{ "type": "genome", "identifier": "GCA_022722355.1", "organism": "Bifidobacterium longum", "title": "Bifidobacterium longum", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Georgia Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022722355.1", "bioproject": "PRJNA747761", "biosample": "SAMN20301941", "wgs_master": "JAIJLN000000000.1", "refseq_category": "na", "taxid": "216816", "species_taxid": "216816", "organism_name": "Bifidobacterium longum", "infraspecific_name": "", "isolate": "Map_61_012", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/28", "asm_name": "ASM2272235v1", "submitter": "Georgia Institute of Technology", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/722/355/GCA_022722355.1_ASM2272235v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-28", "dateModified": "2022-03-28", "datePublished": "2022-03-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium longum" ], "sample_taxid": [ "216816" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mozambique" ], "sample_host_location_id": [], "data_size": "0.587 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 71.81, "contamination": 10.88, "strain_heterogeneity": 80.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2044695", "Number of Sequences": "673", "Longest Sequences (bp)": "24884", "N50 (bp)": "4042", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.7", "Number of CDSs": "1283", "Average Protein Length": "282.9", "Coding Ratio (%)": "53.2", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=ATCC 15697", "accession": "GCA_000020425.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 97.6553, "matched_fragments": 297, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=NCTC11817", "accession": "GCA_900637215.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 97.6212, "matched_fragments": 298, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=JCM 1222", "accession": "GCA_000269965.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 97.5955, "matched_fragments": 299, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=DSM 20088", "accession": "GCA_000771105.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 97.4705, "matched_fragments": 294, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. suis", "strain": "strain=DSM 20211", "accession": "GCA_000771285.1", "taxid": 1695, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 95.6931, "matched_fragments": 256, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. suillum", "strain": "strain=SU-851", "accession": "GCA_016882605.1", "taxid": 1931217, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 95.6617, "matched_fragments": 258, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum subsp. suillum", "strain": "strain=JCM 19995", "accession": "GCA_017132755.1", "taxid": 1931217, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 95.6449, "matched_fragments": 259, "total_fragments": 327, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium longum", "strain": "strain=NCTC11818", "accession": "GCA_900637335.1", "taxid": 216816, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 94.0717, "matched_fragments": 249, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium longum subsp. longum", "strain": "strain=JCM 1217", "accession": "GCA_000196555.1", "taxid": 1679, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 94.0713, "matched_fragments": 249, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium miconisargentati", "strain": "strain=82T25", "accession": "GCA_019331675.1", "taxid": 2834437, "species_taxid": 2834437, "relation_to_type": "type", "validated": true, "ani": 82.8925, "matched_fragments": 211, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 71.81, "contamination": 10.88, "strain_heterogeneity": 80.0 }, "gtdb_result": [ { "accession": "GCF_000269965.1", "gtdb_species": "s__Bifidobacterium infantis", "ani": 97.5955, "matched_fragments": 299, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.68", "min_intra_species_ani": "97.44", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 49, "status": "conclusive" }, { "accession": "GCF_000196555.1", "gtdb_species": "s__Bifidobacterium longum", "ani": 94.0713, "matched_fragments": 249, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.67", "num_clustered_genomes": 481, "status": "-" }, { "accession": "GCF_001025175.1", "gtdb_species": "s__Bifidobacterium breve", "ani": 86.1176, "matched_fragments": 236, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 170, "status": "-" }, { "accession": "GCF_018555355.1", "gtdb_species": "s__Bifidobacterium sp018555355", "ani": 82.8414, "matched_fragments": 208, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003129905.1", "gtdb_species": "s__Bifidobacterium callitrichidarum", "ani": 82.7505, "matched_fragments": 205, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_002259745.1", "gtdb_species": "s__Bifidobacterium myosotis", "ani": 81.9733, "matched_fragments": 197, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000741695.1", "gtdb_species": "s__Bifidobacterium reuteri", "ani": 81.6911, "matched_fragments": 183, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "97.71", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000741785.1", "gtdb_species": "s__Bifidobacterium stellenboschense", "ani": 81.1239, "matched_fragments": 173, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_012932425.1", "gtdb_species": "s__Bifidobacterium sp012932425", "ani": 80.8034, "matched_fragments": 167, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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": -0.022, "cell_length": 0.328, "doubling_h": 0.178, "growth_tmp": 37.0, "optimum_tmp": 37.585, "optimum_ph": 6.377, "genome_size": 2455596.336, "gc_content": 60.482, "coding_genes": 1972.344, "rRNA16S_genes": 3.5, "tRNA_genes": 60.2, "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": 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__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__Bifidobacterium infantis" ], "_genome_taxon": [ "Bifidobacterium", "longum", "d__Bacteria", "p__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__Bifidobacterium infantis", "Bacteria", "Actinomycetota", "Actinomycetes", "Actinomycetales", "Bifidobacteriaceae", "Bifidobacterium", "Bifidobacterium", "infantis" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }