subject A, saliva
BioSample: SAMD01788875 · Study: PRJDB39890 · Body site: saliva
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 | 12.07191% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 8.36252% |
| Veillonella rodentium | Veillonella | Bacillota | 7.80934% |
| Veillonella dispar | Veillonella | Bacillota | 5.79027% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 4.89664% |
| Streptococcus anginosus | Streptococcus | Bacillota | 4.57307% |
| Streptococcus salivarius | Streptococcus | Bacillota | 4.51608% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 3.97774% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 2.90987% |
| Catonella morbi | Catonella | Bacillota | 2.76354% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 2.50954% |
| Neisseria elongata | Neisseria | Pseudomonadota | 2.26854% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 1.66912% |
| Veillonella seminalis | Veillonella | Bacillota | 1.53615% |
| Prevotella intermedia | Prevotella | Bacteroidota | 1.32978% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 1.25318% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 1.24581% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.20027% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 1.18138% |
| Neisseria animalis | Neisseria | Pseudomonadota | 0.99787% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.99250% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.90312% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.86467% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.86156% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.85026% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.82429% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.77747% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 0.71246% |
| Gemella palaticanis | Gemella | Bacillota | 0.70817% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.70683% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.70548% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.68427% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.68422% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.66272% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.64122% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.63882% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.59030% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.58186% |
| Streptococcus downei | Streptococcus | Bacillota | 0.58177% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 0.53997% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.49497% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.47100% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.46003% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.45561% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.42633% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.42160% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.39267% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.38019% |
| Gemella haemolysans | Gemella | Bacillota | 0.37458% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.36843% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 0.34873% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.34367% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.33727% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.30833% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.30141% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.28469% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.28356% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.27541% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.27048% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 0.26585% |
| Veillonella infantium | Veillonella | Bacillota | 0.25223% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.24391% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.23474% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.22700% |
| Neisseria weaveri | Neisseria | Pseudomonadota | 0.22055% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.21822% |
| Veillonella rogosae | Veillonella | Bacillota | 0.20373% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.20114% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.18149% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.16338% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.16314% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.14999% |
| Neisseria arctica | Neisseria | Pseudomonadota | 0.14726% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 0.14625% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.14494% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.14328% |
| Prevotella oris | Prevotella | Bacteroidota | 0.13305% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.12919% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.12749% |
| Neisseria cinerea | Neisseria | Pseudomonadota | 0.12498% |
| Megasphaera hexanoica | Megasphaera | Bacillota | 0.12176% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.11594% |
| Capnocytophaga haemolytica | Capnocytophaga | Bacteroidota | 0.11367% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.11092% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.11028% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.10947% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.10499% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.10486% |
| Veillonella tobetsuensis | Veillonella | Bacillota | 0.10373% |
| Lachnoanaerobaculum gingivalis | Lachnoanaerobaculum | Bacillota | 0.10360% |
| Neisseria perflava | Neisseria | Pseudomonadota | 0.09629% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.09451% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.09434% |
| Prevotella bryantii | Prevotella | Bacteroidota | 0.09311% |
| Streptococcus milleri | Streptococcus | Bacillota | 0.08786% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.08556% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.07875% |
| Fusobacterium necrophorum | Fusobacterium | Fusobacteriota | 0.07500% |
97 of 98 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 |
|---|---|---|
| DRR893436_1.fastq.gz | FASTQ / 163516821 | b9dc2ea7b6dee699beffea74bf4b692e |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 2aba38988a4c9ebd36e00dc986f7a3d8038f81a61f64ad4a5c40abf7fb4e6d79 |
| median_read_length | 1593.0 |
| reads_in_length_window | 29149 |
| 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": 3093, "elapsed_seconds": 2.6492884550000007, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 32, "fraction": 0.16, "adapters_found": {"BC_FLANK": 2, "27F": 30}, "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 | DRR893436 |
|---|---|
| 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 | 194585107 |
| 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 SAMD01788875 |
| 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 | DRX871274 |
| experiment_alias | DRX871274 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: MinION sequencing of SAMD01788875 |
| 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/DRR893436/DRR893436_1.fastq.gz |
| fastq_bytes | 163516821 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893436/DRR893436_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/DRR893/DRR893436/DRR893436_1.fastq.gz |
| fastq_md5 | b9dc2ea7b6dee699beffea74bf4b692e |
| 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 | saliva |
| 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, AS |
| 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 | 124068 |
| 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 | DRR893436 |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMD01788875 |
| sample_alias | SAMD01788875 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | subject A, saliva |
| 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, saliva |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | DRS624241 |
| 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 | SAMD01788875 |
|---|---|
| title | subject A, saliva |
| description | Not reported |
| host_subject_id | A |
|---|---|
| collection_date | 2022 |
| INSDC secondary accession | DRS624241 |
| NCBI submission package | Generic.1.0 |
| organism | human oral metagenome |
| host | Homo sapiens |
| geo_loc_name | Japan:Osaka |
| lat_lon | missing |
| isolation_source | saliva |
| sample_name | AS |
| BioSampleModel | Generic |
| ENA-FIRST-PUBLIC | 2025-12-12 |
| ENA-LAST-UPDATE | 2025-12-13 |
| run | DRR893436 |
|---|---|
| sample | SAMD01788875 |
| study | PRJDB39890 |
| title | subject A, saliva |
| alias | SAMD01788875 |
| site | saliva |
| 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 | 30000 |
| species_reported | 98 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.