{ "type": "genome", "identifier": "GCF_900156885.1", "organism": "Limosilactobacillus caccae", "title": "Limosilactobacillus caccae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900156885.1", "bioproject": "PRJNA224116", "biosample": "SAMEA49226668", "wgs_master": "FTOY00000000.1", "refseq_category": "reference genome", "taxid": "1926284", "species_taxid": "1926284", "organism_name": "Limosilactobacillus caccae", "infraspecific_name": "strain=Marseille-P3519T", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/15", "asm_name": "PRJEB18962", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900156885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/156/885/GCF_900156885.1_PRJEB18962", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2237367", "genome_size_ungapped": "2237367", "gc_percent": "45.500000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900156885.1-RS_2024_07_29", "annotation_date": "2024-07-29", "total_gene_count": "2113", "protein_coding_gene_count": "2026", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-15", "dateModified": "2017-01-15", "datePublished": "2017-01-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Limosilactobacillus caccae" ], "sample_taxid": [ "1926284" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.636 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)": "2237367", "Number of Sequences": "11", "Longest Sequences (bp)": "909365", "N50 (bp)": "629577", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.4", "Number of CDSs": "2055", "Average Protein Length": "322.5", "Coding Ratio (%)": "88.9", "Number of rRNAs": "6", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Limosilactobacillus balticus", "strain": "strain=BG-AF3-A", "accession": "GCA_014145615.1", "taxid": 2759747, "species_taxid": 2759747, "relation_to_type": "type", "validated": true, "ani": 80.8867, "matched_fragments": 278, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. rodentium", "strain": "strain=100-23", "accession": "GCA_000168255.1", "taxid": 349123, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.8399, "matched_fragments": 273, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. reuteri", "strain": "strain=DSM 20016", "accession": "GCA_000016825.1", "taxid": 557436, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.6504, "matched_fragments": 255, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. reuteri", "strain": "strain=DSM 20016", "accession": "GCA_001434615.1", "taxid": 557436, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.5672, "matched_fragments": 242, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus albertensis", "strain": "strain=Lr3000", "accession": "GCA_014145555.1", "taxid": 2759752, "species_taxid": 2759752, "relation_to_type": "type", "validated": true, "ani": 80.5561, "matched_fragments": 283, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. reuteri", "strain": "strain=JCM 1112", "accession": "GCA_000010005.1", "taxid": 557436, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.49, "matched_fragments": 269, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. murium", "strain": "strain=lpuph1", "accession": "GCA_000179455.1", "taxid": 863368, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.3877, "matched_fragments": 246, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus reuteri subsp. suis", "strain": "strain=ATCC 53608", "accession": "GCA_000236455.2", "taxid": 927703, "species_taxid": 1598, "relation_to_type": "type", "validated": true, "ani": 80.2708, "matched_fragments": 258, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus rudii", "strain": "strain=STM3_1", "accession": "GCA_014145455.1", "taxid": 2759755, "species_taxid": 2759755, "relation_to_type": "type", "validated": true, "ani": 80.1429, "matched_fragments": 265, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus avistercoris", "strain": "strain=Sa3CUN2", "accession": "GCA_014836425.1", "taxid": 2762243, "species_taxid": 2762243, "relation_to_type": "type", "validated": true, "ani": 80.1377, "matched_fragments": 155, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus caviae", "strain": "strain=CCM 8609", "accession": "GCA_014635905.1", "taxid": 1769424, "species_taxid": 1769424, "relation_to_type": "type", "validated": true, "ani": 80.0218, "matched_fragments": 276, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus agrestis", "strain": "strain=WF-MT5-A", "accession": "GCA_014145585.1", "taxid": 2759748, "species_taxid": 2759748, "relation_to_type": "type", "validated": true, "ani": 79.96, "matched_fragments": 231, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=ATCC 49540", "accession": "GCA_000159435.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 79.9438, "matched_fragments": 151, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=DSM 5837", "accession": "GCA_001435915.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 79.8588, "matched_fragments": 145, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus fastidiosus", "strain": "strain=WF-MO7-1", "accession": "GCA_014145505.1", "taxid": 2759855, "species_taxid": 2759855, "relation_to_type": "type", "validated": true, "ani": 79.7542, "matched_fragments": 138, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus panis", "strain": "strain=DSM 6035", "accession": "GCA_001435935.1", "taxid": 47493, "species_taxid": 47493, "relation_to_type": "type", "validated": true, "ani": 79.321, "matched_fragments": 186, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus panis", "strain": "strain=DSM 6035", "accession": "GCA_001027985.1", "taxid": 47493, "species_taxid": 47493, "relation_to_type": "type", "validated": true, "ani": 79.2844, "matched_fragments": 189, "total_fragments": 741, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900156885.1", "gtdb_species": "s__Limosilactobacillus sp900156885", "ani": 100.0, "matched_fragments": 741, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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": "conclusive" }, { "accession": "GCF_014145615.1", "gtdb_species": "s__Limosilactobacillus balticus", "ani": 80.8706, "matched_fragments": 278, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000016825.1", "gtdb_species": "s__Limosilactobacillus reuteri", "ani": 80.6259, "matched_fragments": 256, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.73", "min_intra_species_ani": "95.25", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.75", "num_clustered_genomes": 135, "status": "-" }, { "accession": "GCF_013694365.1", "gtdb_species": "s__Limosilactobacillus reuteri_E", "ani": 80.5802, "matched_fragments": 232, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.28", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.72", "num_clustered_genomes": 58, "status": "-" }, { "accession": "GCA_003072625.1", "gtdb_species": "s__Limosilactobacillus reuteri_D", "ani": 80.3902, "matched_fragments": 249, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.43", "min_intra_species_ani": "95.30", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.72", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_014836425.1", "gtdb_species": "s__Limosilactobacillus sp014836425", "ani": 80.2488, "matched_fragments": 152, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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_014145455.1", "gtdb_species": "s__Limosilactobacillus rudii", "ani": 80.1697, "matched_fragments": 264, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014145585.1", "gtdb_species": "s__Limosilactobacillus agrestis", "ani": 79.96, "matched_fragments": 231, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000159435.1", "gtdb_species": "s__Limosilactobacillus vaginalis", "ani": 79.9542, "matched_fragments": 150, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.39", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.86", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_019117285.1", "gtdb_species": "s__Limosilactobacillus intestinigallinarum", "ani": 79.4959, "matched_fragments": 116, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001435935.1", "gtdb_species": "s__Limosilactobacillus panis", "ani": 79.321, "matched_fragments": 186, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000160835.1", "gtdb_species": "s__Limosilactobacillus antri", "ani": 79.1975, "matched_fragments": 164, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_905214235.1", "gtdb_species": "s__Limosilactobacillus sp905214235", "ani": 79.0468, "matched_fragments": 197, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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": "GCA_019117185.1", "gtdb_species": "s__Limosilactobacillus intestinipullorum", "ani": 78.7105, "matched_fragments": 160, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.14", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018883805.1", "gtdb_species": "s__Limosilactobacillus merdavium", "ani": 78.6296, "matched_fragments": 123, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.07", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002299975.1", "gtdb_species": "s__Limosilactobacillus sp002299975", "ani": 77.9503, "matched_fragments": 122, "total_fragments": 741, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.38", "min_intra_species_ani": "99.38", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Limosilactobacillus", "caccae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }