{ "type": "genome", "identifier": "GCF_900129135.1", "organism": "Lactonifactor longoviformis DSM 17459", "title": "Lactonifactor longoviformis DSM 17459", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900129135.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745158", "wgs_master": "FQVI00000000.1", "refseq_category": "reference genome", "taxid": "1122155", "species_taxid": "341220", "organism_name": "Lactonifactor longoviformis DSM 17459", "infraspecific_name": "strain=DSM 17459", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2585428044 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900129135.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/129/135/GCF_900129135.1_IMG-taxon_2585428044_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4839287", "genome_size_ungapped": "4838947", "gc_percent": "46.500000", "replicon_count": "0", "scaffold_count": "76", "contig_count": "76", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900129135.1-RS_2024_04_12", "annotation_date": "2024-04-12", "total_gene_count": "4510", "protein_coding_gene_count": "4355", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactonifactor longoviformis DSM 17459" ], "sample_taxid": [ "1122155" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.374 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)": "4839287", "Number of Sequences": "76", "Longest Sequences (bp)": "572444", "N50 (bp)": "144569", "Gap Ratio (%)": "0.007026", "GCcontent (%)": "46.4", "Number of CDSs": "4390", "Average Protein Length": "328.9", "Coding Ratio (%)": "89.5", "Number of rRNAs": "0", "Number of tRNAs": "60", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactonifactor longoviformis", "strain": "strain=DSM 17459", "accession": "GCA_900129135.1", "taxid": 341220, "species_taxid": 341220, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1568, "total_fragments": 1573, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactonifactor longoviformis", "strain": "strain=DSM 17459", "accession": "GCA_002915525.1", "taxid": 341220, "species_taxid": 341220, "relation_to_type": "suspected-type", "validated": true, "ani": 99.7329, "matched_fragments": 1212, "total_fragments": 1573, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Blautia wexlerae", "strain": "strain=DSM 19850", "accession": "GCA_000484655.1", "taxid": 418240, "species_taxid": 418240, "relation_to_type": "suspected-type", "validated": true, "ani": 81.6584, "matched_fragments": 110, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia wexlerae", "strain": "strain=DSM 19850", "accession": "GCA_025148125.1", "taxid": 418240, "species_taxid": 418240, "relation_to_type": "suspected-type", "validated": true, "ani": 81.574, "matched_fragments": 123, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] scindens", "strain": "strain=ATCC 35704", "accession": "GCA_000154505.1", "taxid": 29347, "species_taxid": 29347, "relation_to_type": "suspected-type", "validated": true, "ani": 80.5417, "matched_fragments": 83, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerostipes butyraticus", "strain": "strain=JCM 17466", "accession": "GCA_016586355.1", "taxid": 645466, "species_taxid": 645466, "relation_to_type": "type", "validated": true, "ani": 80.2335, "matched_fragments": 57, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eisenbergiella tayi", "strain": "strain=DSM 26961", "accession": "GCA_001881565.1", "taxid": 1432052, "species_taxid": 1432052, "relation_to_type": "type", "validated": true, "ani": 79.8536, "matched_fragments": 72, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Wansuia hejianensis", "strain": "strain=NSJ-29", "accession": "GCA_014337215.1", "taxid": 2763667, "species_taxid": 2763667, "relation_to_type": "type", "validated": true, "ani": 79.3592, "matched_fragments": 76, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mediterraneibacter butyricigenes", "strain": "strain=KCTC 15684", "accession": "GCA_003574295.1", "taxid": 2316025, "species_taxid": 2316025, "relation_to_type": "type", "validated": true, "ani": 78.5745, "matched_fragments": 77, "total_fragments": 1573, "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": 78.125, "matched_fragments": 99, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia argi", "strain": "strain=KCTC 15426", "accession": "GCA_003287895.1", "taxid": 1912897, "species_taxid": 1912897, "relation_to_type": "type", "validated": true, "ani": 78.075, "matched_fragments": 120, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia hydrogenotrophica", "strain": "strain=DSM 10507", "accession": "GCA_000157975.1", "taxid": 53443, "species_taxid": 53443, "relation_to_type": "type", "validated": true, "ani": 77.7548, "matched_fragments": 84, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novisyntrophococcus fermenticellae", "strain": "strain=JN500902", "accession": "GCA_018866245.1", "taxid": 2068655, "species_taxid": 2068655, "relation_to_type": "type", "validated": true, "ani": 77.4182, "matched_fragments": 67, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hominisplanchenecus faecis", "strain": "strain=CLA-AA-H246", "accession": "GCA_020687205.1", "taxid": 2885351, "species_taxid": 2885351, "relation_to_type": "type", "validated": true, "ani": 77.2471, "matched_fragments": 79, "total_fragments": 1573, "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": 77.0859, "matched_fragments": 62, "total_fragments": 1573, "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": 77.0756, "matched_fragments": 64, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marvinbryantia formatexigens", "strain": "strain=DSM 14469", "accession": "GCA_000173815.1", "taxid": 168384, "species_taxid": 168384, "relation_to_type": "type", "validated": true, "ani": 77.0727, "matched_fragments": 64, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Murimonas intestini", "strain": "strain=DSM 26524", "accession": "GCA_024622195.1", "taxid": 1337051, "species_taxid": 1337051, "relation_to_type": "type", "validated": true, "ani": 76.8223, "matched_fragments": 103, "total_fragments": 1573, "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": 76.6227, "matched_fragments": 51, "total_fragments": 1573, "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": 76.5238, "matched_fragments": 51, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacrimispora aerotolerans", "strain": "strain=DSM 5434", "accession": "GCA_000687555.1", "taxid": 36832, "species_taxid": 36832, "relation_to_type": "type", "validated": true, "ani": 76.5163, "matched_fragments": 55, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900129135.1", "gtdb_species": "s__Lactonifactor longoviformis", "ani": 100.0, "matched_fragments": 1568, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lactonifactor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_009677585.1", "gtdb_species": "s__Lactonifactor sp009677585", "ani": 93.3173, "matched_fragments": 1246, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lactonifactor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_013304385.1", "gtdb_species": "s__Blautia_A sp900066505", "ani": 78.1464, "matched_fragments": 89, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003287895.1", "gtdb_species": "s__Blautia argi", "ani": 78.0449, "matched_fragments": 121, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.67", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_902362715.1", "gtdb_species": "s__Eubacterium_I sp900066595", "ani": 77.9534, "matched_fragments": 60, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900461125.1", "gtdb_species": "s__Blautia coccoides", "ani": 77.5643, "matched_fragments": 153, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.47", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_002899675.1", "gtdb_species": "s__CHH4-2 sp002899675", "ani": 77.5063, "matched_fragments": 75, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018374355.1", "gtdb_species": "s__Oliverpabstia sp018374355", "ani": 77.1088, "matched_fragments": 107, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia", "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_900539525.1", "gtdb_species": "s__CAG-56 sp900539525", "ani": 76.8948, "matched_fragments": 65, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019118685.1", "gtdb_species": "s__Blautia merdipullorum", "ani": 76.7582, "matched_fragments": 110, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "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_019112785.1", "gtdb_species": "s__Blautia stercorigallinarum", "ani": 76.7561, "matched_fragments": 107, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900765525.1", "gtdb_species": "s__Blautia pullicola", "ani": 76.746, "matched_fragments": 116, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.76", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_900762665.1", "gtdb_species": "s__CAG-56 sp900762665", "ani": 76.7072, "matched_fragments": 90, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000155205.1", "gtdb_species": "s__Mediterraneibacter lactaris", "ani": 76.553, "matched_fragments": 50, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.36", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCA_018714325.1", "gtdb_species": "s__Pelethocola excrementipullorum", "ani": 76.4578, "matched_fragments": 74, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola", "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_018713585.1", "gtdb_species": "s__Pullilachnospira stercoravium", "ani": 76.286, "matched_fragments": 73, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_018711815.1", "gtdb_species": "s__Egerieimonas intestinavium", "ani": 76.0019, "matched_fragments": 76, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas", "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_019120545.1", "gtdb_species": "s__Blautia stercoripullorum", "ani": 75.8154, "matched_fragments": 85, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "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_019119235.1", "gtdb_species": "s__Blautia_A excrementigallinarum", "ani": 75.7227, "matched_fragments": 51, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4839287.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Lactonifactor", "longoviformis", "DSM", "17459" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }