{ "type": "genome", "identifier": "GCA_022757685.1", "organism": "Lactobacillus crispatus", "title": "Lactobacillus crispatus", "description": "derived from metagenome; genome length too small", "data type": "Genome sequencing and assembly", "organization": "Massachusetts General Hospital", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022757685.1", "bioproject": "PRJNA799762", "biosample": "SAMN25208356", "wgs_master": "JALBQD000000000.1", "refseq_category": "na", "taxid": "47770", "species_taxid": "47770", "organism_name": "Lactobacillus crispatus", "infraspecific_name": "", "isolate": "MHKL_MAG_00237", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/29", "asm_name": "ASM2275768v1", "submitter": "Massachusetts General Hospital", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/757/685/GCA_022757685.1_ASM2275768v1", "excluded_from_refseq": "derived from metagenome; genome length too small", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-29", "dateModified": "2022-03-29", "datePublished": "2022-03-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactobacillus crispatus" ], "sample_taxid": [ "47770" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.271 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "953283", "Number of Sequences": "74", "Longest Sequences (bp)": "99449", "N50 (bp)": "18462", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.4", "Number of CDSs": "915", "Average Protein Length": "309.2", "Coding Ratio (%)": "89.0", "Number of rRNAs": "0", "Number of tRNAs": "18", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactobacillus crispatus", "strain": "strain=DSM 20584", "accession": "GCA_001434005.1", "taxid": 47770, "species_taxid": 47770, "relation_to_type": "type", "validated": true, "ani": 97.3409, "matched_fragments": 223, "total_fragments": 280, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactobacillus crispatus", "strain": "strain=ATCC 33820", "accession": "GCA_002088015.1", "taxid": 47770, "species_taxid": 47770, "relation_to_type": "type", "validated": true, "ani": 97.2934, "matched_fragments": 227, "total_fragments": 280, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactobacillus crispatus", "strain": "strain=NCK2488", "accession": "GCA_008694755.1", "taxid": 47770, "species_taxid": 47770, "relation_to_type": "type", "validated": true, "ani": 97.2911, "matched_fragments": 221, "total_fragments": 280, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactobacillus crispatus", "strain": "strain=ATCC 33820", "accession": "GCA_018987235.1", "taxid": 47770, "species_taxid": 47770, "relation_to_type": "suspected-type", "validated": true, "ani": 97.2852, "matched_fragments": 235, "total_fragments": 280, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactobacillus gasseri", "strain": "strain=ATCC 33323", "accession": "GCA_008868295.1", "taxid": 1596, "species_taxid": 1596, "relation_to_type": "type", "validated": true, "ani": 85.2957, "matched_fragments": 100, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus gasseri", "strain": "strain=ATCC 33323", "accession": "GCA_000014425.1", "taxid": 1596, "species_taxid": 1596, "relation_to_type": "type", "validated": true, "ani": 85.0917, "matched_fragments": 100, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus gasseri", "strain": "strain=NCTC13722", "accession": "GCA_900452355.1", "taxid": 1596, "species_taxid": 1596, "relation_to_type": "type", "validated": true, "ani": 84.9639, "matched_fragments": 101, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus paragasseri", "strain": "strain=JCM 5343", "accession": "GCA_003307275.1", "taxid": 2107999, "species_taxid": 2107999, "relation_to_type": "type", "validated": true, "ani": 83.4778, "matched_fragments": 101, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus paragasseri", "strain": "strain=JCM 5343", "accession": "GCA_003584685.1", "taxid": 2107999, "species_taxid": 2107999, "relation_to_type": "type", "validated": true, "ani": 83.0939, "matched_fragments": 105, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus ultunensis", "strain": "strain=DSM 16047", "accession": "GCA_001436305.1", "taxid": 227945, "species_taxid": 227945, "relation_to_type": "type", "validated": true, "ani": 81.0547, "matched_fragments": 158, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus intestinalis", "strain": "strain=DSM 6629", "accession": "GCA_024397795.1", "taxid": 151781, "species_taxid": 151781, "relation_to_type": "type", "validated": true, "ani": 79.5918, "matched_fragments": 103, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus rodentium", "strain": "strain=DSM 24759", "accession": "GCA_024622425.1", "taxid": 947835, "species_taxid": 947835, "relation_to_type": "type", "validated": true, "ani": 78.096, "matched_fragments": 57, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus apis", "strain": "strain=LMG 26964", "accession": "GCA_002837055.1", "taxid": 303541, "species_taxid": 303541, "relation_to_type": "type", "validated": true, "ani": 77.4681, "matched_fragments": 57, "total_fragments": 280, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018987235.1", "gtdb_species": "s__Lactobacillus crispatus", "ani": 97.0941, "matched_fragments": 237, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "96.25", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.70", "num_clustered_genomes": 161, "status": "conclusive" }, { "accession": "GCF_000014425.1", "gtdb_species": "s__Lactobacillus gasseri", "ani": 85.0917, "matched_fragments": 100, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "96.79", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_003584685.1", "gtdb_species": "s__Lactobacillus paragasseri", "ani": 83.0939, "matched_fragments": 105, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 40, "status": "-" }, { "accession": "GCF_000615285.1", "gtdb_species": "s__Lactobacillus kitasatonis", "ani": 82.2375, "matched_fragments": 153, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002706375.1", "gtdb_species": "s__Lactobacillus amylovorus", "ani": 82.0119, "matched_fragments": 153, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.43", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_001434975.1", "gtdb_species": "s__Lactobacillus gallinarum", "ani": 81.7325, "matched_fragments": 159, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_001591845.1", "gtdb_species": "s__Lactobacillus acidophilus", "ani": 81.5732, "matched_fragments": 147, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.94", "num_clustered_genomes": 59, "status": "-" }, { "accession": "GCF_000160855.1", "gtdb_species": "s__Lactobacillus helveticus", "ani": 81.3163, "matched_fragments": 163, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "96.37", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.75", "num_clustered_genomes": 146, "status": "-" }, { "accession": "GCF_001436305.1", "gtdb_species": "s__Lactobacillus ultunensis", "ani": 80.9898, "matched_fragments": 160, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001436695.1", "gtdb_species": "s__Lactobacillus taiwanensis", "ani": 80.1151, "matched_fragments": 89, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 31, "status": "-" }, { "accession": "GCF_000159355.1", "gtdb_species": "s__Lactobacillus johnsonii", "ani": 79.8613, "matched_fragments": 81, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.89", "min_intra_species_ani": "95.28", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.57", "num_clustered_genomes": 61, "status": "-" }, { "accession": "GCA_910589175.1", "gtdb_species": "s__Lactobacillus sp910589175", "ani": 79.6991, "matched_fragments": 83, "total_fragments": 280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "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": -0.097, "cell_length": 0.361, "doubling_h": -0.086, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 6.027, "genome_size": 2217171.864, "gc_content": 36.743, "coding_genes": 2024.0, "rRNA16S_genes": 5.074, "tRNA_genes": 63.614, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "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__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Lactobacillus crispatus" ], "_genome_taxon": [ "Lactobacillus", "crispatus", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Lactobacillus crispatus", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Lactobacillaceae", "Lactobacillus", "Lactobacillus", "crispatus" ], "_meo": [ { "id": "MEO_0000523", "label": "vagina" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }