subject B, interdental plaque
BioSample: SAMD01788874 · 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 |
|---|---|---|---|
| Campylobacter curvus | Campylobacter | Pseudomonadota | 10.49200% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 6.92101% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 6.58736% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 6.17524% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 5.03810% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 4.57025% |
| Streptococcus anginosus | Streptococcus | Bacillota | 3.71227% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 3.62268% |
| Streptococcus salivarius | Streptococcus | Bacillota | 3.27472% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 3.22807% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 3.18395% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 3.01838% |
| Neisseria elongata | Neisseria | Pseudomonadota | 2.54453% |
| Selenomonas sputigena | Selenomonas | Bacillota | 2.53967% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 2.36388% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 2.31893% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 1.72544% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 1.15975% |
| Veillonella parvula | Veillonella | Bacillota | 1.15743% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 1.14261% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 1.13995% |
| Capnocytophaga haemolytica | Capnocytophaga | Bacteroidota | 1.13210% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 1.09499% |
| Abiotrophia defectiva | Abiotrophia | Bacillota | 1.07502% |
| Neisseria animalis | Neisseria | Pseudomonadota | 1.05989% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.99892% |
| Campylobacter rectus | Campylobacter | Pseudomonadota | 0.94646% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.87968% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 0.80798% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.80299% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.75685% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.72536% |
| Streptococcus downei | Streptococcus | Bacillota | 0.58588% |
| Veillonella rodentium | Veillonella | Bacillota | 0.56471% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.56088% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.54990% |
| Capnocytophaga canimorsus | Capnocytophaga | Bacteroidota | 0.51381% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.50616% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.48336% |
| Cardiobacterium hominis | Cardiobacterium | Pseudomonadota | 0.47479% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.46279% |
| Fusobacterium necrophorum | Fusobacterium | Fusobacteriota | 0.45030% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 0.43753% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.41225% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 0.40931% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.40705% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.40514% |
| Gemella palaticanis | Gemella | Bacillota | 0.37919% |
| Selenomonas infelix | Selenomonas | Bacillota | 0.36846% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.35021% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.34130% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.32689% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.31432% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.28433% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.28404% |
| Lachnoanaerobaculum gingivalis | Lachnoanaerobaculum | Bacillota | 0.25278% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.23670% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.22246% |
| Elizabethkingia miricola | Elizabethkingia | Bacteroidota | 0.22201% |
| Capnocytophaga ochracea | Capnocytophaga | Bacteroidota | 0.21207% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.21067% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.20748% |
| Veillonella dispar | Veillonella | Bacillota | 0.20123% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.18793% |
| Selenomonas lacticifex | Selenomonas | Bacillota | 0.17963% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.17393% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.16137% |
| Neisseria arctica | Neisseria | Pseudomonadota | 0.15621% |
| Capnocytophaga granulosa | Capnocytophaga | Bacteroidota | 0.15248% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 0.14822% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.14709% |
| Veillonella seminalis | Veillonella | Bacillota | 0.14488% |
| Lachnoanaerobaculum saburreum | Lachnoanaerobaculum | Bacillota | 0.14481% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.13389% |
| Gemella haemolysans | Gemella | Bacillota | 0.11682% |
| Cardiobacterium valvarum | Cardiobacterium | Pseudomonadota | 0.10946% |
| Campylobacter ureolyticus | Campylobacter | Pseudomonadota | 0.10508% |
| Fusobacterium hwasookii | Fusobacterium | Fusobacteriota | 0.10373% |
77 of 78 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 |
|---|---|---|
| DRR893435_1.fastq.gz | FASTQ / 143536058 | 9cea6ee5cb24a9273165eb215f655d52 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | a28bde4740be9b27a5a6bdab87607598ce8551b7b3878cbb1f2c3fda9d754b2a |
| median_read_length | 1573.0 |
| reads_in_length_window | 29076 |
| 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": 4066, "elapsed_seconds": 2.478284213000002, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 22, "fraction": 0.11, "adapters_found": {"27F": 22}, "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 | DRR893435 |
|---|---|
| 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 | 169691152 |
| 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 SAMD01788874 |
| 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 | DRX871273 |
| experiment_alias | DRX871273 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: MinION sequencing of SAMD01788874 |
| 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/DRR893435/DRR893435_1.fastq.gz |
| fastq_bytes | 143536058 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893435/DRR893435_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893435/DRR893435_1.fastq.gz |
| fastq_md5 | 9cea6ee5cb24a9273165eb215f655d52 |
| 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, BP |
| 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 | 109299 |
| 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 | DRR893435 |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMD01788874 |
| sample_alias | SAMD01788874 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | subject B, 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 B, 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 | DRS624240 |
| 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 | SAMD01788874 |
|---|---|
| title | subject B, interdental plaque |
| description | Not reported |
| host_subject_id | B |
|---|---|
| collection_date | 2022 |
| INSDC secondary accession | DRS624240 |
| 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 | BP |
| BioSampleModel | Generic |
| ENA-FIRST-PUBLIC | 2025-12-12 |
| ENA-LAST-UPDATE | 2025-12-13 |
| run | DRR893435 |
|---|---|
| sample | SAMD01788874 |
| study | PRJDB39890 |
| title | subject B, interdental plaque |
| alias | SAMD01788874 |
| site | interdental plaque |
| subject | B |
| 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 | 78 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.