{ "type": "genome", "identifier": "GCA_022649875.1", "organism": "Lactobacillus sp.", "title": "Lactobacillus sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022649875.1", "bioproject": "PRJNA768587", "biosample": "SAMN22412660", "wgs_master": "JALCOV000000000.1", "refseq_category": "na", "taxid": "1591", "species_taxid": "1591", "organism_name": "Lactobacillus sp.", "infraspecific_name": "", "isolate": "UW_DM_LAC1_4", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/21", "asm_name": "ASM2264987v1", "submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/649/875/GCA_022649875.1_ASM2264987v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-21", "dateModified": "2022-03-21", "datePublished": "2022-03-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactobacillus sp." ], "sample_taxid": [ "1591" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Madison, WI", "Freezer" ], "sample_host_location_id": [], "data_size": "0.340 MB", "sample_ph_range": { "min": 55.0, "max": 55.0 }, "sample_temperature_range": { "min": 35.0, "max": 80.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1189571", "Number of Sequences": "26", "Longest Sequences (bp)": "100627", "N50 (bp)": "71540", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.9", "Number of CDSs": "1114", "Average Protein Length": "316.2", "Coding Ratio (%)": "88.8", "Number of rRNAs": "0", "Number of tRNAs": "19", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_004354545.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.5643, "matched_fragments": 57, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_000178475.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.5621, "matched_fragments": 56, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_001435665.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.5301, "matched_fragments": 55, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus kalixensis", "strain": "strain=DSM 16043", "accession": "GCA_001434335.1", "taxid": 227944, "species_taxid": 227944, "relation_to_type": "type", "validated": true, "ani": 78.1552, "matched_fragments": 58, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus kitasatonis", "strain": "strain=JCM 1039", "accession": "GCA_000615285.1", "taxid": 237446, "species_taxid": 237446, "relation_to_type": "type", "validated": true, "ani": 78.0563, "matched_fragments": 66, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus kitasatonis", "strain": "strain=DSM 16761", "accession": "GCA_001434435.1", "taxid": 237446, "species_taxid": 237446, "relation_to_type": "type", "validated": true, "ani": 78.0186, "matched_fragments": 65, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylovorus", "strain": "strain=DSM 20531", "accession": "GCA_002706375.1", "taxid": 1604, "species_taxid": 1604, "relation_to_type": "type", "validated": true, "ani": 78.0142, "matched_fragments": 62, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylovorus", "strain": "strain=DSM 20531", "accession": "GCA_001433985.1", "taxid": 1604, "species_taxid": 1604, "relation_to_type": "type", "validated": true, "ani": 77.9913, "matched_fragments": 62, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus gallinarum", "strain": "strain=DSM 10532", "accession": "GCA_001434975.1", "taxid": 52242, "species_taxid": 52242, "relation_to_type": "type", "validated": true, "ani": 77.8534, "matched_fragments": 63, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus corticis", "strain": "strain=B40", "accession": "GCA_018327645.1", "taxid": 2201249, "species_taxid": 2201249, "relation_to_type": "type", "validated": true, "ani": 77.8313, "matched_fragments": 59, "total_fragments": 383, "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": 77.7547, "matched_fragments": 57, "total_fragments": 383, "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": 77.6998, "matched_fragments": 58, "total_fragments": 383, "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": 77.678, "matched_fragments": 58, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus gasseri", "strain": "strain=ATCC 33323", "accession": "GCA_008868295.1", "taxid": 1596, "species_taxid": 1596, "relation_to_type": "type", "validated": true, "ani": 77.6396, "matched_fragments": 60, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus hominis", "strain": "strain=type strain:CRBIP 24.179", "accession": "GCA_000296835.1", "taxid": 1203033, "species_taxid": 1203033, "relation_to_type": "type", "validated": true, "ani": 77.5348, "matched_fragments": 63, "total_fragments": 383, "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": 77.4967, "matched_fragments": 59, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus helveticus", "strain": "strain=DSM 20075", "accession": "GCA_000160855.1", "taxid": 1587, "species_taxid": 1587, "relation_to_type": "type", "validated": true, "ani": 77.2971, "matched_fragments": 67, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus helveticus", "strain": "strain=CGMCC 1.1877", "accession": "GCA_001434945.1", "taxid": 1587, "species_taxid": 1587, "relation_to_type": "type", "validated": true, "ani": 77.2608, "matched_fragments": 64, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus helveticus", "strain": "strain=JCM 1120", "accession": "GCA_015698225.1", "taxid": 1587, "species_taxid": 1587, "relation_to_type": "type", "validated": true, "ani": 77.203, "matched_fragments": 69, "total_fragments": 383, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000178475.1", "gtdb_species": "s__Lactobacillus amylolyticus", "ani": 78.5621, "matched_fragments": 56, "total_fragments": 383, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_905214545.1", "gtdb_species": "s__Lactobacillus sp905214545", "ani": 78.3644, "matched_fragments": 76, "total_fragments": 383, "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": "-" }, { "accession": "GCF_001434335.1", "gtdb_species": "s__Lactobacillus kalixensis", "ani": 78.1552, "matched_fragments": 58, "total_fragments": 383, "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": "-" }, { "accession": "GCF_000615285.1", "gtdb_species": "s__Lactobacillus kitasatonis", "ani": 78.0563, "matched_fragments": 66, "total_fragments": 383, "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": 78.0142, "matched_fragments": 62, "total_fragments": 383, "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": "GCA_910589675.1", "gtdb_species": "s__Lactobacillus sp910589675", "ani": 77.9366, "matched_fragments": 52, "total_fragments": 383, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.73", "min_intra_species_af": "0.71", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001434975.1", "gtdb_species": "s__Lactobacillus gallinarum", "ani": 77.9085, "matched_fragments": 62, "total_fragments": 383, "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_018327645.1", "gtdb_species": "s__Lactobacillus corticis", "ani": 77.8313, "matched_fragments": 59, "total_fragments": 383, "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": "-" }, { "accession": "GCF_000615445.1", "gtdb_species": "s__Lactobacillus hamsteri", "ani": 77.7767, "matched_fragments": 61, "total_fragments": 383, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003584685.1", "gtdb_species": "s__Lactobacillus paragasseri", "ani": 77.6998, "matched_fragments": 58, "total_fragments": 383, "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_900103655.1", "gtdb_species": "s__Lactobacillus kefiranofaciens", "ani": 77.6322, "matched_fragments": 64, "total_fragments": 383, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.62", "min_intra_species_ani": "99.18", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.85", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000014425.1", "gtdb_species": "s__Lactobacillus gasseri", "ani": 77.6222, "matched_fragments": 59, "total_fragments": 383, "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_000296835.1", "gtdb_species": "s__Lactobacillus hominis", "ani": 77.5348, "matched_fragments": 63, "total_fragments": 383, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000160855.1", "gtdb_species": "s__Lactobacillus helveticus", "ani": 77.2971, "matched_fragments": 67, "total_fragments": 383, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.148, "cell_length": 0.354, "doubling_h": -0.086, "growth_tmp": 32.808, "optimum_tmp": 31.646, "optimum_ph": 6.027, "genome_size": 2295637.558, "gc_content": 40.393, "coding_genes": 2119.007, "rRNA16S_genes": 5.074, "tRNA_genes": 63.614, "gram_stain": 1.0, "sporulation": 0.009, "motility": 0.08, "range_salinity": 0.0, "facultative_respiration": 0.155, "anaerobic_respiration": 0.175, "aerobic_respiration": 0.668, "mesophilic_range_tmp": 0.977, "thermophilic_range_tmp": 0.022, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.983, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.016, "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 sp022483245" ], "_genome_taxon": [ "Lactobacillus", "sp.", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Lactobacillus sp022483245", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Lactobacillaceae", "Lactobacillus", "Lactobacillus", "sp022483245" ], "_meo": [ { "id": "MEO_0000119", "label": "bioreactor" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }