbryantia formatexigens", "strain": "strain=DSM 14469", "accession": "GCA_025148285.1", "taxid": 168384, "species_taxid": 168384, "relation_to_type": "type", "validated": true, "ani": 76.195, "matched_fragments": 61, "total_fragments": 836, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 77.08, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_019118545.1", "gtdb_species": "s__Mediterraneibacter merdavium", "ani": 100.0, "matched_fragments": 830, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "99.49", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_904418845.1", "gtdb_species": "s__Mediterraneibacter sp904418845", "ani": 85.5618, "matched_fragments": 546, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_900761655.1", "gtdb_species": "s__Mediterraneibacter sp900761655", "ani": 83.7435, "matched_fragments": 407, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_019117065.1", "gtdb_species": "s__Mediterraneibacter pullicola", "ani": 81.0978, "matched_fragments": 430, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.71", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002161355.1", "gtdb_species": "s__Mediterraneibacter caccavium", "ani": 80.0804, "matched_fragments": 350, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_019120595.1", "gtdb_species": "s__Mediterraneibacter tabaqchaliae", "ani": 79.4173, "matched_fragments": 292, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_019116185.1", "gtdb_species": "s__Mediterraneibacter stercorigallinarum", "ani": 78.8987, "matched_fragments": 267, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.63", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019112735.1", "gtdb_species": "s__Mediterraneibacter guildfordensis", "ani": 78.6532, "matched_fragments": 266, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_019114745.1", "gtdb_species": "s__Mediterraneibacter colneyensis", "ani": 78.341, "matched_fragments": 205, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019120275.1", "gtdb_species": "s__Mediterraneibacter excrementavium", "ani": 78.3281, "matched_fragments": 229, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_019119205.1", "gtdb_species": "s__Mediterraneibacter intestinavium", "ani": 78.3161, "matched_fragments": 232, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.10", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019118885.1", "gtdb_species": "s__Mediterraneibacter surreyensis", "ani": 78.2748, "matched_fragments": 266, "total_fragments": 836, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.76", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Mediterraneibacter", "s__Mediterraneibacter merdavium" ], "_genome_taxon": [ "Candidatus", "Mediterraneibacter", "merdavium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Mediterraneibacter", "s__Mediterraneibacter merdavium", "Bacteria", "Bacillota", "A", "Clostridia", "Lachnospirales", "Lachnospiraceae", "Mediterraneibacter", "Mediterraneibacter", "merdavium" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }