{ "type": "genome", "identifier": "GCF_000741615.1", "organism": "Bifidobacterium merycicum", "title": "Bifidobacterium merycicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000741615.1", "bioproject": "PRJNA224116", "biosample": "SAMN02673440", "wgs_master": "JGZC00000000.1", "refseq_category": "na", "taxid": "78345", "species_taxid": "78345", "organism_name": "Bifidobacterium merycicum", "infraspecific_name": "strain=LMG 11341", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/08/18", "asm_name": "Bifmer", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_000741615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/741/615/GCF_000741615.1_Bifmer", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2280234", "genome_size_ungapped": "2280234", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000741615.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "1907", "protein_coding_gene_count": "1786", "non_coding_gene_count": "63", "pubmed_id": "25085493;25107967" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-08-18", "dateModified": "2014-08-18", "datePublished": "2014-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium merycicum" ], "sample_taxid": [ "78345" ], "sample_host_organism": [ "bovine" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.639 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2280234", "Number of Sequences": "16", "Longest Sequences (bp)": "517378", "N50 (bp)": "328208", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.3", "Number of CDSs": "1855", "Average Protein Length": "349.0", "Coding Ratio (%)": "85.2", "Number of rRNAs": "5", "Number of tRNAs": "56", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium merycicum", "strain": "strain=LMG 11341", "accession": "GCA_000741615.1", "taxid": 78345, "species_taxid": 78345, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 751, "total_fragments": 752, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium merycicum", "strain": "strain=DSM 6492", "accession": "GCA_900129045.1", "taxid": 78345, "species_taxid": 78345, "relation_to_type": "type", "validated": true, "ani": 99.9778, "matched_fragments": 747, "total_fragments": 752, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium merycicum", "strain": "strain=DSM 6492", "accession": "GCA_000770945.1", "taxid": 78345, "species_taxid": 78345, "relation_to_type": "type", "validated": true, "ani": 99.9457, "matched_fragments": 731, "total_fragments": 752, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium pongonis", "strain": "strain=64T4", "accession": "GCA_019331805.1", "taxid": 2834432, "species_taxid": 2834432, "relation_to_type": "type", "validated": true, "ani": 90.747, "matched_fragments": 585, "total_fragments": 752, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium angulatum", "strain": "strain=LMG 11039", "accession": "GCA_000741065.1", "taxid": 1683, "species_taxid": 1683, "relation_to_type": "type", "validated": true, "ani": 88.3422, "matched_fragments": 536, "total_fragments": 752, "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": 81.6634, "matched_fragments": 372, "total_fragments": 752, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas avistercoris", "strain": "strain=Sa3CUA2", "accession": "GCA_014836445.1", "taxid": 2762242, "species_taxid": 2762242, "relation_to_type": "type", "validated": true, "ani": 76.1966, "matched_fragments": 60, "total_fragments": 752, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mariniharenae", "strain": "strain=NEAU-184", "accession": "GCA_008122505.1", "taxid": 2604423, "species_taxid": 2604423, "relation_to_type": "type", "validated": true, "ani": 76.1439, "matched_fragments": 52, "total_fragments": 752, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Promicromonospora umidemergens", "strain": "strain=DSM 22081", "accession": "GCA_024171995.1", "taxid": 629679, "species_taxid": 629679, "relation_to_type": "type", "validated": true, "ani": 75.6117, "matched_fragments": 72, "total_fragments": 752, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900129045.1", "gtdb_species": "s__Bifidobacterium merycicum", "ani": 99.9778, "matched_fragments": 747, "total_fragments": 752, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.29", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_001025155.1", "gtdb_species": "s__Bifidobacterium angulatum", "ani": 88.3237, "matched_fragments": 535, "total_fragments": 752, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.74", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_012932675.1", "gtdb_species": "s__Bifidobacterium sp012932675", "ani": 86.9402, "matched_fragments": 572, "total_fragments": 752, "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_002860365.1", "gtdb_species": "s__Bifidobacterium parmae", "ani": 81.8119, "matched_fragments": 394, "total_fragments": 752, "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_000741785.1", "gtdb_species": "s__Bifidobacterium stellenboschense", "ani": 81.7163, "matched_fragments": 390, "total_fragments": 752, "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_018555635.1", "gtdb_species": "s__Bifidobacterium sp018555635", "ani": 81.6111, "matched_fragments": 378, "total_fragments": 752, "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_018555385.1", "gtdb_species": "s__Bifidobacterium sp018555385", "ani": 81.6093, "matched_fragments": 375, "total_fragments": 752, "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_003129905.1", "gtdb_species": "s__Bifidobacterium callitrichidarum", "ani": 81.4765, "matched_fragments": 372, "total_fragments": 752, "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_001417815.1", "gtdb_species": "s__Bifidobacterium aesculapii", "ani": 81.3287, "matched_fragments": 390, "total_fragments": 752, "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_012932445.1", "gtdb_species": "s__Bifidobacterium sp012932445", "ani": 80.7549, "matched_fragments": 258, "total_fragments": 752, "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": 80.6501, "matched_fragments": 327, "total_fragments": 752, "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_000741215.1", "gtdb_species": "s__Bifidobacterium pullorum_B", "ani": 80.5148, "matched_fragments": 322, "total_fragments": 752, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "95.67", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 17, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.301, "cell_length": 0.328, "doubling_h": 0.178, "growth_tmp": 37.0, "optimum_tmp": 36.466, "optimum_ph": 6.377, "genome_size": 2277458.0, "gc_content": 59.795, "coding_genes": 1746.874, "rRNA16S_genes": 3.765, "tRNA_genes": 52.571, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.043, "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 }, "_genome_taxon": [ "Bifidobacterium", "merycicum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }