{ "type": "genome", "identifier": "GCA_934754385.1", "organism": "uncultured Clostridium sp.", "title": "uncultured Clostridium sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "stanford university school of medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCA_934754385.1", "bioproject": "PRJEB49206", "biosample": "SAMEA13478492", "wgs_master": "CAKVKF000000000.1", "refseq_category": "na", "taxid": "59620", "species_taxid": "59620", "organism_name": "uncultured Clostridium sp.", "infraspecific_name": "", "isolate": "REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_E_13_1725.53", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/16", "asm_name": "ERR7738530_bin.53", "submitter": "stanford university school of medicine", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/934/754/385/GCA_934754385.1_ERR7738530_bin.53", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-16", "dateModified": "2022-04-16", "datePublished": "2022-04-16", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Clostridium sp." ], "sample_taxid": [ "59620" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tanzania" ], "sample_host_location_id": [], "data_size": "0.847 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 76.62, "contamination": 0.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3017828", "Number of Sequences": "696", "Longest Sequences (bp)": "21180", "N50 (bp)": "5226", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.7", "Number of CDSs": "2406", "Average Protein Length": "270.3", "Coding Ratio (%)": "64.7", "Number of rRNAs": "0", "Number of tRNAs": "24", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium paraputrificum", "strain": "strain=NCTC11833", "accession": "GCA_900447045.1", "taxid": 29363, "species_taxid": 29363, "relation_to_type": "type", "validated": true, "ani": 99.0572, "matched_fragments": 591, "total_fragments": 643, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium cibarium", "strain": "strain=Sa3CVN1", "accession": "GCA_014836335.1", "taxid": 2762247, "species_taxid": 2762247, "relation_to_type": "type", "validated": true, "ani": 78.1008, "matched_fragments": 175, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium septicum", "strain": "strain=FDAARGOS_1551", "accession": "GCA_020736665.1", "taxid": 1504, "species_taxid": 1504, "relation_to_type": "type", "validated": true, "ani": 78.0237, "matched_fragments": 149, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium chauvoei", "strain": "strain=DSM 7528", "accession": "GCA_002327185.1", "taxid": 46867, "species_taxid": 46867, "relation_to_type": "type", "validated": true, "ani": 77.9741, "matched_fragments": 139, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tertium", "strain": "strain=DSM 2485", "accession": "GCA_017873245.1", "taxid": 1559, "species_taxid": 1559, "relation_to_type": "type", "validated": true, "ani": 77.782, "matched_fragments": 170, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium gallinarum", "strain": "strain=Sa3CUN1", "accession": "GCA_014836325.1", "taxid": 2762246, "species_taxid": 2762246, "relation_to_type": "type", "validated": true, "ani": 77.7182, "matched_fragments": 150, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saudiense", "strain": "strain=JCC", "accession": "GCA_000577815.1", "taxid": 1414720, "species_taxid": 1414720, "relation_to_type": "type", "validated": true, "ani": 77.6249, "matched_fragments": 152, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium celatum", "strain": "strain=DSM 1785", "accession": "GCA_000320405.1", "taxid": 36834, "species_taxid": 36834, "relation_to_type": "type", "validated": true, "ani": 77.6102, "matched_fragments": 149, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium uliginosum", "strain": "strain=DSM 12992", "accession": "GCA_900112485.1", "taxid": 119641, "species_taxid": 119641, "relation_to_type": "type", "validated": true, "ani": 77.5973, "matched_fragments": 151, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium neonatale", "strain": "strain=LCDC 99A005", "accession": "GCA_002553615.1", "taxid": 137838, "species_taxid": 137838, "relation_to_type": "type", "validated": true, "ani": 77.375, "matched_fragments": 159, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium isatidis", "strain": "strain=DSM 15098", "accession": "GCA_002285495.1", "taxid": 182773, "species_taxid": 182773, "relation_to_type": "type", "validated": true, "ani": 77.2485, "matched_fragments": 116, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium vincentii", "strain": "strain=DSM 10228", "accession": "GCA_002995745.1", "taxid": 52704, "species_taxid": 52704, "relation_to_type": "type", "validated": true, "ani": 77.1626, "matched_fragments": 148, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium chrysemydis", "strain": "strain=PT", "accession": "GCA_015234215.1", "taxid": 2665504, "species_taxid": 2665504, "relation_to_type": "type", "validated": true, "ani": 76.9351, "matched_fragments": 116, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium puniceum", "strain": "strain=DSM 2619", "accession": "GCA_002006345.1", "taxid": 29367, "species_taxid": 29367, "relation_to_type": "type", "validated": true, "ani": 76.913, "matched_fragments": 132, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium zeae", "strain": "strain=CSC2", "accession": "GCA_017312485.1", "taxid": 2759022, "species_taxid": 2759022, "relation_to_type": "type", "validated": true, "ani": 76.7313, "matched_fragments": 92, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium intestinale", "strain": "strain=DSM 6191", "accession": "GCA_900130055.1", "taxid": 36845, "species_taxid": 36845, "relation_to_type": "type", "validated": true, "ani": 76.5128, "matched_fragments": 112, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium simiarum", "strain": "strain=MSJ-4", "accession": "GCA_018919175.1", "taxid": 2841506, "species_taxid": 2841506, "relation_to_type": "type", "validated": true, "ani": 76.0012, "matched_fragments": 67, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium massiliodielmoense", "strain": "strain=MT26", "accession": "GCA_900176615.1", "taxid": 1776385, "species_taxid": 1776385, "relation_to_type": "type", "validated": true, "ani": 75.9891, "matched_fragments": 61, "total_fragments": 643, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 76.62, "contamination": 0.38, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900447045.1", "gtdb_species": "s__Clostridium paraputrificum", "ani": 99.0572, "matched_fragments": 591, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "95.42", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 29, "status": "conclusive" }, { "accession": "GCA_018372875.1", "gtdb_species": "s__Clostridium sp018372875", "ani": 94.0988, "matched_fragments": 533, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900116755.1", "gtdb_species": "s__Clostridium sp900116755", "ani": 78.0961, "matched_fragments": 168, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_015058405.1", "gtdb_species": "s__Clostridium sp015058405", "ani": 78.0923, "matched_fragments": 173, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_002327185.1", "gtdb_species": "s__Clostridium chauvoei", "ani": 77.9984, "matched_fragments": 138, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900539375.1", "gtdb_species": "s__Clostridium sp900539375", "ani": 77.9224, "matched_fragments": 165, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000789395.1", "gtdb_species": "s__Clostridium baratii", "ani": 77.8564, "matched_fragments": 158, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.53", "min_intra_species_ani": "95.37", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_004353185.1", "gtdb_species": "s__Clostridium cuniculi", "ani": 77.8037, "matched_fragments": 147, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "97.60", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_015058375.1", "gtdb_species": "s__Clostridium sp015058375", "ani": 77.7594, "matched_fragments": 130, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_001405015.1", "gtdb_species": "s__Clostridium disporicum", "ani": 77.7585, "matched_fragments": 135, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_015667795.1", "gtdb_species": "s__Clostridium sp015667795", "ani": 77.7119, "matched_fragments": 165, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_012519845.1", "gtdb_species": "s__Clostridium sp012519845", "ani": 77.6636, "matched_fragments": 131, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_015555905.1", "gtdb_species": "s__Clostridium sp015555905", "ani": 77.6386, "matched_fragments": 155, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.73", "min_intra_species_af": "0.73", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000577815.1", "gtdb_species": "s__Clostridium saudiense", "ani": 77.6249, "matched_fragments": 152, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_902785295.1", "gtdb_species": "s__Clostridium sp902785295", "ani": 77.614, "matched_fragments": 133, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_900112485.1", "gtdb_species": "s__Clostridium uliginosum", "ani": 77.5762, "matched_fragments": 152, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_003129525.1", "gtdb_species": "s__Clostridium beijerinckii_D", "ani": 77.1859, "matched_fragments": 121, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_002995745.1", "gtdb_species": "s__Clostridium vincentii", "ani": 77.1801, "matched_fragments": 147, "total_fragments": 643, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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": -0.16, "cell_length": 0.434, "doubling_h": 0.353, "growth_tmp": 33.457, "optimum_tmp": 35.173, "optimum_ph": 6.947, "genome_size": 4165901.003, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 0.945, "sporulation": 0.967, "motility": 0.92, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.944, "thermophilic_range_tmp": 0.055, "psychrophilic_range_tmp": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__Clostridium paraputrificum" ], "_genome_taxon": [ "uncultured", "Clostridium", "sp.", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__Clostridium paraputrificum", "Bacteria", "Bacillota", "A", "Clostridia", "Clostridiales", "Clostridiaceae", "Clostridium", "Clostridium", "paraputrificum" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }