subject A, interdental plaque
BioSample: SAMD01788873 · Study: PRJDB39890 · Body site: interdental plaque
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 |
|---|---|---|---|
| Veillonella parvula | Veillonella | Bacillota | 32.66500% |
| Veillonella rodentium | Veillonella | Bacillota | 16.48858% |
| Streptococcus anginosus | Streptococcus | Bacillota | 5.42604% |
| Streptococcus salivarius | Streptococcus | Bacillota | 4.33970% |
| Veillonella dispar | Veillonella | Bacillota | 3.85387% |
| Veillonella seminalis | Veillonella | Bacillota | 3.80823% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 3.22624% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 3.13628% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 2.06389% |
| Streptococcus gordonii | Streptococcus | Bacillota | 1.81510% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 1.58427% |
| Streptococcus downei | Streptococcus | Bacillota | 1.54972% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 1.40068% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 1.10430% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 1.01825% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.97060% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.84804% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.75635% |
| Lautropia mirabilis | Lautropia | Pseudomonadota | 0.72838% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.61457% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.60563% |
| Veillonella infantium | Veillonella | Bacillota | 0.58680% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.58015% |
| Rothia aeria | Rothia | Actinomycetota | 0.56573% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.54631% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.53836% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.53751% |
| Lawsonella clevelandensis | Lawsonella | Actinomycetota | 0.52330% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.51741% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.48917% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.47161% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.46045% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.43055% |
| Kingella kingae | Kingella | Pseudomonadota | 0.42310% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.38377% |
| Neisseria animalis | Neisseria | Pseudomonadota | 0.35026% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.34533% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.33944% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.26945% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.26877% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.26404% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.25624% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.25458% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.24917% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.24017% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.23943% |
| Veillonella rogosae | Veillonella | Bacillota | 0.23842% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.21744% |
| Actinomyces oris | Actinomyces | Actinomycetota | 0.21215% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.19942% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.18385% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.17736% |
| Eikenella corrodens | Eikenella | Pseudomonadota | 0.17686% |
| Capnocytophaga haemolytica | Capnocytophaga | Bacteroidota | 0.16265% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.15558% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.14143% |
55 of 56 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 |
|---|---|---|
| DRR893434_1.fastq.gz | FASTQ / 131612455 | 2d61b660cb24b8af6a7ae69d49fa595b |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 4b4af930719eda5037d5a6f3e8d7c22d4cddd04a2a9cebde90051b55c93d5bdc |
| median_read_length | 1605.0 |
| reads_in_length_window | 14563 |
| 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": 15000, "reads_skipped": 607, "elapsed_seconds": 1.634690312999993, "reads_submitted": 15000, "reads_after_filter": 15000, "adapter_scan": {"sampled": 200, "matched": 29, "fraction": 0.145, "adapters_found": {"27F": 28, "BC_FLANK": 1}, "should_trim": true}, "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 | DRR893434 |
|---|---|
| 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 | 164322062 |
| 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 | Osaka Dental University |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2022 |
| collection_date_end | 2022-12-31 |
| collection_date_start | 2022-01-01 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Japan:Osaka |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: MinION sequencing of SAMD01788873 |
| 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 | DRX871272 |
| experiment_alias | DRX871272 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: MinION sequencing of SAMD01788873 |
| 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/DRR893/DRR893434/DRR893434_1.fastq.gz |
| fastq_bytes | 131612455 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893434/DRR893434_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893434/DRR893434_1.fastq.gz |
| fastq_md5 | 2d61b660cb24b8af6a7ae69d49fa595b |
| file_location | Not reported |
| first_created | 2025-12-14 |
| first_public | 2025-12-14 |
| 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 | MinION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | interdental plaque |
| last_updated | 2025-12-14 |
| lat | Not reported |
| library_construction_protocol | 16S Barcoding kit (SQK-RAB204). full-length 16S rRNA gene was amplified with 27F/1492R primers. |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | ONT, AP |
| 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 | GENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | Not reported |
| location_end | Not reported |
| location_start | Not reported |
| lon | Not reported |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Generic |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | human oral metagenome |
| protocol_label | Not reported |
| read_count | 103984 |
| 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 | DRR893434 |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMD01788873 |
| sample_alias | SAMD01788873 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | subject A, interdental plaque |
| 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 | subject A, interdental plaque |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | DRS624239 |
| secondary_study_accession | DRP016630 |
| 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 | PRJDB39890 |
| study_alias | DRP016630 |
| study_title | Cross-platform comparison of oral microbiome profiles under a unified reference database |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | DRA025851 |
| 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 | Not reported |
| 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 | SAMD01788873 |
|---|---|
| title | subject A, interdental plaque |
| description | Not reported |
| host_subject_id | A |
|---|---|
| collection_date | 2022 |
| INSDC secondary accession | DRS624239 |
| NCBI submission package | Generic.1.0 |
| organism | human oral metagenome |
| host | Homo sapiens |
| geo_loc_name | Japan:Osaka |
| lat_lon | missing |
| isolation_source | interdental plaque |
| sample_name | AP |
| BioSampleModel | Generic |
| ENA-FIRST-PUBLIC | 2025-12-12 |
| ENA-LAST-UPDATE | 2025-12-13 |
| run | DRR893434 |
|---|---|
| sample | SAMD01788873 |
| study | PRJDB39890 |
| title | subject A, interdental plaque |
| alias | SAMD01788873 |
| site | interdental plaque |
| subject | A |
| 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 | 15000 |
| species_reported | 56 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.