{ "type": "genome", "identifier": "GCA_944376415.1", "organism": "Candidatus Mediterraneibacter merdigallinarum", "title": "Candidatus Mediterraneibacter merdigallinarum", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Institut National pour la Recherche Agronomique (FRANCE)", "publication": [ {} ], "properties": { "assembly_accession": "GCA_944376415.1", "bioproject": "PRJEB53581", "biosample": "SAMEA110135442", "wgs_master": "CALWCN000000000.1", "refseq_category": "na", "taxid": "2838677", "species_taxid": "2838677", "organism_name": "Candidatus Mediterraneibacter merdigallinarum", "infraspecific_name": "", "isolate": "BRZ_HN__bin2", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/30", "asm_name": "BRZ_HN__bin2", "submitter": "Institut National pour la Recherche Agronomique (FRANCE)", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/944/376/415/GCA_944376415.1_BRZ_HN_bin2", "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": "2022-06-30", "dateModified": "2022-06-30", "datePublished": "2022-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Candidatus Mediterraneibacter merdigallinarum" ], "sample_taxid": [ "2838677" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "0.754 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.42, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2646111", "Number of Sequences": "50", "Longest Sequences (bp)": "133074", "N50 (bp)": "71071", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "46.6", "Number of CDSs": "2431", "Average Protein Length": "320.9", "Coding Ratio (%)": "88.4", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "2" }, "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": 79.3703, "matched_fragments": 292, "total_fragments": 860, "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": 77.7171, "matched_fragments": 178, "total_fragments": 860, "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": 77.7122, "matched_fragments": 175, "total_fragments": 860, "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": 77.6693, "matched_fragments": 178, "total_fragments": 860, "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": 77.5976, "matched_fragments": 162, "total_fragments": 860, "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": 77.5372, "matched_fragments": 159, "total_fragments": 860, "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": 77.5251, "matched_fragments": 161, "total_fragments": 860, "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": 77.5219, "matched_fragments": 164, "total_fragments": 860, "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": 77.4769, "matched_fragments": 167, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprococcus comes", "strain": "strain=ATCC 27758", "accession": "GCA_025149785.1", "taxid": 410072, "species_taxid": 410072, "relation_to_type": "type", "validated": true, "ani": 76.8017, "matched_fragments": 86, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] hylemonae", "strain": "strain=DSM 15053", "accession": "GCA_008281175.1", "taxid": 89153, "species_taxid": 89153, "relation_to_type": "type", "validated": true, "ani": 76.7868, "matched_fragments": 74, "total_fragments": 860, "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": 76.7497, "matched_fragments": 100, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] hylemonae", "strain": "strain=DSM 15053", "accession": "GCA_000156515.1", "taxid": 89153, "species_taxid": 89153, "relation_to_type": "type", "validated": true, "ani": 76.6941, "matched_fragments": 76, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hespellia stercorisuis", "strain": "strain=DSM 15480", "accession": "GCA_900142165.1", "taxid": 180311, "species_taxid": 180311, "relation_to_type": "type", "validated": true, "ani": 76.6625, "matched_fragments": 94, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia caecimuris", "strain": "strain=DSM 29492", "accession": "GCA_024622975.1", "taxid": 1796615, "species_taxid": 1796615, "relation_to_type": "type", "validated": true, "ani": 76.5526, "matched_fragments": 82, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1 82", "accession": "GCA_025151715.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 76.3374, "matched_fragments": 50, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_000156535.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 76.3293, "matched_fragments": 50, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_900537995.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 76.3066, "matched_fragments": 51, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprococcus phoceensis", "strain": "strain=Marseille-P3062", "accession": "GCA_900104635.1", "taxid": 1870993, "species_taxid": 1870993, "relation_to_type": "type", "validated": true, "ani": 76.199, "matched_fragments": 74, "total_fragments": 860, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.42, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_019117305.1", "gtdb_species": "s__Mediterraneibacter merdigallinarum", "ani": 97.8082, "matched_fragments": 602, "total_fragments": 860, "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": "conclusive" }, { "accession": "GCA_019112765.1", "gtdb_species": "s__Mediterraneibacter norwichensis", "ani": 89.6414, "matched_fragments": 586, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "97.86", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.76", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900553885.1", "gtdb_species": "s__Mediterraneibacter sp900553885", "ani": 86.584, "matched_fragments": 616, "total_fragments": 860, "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_019115385.1", "gtdb_species": "s__Mediterraneibacter avicola", "ani": 81.7899, "matched_fragments": 475, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019119745.1", "gtdb_species": "s__Mediterraneibacter gallistercoris", "ani": 79.314, "matched_fragments": 231, "total_fragments": 860, "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_019119995.1", "gtdb_species": "s__Mediterraneibacter faecavium", "ani": 79.164, "matched_fragments": 267, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019118885.1", "gtdb_species": "s__Mediterraneibacter surreyensis", "ani": 79.079, "matched_fragments": 255, "total_fragments": 860, "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": "-" }, { "accession": "GCF_900120155.1", "gtdb_species": "s__Mediterraneibacter sp900120155", "ani": 78.554, "matched_fragments": 258, "total_fragments": 860, "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_904419285.1", "gtdb_species": "s__Mediterraneibacter caccogallinarum", "ani": 78.4006, "matched_fragments": 288, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_019115765.1", "gtdb_species": "s__Mediterraneibacter stercoripullorum", "ani": 78.383, "matched_fragments": 254, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019116885.1", "gtdb_species": "s__Mediterraneibacter pullistercoris", "ani": 78.3445, "matched_fragments": 225, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019114745.1", "gtdb_species": "s__Mediterraneibacter colneyensis", "ani": 78.2701, "matched_fragments": 196, "total_fragments": 860, "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": 78.1953, "matched_fragments": 235, "total_fragments": 860, "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_019120595.1", "gtdb_species": "s__Mediterraneibacter tabaqchaliae", "ani": 78.0003, "matched_fragments": 220, "total_fragments": 860, "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": "GCF_000153925.1", "gtdb_species": "s__Mediterraneibacter torques", "ani": 77.7074, "matched_fragments": 174, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCA_900544395.1", "gtdb_species": "s__Ruminococcus_B sp900544395", "ani": 77.2417, "matched_fragments": 142, "total_fragments": 860, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "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 merdigallinarum" ], "_genome_taxon": [ "Candidatus", "Mediterraneibacter", "merdigallinarum", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Mediterraneibacter", "s__Mediterraneibacter merdigallinarum", "Bacteria", "Bacillota", "A", "Clostridia", "Lachnospirales", "Lachnospiraceae", "Mediterraneibacter", "Mediterraneibacter", "merdigallinarum" ], "_meo": [ { "id": "MEO_0000460", "label": "cecum" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }