{ "type": "genome", "identifier": "GCF_020687545.1", "organism": "Ruminococcus turbiniformis", "title": "Ruminococcus turbiniformis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "RWTH Aachen University Hospital", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020687545.1", "bioproject": "PRJNA224116", "biosample": "SAMN22081872", "wgs_master": "JAJEQX000000000.1", "refseq_category": "reference genome", "taxid": "2881258", "species_taxid": "2881258", "organism_name": "Ruminococcus turbiniformis", "infraspecific_name": "strain=CLA-AA-H200", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/31", "asm_name": "ASM2068754v1", "asm_submitter": "RWTH Aachen University Hospital", "gbrs_paired_asm": "GCA_020687545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/687/545/GCF_020687545.1_ASM2068754v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3813516", "genome_size_ungapped": "3813516", "gc_percent": "49.000000", "replicon_count": "0", "scaffold_count": "94", "contig_count": "94", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020687545.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3706", "protein_coding_gene_count": "3565", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-31", "dateModified": "2021-10-31", "datePublished": "2021-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Ruminococcus turbiniformis" ], "sample_taxid": [ "2881258" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Aachen" ], "sample_host_location_id": [], "data_size": "1.087 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3813516", "Number of Sequences": "94", "Longest Sequences (bp)": "244676", "N50 (bp)": "92015", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.2", "Number of CDSs": "3642", "Average Protein Length": "309.7", "Coding Ratio (%)": "88.7", "Number of rRNAs": "1", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Massilistercora timonensis", "strain": "strain=Marseille-P3756", "accession": "GCA_900312975.1", "taxid": 2086584, "species_taxid": 2086584, "relation_to_type": "type", "validated": true, "ani": 82.993, "matched_fragments": 175, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mediterraneibacter catenae", "strain": "strain=SW178", "accession": "GCA_008691045.1", "taxid": 2594882, "species_taxid": 2594882, "relation_to_type": "type", "validated": true, "ani": 79.7397, "matched_fragments": 349, "total_fragments": 1220, "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": 78.4657, "matched_fragments": 158, "total_fragments": 1220, "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": 78.4601, "matched_fragments": 160, "total_fragments": 1220, "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": 78.4398, "matched_fragments": 184, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sellimonas caecigallum", "strain": "strain=SW451", "accession": "GCA_019754295.1", "taxid": 2592333, "species_taxid": 2592333, "relation_to_type": "type", "validated": true, "ani": 77.943, "matched_fragments": 112, "total_fragments": 1220, "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": 77.9316, "matched_fragments": 163, "total_fragments": 1220, "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": 77.9302, "matched_fragments": 165, "total_fragments": 1220, "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": 77.9212, "matched_fragments": 162, "total_fragments": 1220, "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": 77.9145, "matched_fragments": 167, "total_fragments": 1220, "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": 77.7309, "matched_fragments": 146, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sporofaciens musculi", "strain": "strain=WCA-9-b2", "accession": "GCA_009830285.1", "taxid": 2681861, "species_taxid": 2681861, "relation_to_type": "type", "validated": true, "ani": 77.5098, "matched_fragments": 85, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea formicigenerans", "strain": "strain=ATCC 27755", "accession": "GCA_000169235.1", "taxid": 39486, "species_taxid": 39486, "relation_to_type": "suspected-type", "validated": true, "ani": 77.4311, "matched_fragments": 94, "total_fragments": 1220, "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": 77.3624, "matched_fragments": 178, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea formicigenerans", "strain": "strain=ATCC 27755", "accession": "GCA_025150245.1", "taxid": 39486, "species_taxid": 39486, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3342, "matched_fragments": 91, "total_fragments": 1220, "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": 76.9913, "matched_fragments": 87, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterocloster asparagiformis", "strain": "strain=DSM 15981", "accession": "GCA_025149125.1", "taxid": 333367, "species_taxid": 333367, "relation_to_type": "type", "validated": true, "ani": 76.8746, "matched_fragments": 63, "total_fragments": 1220, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002161355.1", "gtdb_species": "s__Mediterraneibacter caccavium", "ani": 80.8772, "matched_fragments": 372, "total_fragments": 1220, "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": "GCF_002160525.1", "gtdb_species": "s__Mediterraneibacter cottocaccae", "ani": 80.7263, "matched_fragments": 402, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.78", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016902345.1", "gtdb_species": "s__Mediterraneibacter glycyrrhizinilyticus_A", "ani": 80.2926, "matched_fragments": 381, "total_fragments": 1220, "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_002159505.1", "gtdb_species": "s__Mediterraneibacter ornithocaccae", "ani": 80.0794, "matched_fragments": 343, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.93", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_019113645.1", "gtdb_species": "s__Mediterraneibacter vanvlietii", "ani": 79.4863, "matched_fragments": 379, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_019119995.1", "gtdb_species": "s__Mediterraneibacter faecavium", "ani": 79.3657, "matched_fragments": 339, "total_fragments": 1220, "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_019112735.1", "gtdb_species": "s__Mediterraneibacter guildfordensis", "ani": 79.2297, "matched_fragments": 308, "total_fragments": 1220, "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": 79.1507, "matched_fragments": 277, "total_fragments": 1220, "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_900555215.1", "gtdb_species": "s__Mediterraneibacter excrementipullorum", "ani": 79.123, "matched_fragments": 181, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.77", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.72", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_904377845.1", "gtdb_species": "s__Mediterraneibacter sp904377845", "ani": 79.0295, "matched_fragments": 315, "total_fragments": 1220, "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_019120575.1", "gtdb_species": "s__Mediterraneibacter quadrami", "ani": 78.8766, "matched_fragments": 306, "total_fragments": 1220, "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_900751785.1", "gtdb_species": "s__Mediterraneibacter faecigallinarum", "ani": 78.864, "matched_fragments": 283, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_019118885.1", "gtdb_species": "s__Mediterraneibacter surreyensis", "ani": 78.8009, "matched_fragments": 326, "total_fragments": 1220, "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": "GCA_019116185.1", "gtdb_species": "s__Mediterraneibacter stercorigallinarum", "ani": 78.7461, "matched_fragments": 242, "total_fragments": 1220, "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_019114745.1", "gtdb_species": "s__Mediterraneibacter colneyensis", "ani": 78.7226, "matched_fragments": 261, "total_fragments": 1220, "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_019119745.1", "gtdb_species": "s__Mediterraneibacter gallistercoris", "ani": 78.7066, "matched_fragments": 283, "total_fragments": 1220, "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": 78.6996, "matched_fragments": 269, "total_fragments": 1220, "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_019120075.1", "gtdb_species": "s__Mediterraneibacter excrementigallinarum_A", "ani": 78.6917, "matched_fragments": 283, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.40", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_019115385.1", "gtdb_species": "s__Mediterraneibacter avicola", "ani": 78.6675, "matched_fragments": 243, "total_fragments": 1220, "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_019118665.1", "gtdb_species": "s__Mediterraneibacter intestinipullorum", "ani": 78.5774, "matched_fragments": 266, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000153925.1", "gtdb_species": "s__Mediterraneibacter torques", "ani": 78.4269, "matched_fragments": 184, "total_fragments": 1220, "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": "GCF_001028025.1", "gtdb_species": "s__Muricomes fissicatena_A", "ani": 77.6387, "matched_fragments": 138, "total_fragments": 1220, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": -0.18, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.7, "optimum_ph": 7.0, "genome_size": 3334855.36, "gc_content": 43.875, "coding_genes": 2772.666, "rRNA16S_genes": 4.0, "tRNA_genes": 64.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Ruminococcus", "turbiniformis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }