{ "type": "genome", "identifier": "GCF_018555435.2", "organism": "Bifidobacterium amazonense", "title": "Bifidobacterium amazonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018555435.2", "bioproject": "PRJNA224116", "biosample": "SAMN17736106", "wgs_master": "JAFEJT000000000.2", "refseq_category": "reference genome", "taxid": "2809027", "species_taxid": "2809027", "organism_name": "Bifidobacterium amazonense", "infraspecific_name": "strain=MA1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/15", "asm_name": "ASM1855543v2", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_018555435.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/555/435/GCF_018555435.2_ASM1855543v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3348570", "genome_size_ungapped": "3348477", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "133", "contig_count": "133", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018555435.2-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2737", "protein_coding_gene_count": "2600", "non_coding_gene_count": "80", "pubmed_id": "33973321;34715437" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-15", "dateModified": "2022-03-15", "datePublished": "2022-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium amazonense" ], "sample_taxid": [ "2809027" ], "sample_host_organism": [ "Mico argentatus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "0.926 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)": "3348570", "Number of Sequences": "133", "Longest Sequences (bp)": "164649", "N50 (bp)": "43704", "Gap Ratio (%)": "0.002777", "GCcontent (%)": "64.4", "Number of CDSs": "2587", "Average Protein Length": "360.1", "Coding Ratio (%)": "83.5", "Number of rRNAs": "3", "Number of tRNAs": "71", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium amazonense", "strain": "strain=MA1", "accession": "GCA_018555435.2", "taxid": 2809027, "species_taxid": 2809027, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1030, "total_fragments": 1047, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium miconis", "strain": "strain=82T10", "accession": "GCA_019331735.1", "taxid": 2834435, "species_taxid": 2834435, "relation_to_type": "type", "validated": true, "ani": 90.9477, "matched_fragments": 750, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium biavatii", "strain": "strain=DSM 23969", "accession": "GCA_000771645.1", "taxid": 762212, "species_taxid": 762212, "relation_to_type": "type", "validated": true, "ani": 90.868, "matched_fragments": 766, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium biavatii", "strain": "strain=DSM 23969", "accession": "GCA_000741165.1", "taxid": 762212, "species_taxid": 762212, "relation_to_type": "type", "validated": true, "ani": 90.7747, "matched_fragments": 759, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium simiiventris", "strain": "strain=81T8", "accession": "GCA_019331715.1", "taxid": 2834434, "species_taxid": 2834434, "relation_to_type": "type", "validated": true, "ani": 87.0427, "matched_fragments": 651, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium ramosum", "strain": "strain=TREM", "accession": "GCA_010667665.1", "taxid": 1798158, "species_taxid": 1798158, "relation_to_type": "type", "validated": true, "ani": 86.7432, "matched_fragments": 661, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium aerophilum", "strain": "strain=TRE17", "accession": "GCA_010667685.1", "taxid": 1798155, "species_taxid": 1798155, "relation_to_type": "type", "validated": true, "ani": 86.6572, "matched_fragments": 608, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium samirii", "strain": "strain=2033B", "accession": "GCA_003952945.1", "taxid": 2306974, "species_taxid": 2306974, "relation_to_type": "type", "validated": true, "ani": 84.7886, "matched_fragments": 528, "total_fragments": 1047, "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": 83.2937, "matched_fragments": 526, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium pseudolongum subsp. pseudolongum", "strain": "strain=ATCC 25526", "accession": "GCA_022691205.1", "taxid": 31954, "species_taxid": 1694, "relation_to_type": "type", "validated": true, "ani": 80.2552, "matched_fragments": 318, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium mizhiense", "strain": "strain=S053-2", "accession": "GCA_020884755.1", "taxid": 2879940, "species_taxid": 2879940, "relation_to_type": "type", "validated": true, "ani": 77.9384, "matched_fragments": 154, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas palmilytica", "strain": "strain=EW123", "accession": "GCA_021590045.1", "taxid": 2608402, "species_taxid": 2608402, "relation_to_type": "type", "validated": true, "ani": 76.888, "matched_fragments": 169, "total_fragments": 1047, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000741165.1", "gtdb_species": "s__Bifidobacterium biavatii", "ani": 90.7802, "matched_fragments": 759, "total_fragments": 1047, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018555335.1", "gtdb_species": "s__Bifidobacterium sp018555335", "ani": 86.8632, "matched_fragments": 646, "total_fragments": 1047, "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_009299505.1", "gtdb_species": "s__Bifidobacterium ramosum", "ani": 86.7681, "matched_fragments": 655, "total_fragments": 1047, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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": 2, "status": "-" }, { "accession": "GCF_010667685.1", "gtdb_species": "s__Bifidobacterium aerophilum", "ani": 86.6098, "matched_fragments": 610, "total_fragments": 1047, "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": 84.9878, "matched_fragments": 580, "total_fragments": 1047, "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_003952945.1", "gtdb_species": "s__Bifidobacterium samirii", "ani": 84.7653, "matched_fragments": 529, "total_fragments": 1047, "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_001042635.1", "gtdb_species": "s__Bifidobacterium scardovii", "ani": 84.0848, "matched_fragments": 563, "total_fragments": 1047, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.51", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_018555635.1", "gtdb_species": "s__Bifidobacterium sp018555635", "ani": 83.9972, "matched_fragments": 518, "total_fragments": 1047, "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_009078285.1", "gtdb_species": "s__Bifidobacterium jacchi", "ani": 82.5823, "matched_fragments": 445, "total_fragments": 1047, "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": 36.851, "optimum_tmp": 36.466, "optimum_ph": 6.377, "genome_size": 2304203.81, "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": 0.147, "anaerobic_respiration": 0.823, "aerobic_respiration": 0.029, "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", "amazonense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }