Metagenome or environmental sample from human oral metagenome
BioSample: SAMN28173408 · Study: PRJNA836758 · Body site: Extracted Tooth
Interactive report · NCBI SRA · ENA
Relative abundance is normalized among reported taxa. No reported taxa does not establish absence of organisms.
| Species | Genus | Phylum | Abundance |
|---|---|---|---|
| Phocaeicola abscessus | Phocaeicola | Bacteroidota | 20.76788% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 17.39471% |
| Tannerella forsythia | Tannerella | Bacteroidota | 12.32303% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 6.18753% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 4.49507% |
| Eubacterium ramulus | Eubacterium | Bacillota | 4.36073% |
| Prevotella oralis | Prevotella | Bacteroidota | 3.27167% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 3.19647% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 2.76605% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 2.71489% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 2.53469% |
| Mogibacterium pumilum | Mogibacterium | Bacillota | 1.46565% |
| Eubacterium limosum | Eubacterium | Bacillota | 1.25644% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 1.20113% |
| Desulfobulbus oralis | Desulfobulbus | Thermodesulfobacteriota | 1.18193% |
| Prevotella buccalis | Prevotella | Bacteroidota | 1.15760% |
| Dialister invisus | Dialister | Bacillota | 1.10240% |
| Pseudoramibacter alactolyticus | Pseudoramibacter | Bacillota | 1.00608% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.81756% |
| Prevotella oris | Prevotella | Bacteroidota | 0.75900% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.72519% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.71085% |
| Phocaeicola vulgatus | Phocaeicola | Bacteroidota | 0.68907% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.67245% |
| Prevotella brevis | Prevotella | Bacteroidota | 0.62120% |
| Mogibacterium vescum | Mogibacterium | Bacillota | 0.58325% |
| Eubacterium ventriosum | Eubacterium | Bacillota | 0.51574% |
| Mogibacterium neglectum | Mogibacterium | Bacillota | 0.48454% |
| Pseudomonas aeruginosa | Pseudomonas | Pseudomonadota | 0.47127% |
| Eubacterium multiforme | Eubacterium | Bacillota | 0.44072% |
| Alterileibacterium massiliense | Alterileibacterium | Bacillota | 0.43653% |
| Phocaeicola dorei | Phocaeicola | Bacteroidota | 0.35895% |
| Stutzerimonas stutzeri | Stutzerimonas | Pseudomonadota | 0.30611% |
| Dialister hominis | Dialister | Bacillota | 0.28286% |
| Eubacterium barkeri | Eubacterium | Bacillota | 0.28237% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.26176% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.24680% |
| Prevotella buccae | Prevotella | Bacteroidota | 0.23222% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 0.22980% |
| Megasphaera hexanoica | Megasphaera | Bacillota | 0.15511% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.15299% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.15133% |
| Phocaeicola sartorii | Phocaeicola | Bacteroidota | 0.14211% |
| Prevotella corporis | Prevotella | Bacteroidota | 0.13937% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.13299% |
| Eubacterium oxidoreducens | Eubacterium | Bacillota | 0.11180% |
| Prevotella maculosa | Prevotella | Bacteroidota | 0.11080% |
| Prevotella bivia | Prevotella | Bacteroidota | 0.10480% |
| Megasphaera coli | Megasphaera | Bacillota | 0.09718% |
| Prevotella baroniae | Prevotella | Bacteroidota | 0.09563% |
| Eubacterium uniforme | Eubacterium | Bacillota | 0.09374% |
51 of 51 reported species have an eligible reference. MAFFT alignment and FastTree GTR+CAT tree, pruned to this sample. This is not a phylogeny inferred from sample reads or ASVs. Root placement is arbitrary; branch lengths are substitutions per site.
Files contain the original full run. Downloads are hosted by ENA.
| File | Type / bytes | MD5 |
|---|---|---|
| SRR19631903_1.fastq.gz | FASTQ / 200333413 | e10b2904885767985e0b7fc716af3f89 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 468786c776b4272e40eb9c56be53b3b22e2d97cd5580f348865fb6bc4b0767ab |
| median_read_length | 1447.0 |
| reads_in_length_window | 25990 |
| length_window_bp | [1200, 2000] |
| quality_scores | Unavailable in fetched FASTA; no measured quality filtering |
| classifier_stats | {"marker": "16s", "pipeline": "v18.8", "gpu": "RTX-PRO-6000", "input_path": "volume-fastq-gz", "reads_in": 30000, "reads_skipped": 4674, "elapsed_seconds": 2.7174241979999962, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 2, "fraction": 0.01, "adapters_found": {"BC_FLANK": 2}, "should_trim": false}, "porechop_ran": false, "porechop_reason": "fast-path: no adapter trimming required"} |
All retrieved values are included. Blank source values are displayed as “Not reported”. Expand the sections below to inspect the full record.
| run_accession | SRR19631903 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | Not reported |
| bam_bytes | Not reported |
| bam_file_role | Not reported |
| bam_ftp | Not reported |
| bam_galaxy | Not reported |
| bam_md5 | Not reported |
| base_count | 210793113 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Not reported |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB11589611 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2021-12-02 |
| collection_date_end | 2021-12-02 |
| collection_date_start | 2021-12-02 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | India: Chennai |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Not reported |
| environment_feature | Not reported |
| environment_material | Not reported |
| environmental_medium | Not reported |
| environmental_sample | Not reported |
| experiment_accession | SRX15682446 |
| experiment_alias | TM 4 |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples |
| experimental_factor | Not reported |
| experimental_protocol | Not reported |
| extraction_protocol | Not reported |
| faang_library_selection | Not reported |
| fastq_aspera | fasp.sra.ebi.ac.uk:/vol1/fastq/SRR196/003/SRR19631903/SRR19631903_1.fastq.gz |
| fastq_bytes | 200333413 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/003/SRR19631903/SRR19631903_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/003/SRR19631903/SRR19631903_1.fastq.gz |
| fastq_md5 | e10b2904885767985e0b7fc716af3f89 |
| file_location | Not reported |
| first_created | 2023-08-27 |
| first_public | 2023-08-27 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Homo sapiens |
| host_body_site | Not reported |
| host_genotype | Not reported |
| host_gravidity | Not reported |
| host_growth_conditions | Not reported |
| host_phenotype | Not reported |
| host_scientific_name | Homo sapiens |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | 9606 |
| identified_by | Not reported |
| instrument_model | GridION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Extracted Tooth |
| last_updated | 2023-08-27 |
| lat | 13.0827 |
| library_construction_protocol | Not reported |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | TM 4 |
| library_pcr_isolation_protocol | Not reported |
| library_prep_date | Not reported |
| library_prep_date_format | Not reported |
| library_prep_latitude | Not reported |
| library_prep_location | Not reported |
| library_prep_longitude | Not reported |
| library_selection | PCR |
| library_source | METAGENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | 13.0827 N 80.2707 E |
| location_end | 13.0827 N 80.2707 E |
| location_start | 13.0827 N 80.2707 E |
| lon | 80.2707 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Metagenome or environmental |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | Not reported |
| protocol_label | Not reported |
| read_count | 154360 |
| read_strand | Not reported |
| restriction_enzyme | Not reported |
| restriction_enzyme_target_sequence | Not reported |
| restriction_site | Not reported |
| rna_integrity_num | Not reported |
| rna_prep_3_protocol | Not reported |
| rna_prep_5_protocol | Not reported |
| rna_purity_230_ratio | Not reported |
| rna_purity_280_ratio | Not reported |
| rt_prep_protocol | Not reported |
| run_alias | TM4.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN28173408 |
| sample_alias | TM 4 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Metagenome or environmental sample from human oral metagenome |
| sample_material | Not reported |
| sample_prep_interval | Not reported |
| sample_prep_interval_units | Not reported |
| sample_storage | Not reported |
| sample_storage_processing | Not reported |
| sample_title | Metagenome or environmental sample from human oral metagenome |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS13380274 |
| secondary_study_accession | SRP379752 |
| sequencing_date | Not reported |
| sequencing_date_format | Not reported |
| sequencing_location | Not reported |
| sequencing_longitude | Not reported |
| sequencing_method | Not reported |
| sequencing_primer_catalog | Not reported |
| sequencing_primer_lot | Not reported |
| sequencing_primer_provider | Not reported |
| serotype | Not reported |
| serovar | Not reported |
| sex | Not reported |
| specimen_voucher | Not reported |
| sra_aspera | Not reported |
| sra_bytes | Not reported |
| sra_file_role | Not reported |
| sra_ftp | Not reported |
| sra_galaxy | Not reported |
| sra_md5 | Not reported |
| status | public |
| strain | Not reported |
| study_accession | PRJNA836758 |
| study_alias | PRJNA836758 |
| study_title | 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples using Nanopore Sequencing Platform |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1435979 |
| submission_tool | Not reported |
| submitted_aspera | Not reported |
| submitted_bytes | Not reported |
| submitted_file_role | Not reported |
| submitted_format | Not reported |
| submitted_ftp | Not reported |
| submitted_galaxy | Not reported |
| submitted_host_sex | Not reported |
| submitted_md5 | Not reported |
| submitted_read_type | Not reported |
| surveillance_target | Not reported |
| tag | env_geo;env_geo:terrestrial |
| target_gene | Not reported |
| tax_id | 447426 |
| tax_lineage | 1;2787823;12908;408169;410656;447426 |
| taxonomic_classification | Not reported |
| taxonomic_identity_marker | Not reported |
| temperature | Not reported |
| tissue_lib | Not reported |
| tissue_type | Not reported |
| transposase_protocol | Not reported |
| variety | Not reported |
| alias | TM 4 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2021-12-02 |
|---|---|
| INSDC secondary accession | SRS13380274 |
| NCBI submission package | Metagenome.environmental.1.0 |
| organism | human oral metagenome |
| host | Homo sapiens |
| geo_loc_name | India: Chennai |
| lat_lon | 13.0827 N 80.2707 E |
| isolation_source | Extracted Tooth |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2023-08-09 |
| ENA-LAST-UPDATE | 2023-08-09 |
| run | SRR19631903 |
|---|---|
| sample | SAMN28173408 |
| study | PRJNA836758 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | TM 4 |
| site | Extracted Tooth |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 51 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.