SWS3 PD58
BioSample: SAMN48098252 · Study: PRJNA1242173 · 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 |
|---|---|---|---|
| Helcococcus kunzii | Helcococcus | Bacillota | 16.73139% |
| Helcococcus seattlensis | Helcococcus | Bacillota | 11.15848% |
| Helcococcus ovis | Helcococcus | Bacillota | 8.93205% |
| Veillonella parvula | Veillonella | Bacillota | 6.89947% |
| Parvimonas micra | Parvimonas | Bacillota | 5.08627% |
| Porphyromonas pasteri | Porphyromonas | Bacteroidota | 4.69658% |
| Neisseria subflava | Neisseria | Pseudomonadota | 3.47885% |
| Streptococcus oralis | Streptococcus | Bacillota | 3.16134% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 3.14086% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 2.80253% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 2.59388% |
| Solobacterium moorei | Solobacterium | Bacillota | 2.44728% |
| Streptococcus mitis | Streptococcus | Bacillota | 2.19850% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 2.02456% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 1.99618% |
| Granulicatella elegans | Granulicatella | Bacillota | 1.84494% |
| Lancefieldella parvula | Lancefieldella | Actinomycetota | 1.71986% |
| Capnocytophaga ochracea | Capnocytophaga | Bacteroidota | 1.35866% |
| Prevotella nanceiensis | Prevotella | Bacteroidota | 1.17289% |
| Streptococcus viridans | Streptococcus | Bacillota | 1.09300% |
| Gemella haemolysans | Gemella | Bacillota | 0.92962% |
| Schaalia odontolytica | Schaalia | Actinomycetota | 0.82328% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.81194% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.74524% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.74269% |
| Metamycoplasma orale | Metamycoplasma | Mycoplasmatota | 0.71050% |
| Veillonella dispar | Veillonella | Bacillota | 0.65100% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.62353% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.58084% |
| Prevotella pallens | Prevotella | Bacteroidota | 0.54133% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.50339% |
| Treponema brennaborense | Treponema | Spirochaetota | 0.46239% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.44595% |
| Malacoplasma penetrans | Malacoplasma | Mycoplasmatota | 0.41728% |
| Treponema phagedenis | Treponema | Spirochaetota | 0.41167% |
| Prevotella salivae | Prevotella | Bacteroidota | 0.39470% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.36942% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.34294% |
| Rothia aeria | Rothia | Actinomycetota | 0.31578% |
| Prevotella oris | Prevotella | Bacteroidota | 0.30619% |
| Treponema socranskii | Treponema | Spirochaetota | 0.29886% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.29232% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.28281% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.26943% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.25375% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.25255% |
| Neisseria cinerea | Neisseria | Pseudomonadota | 0.24281% |
| Prevotella shahii | Prevotella | Bacteroidota | 0.23683% |
| Neisseria sicca | Neisseria | Pseudomonadota | 0.23479% |
| Rothia dentocariosa | Rothia | Actinomycetota | 0.21992% |
| Rothia mucilaginosa | Rothia | Actinomycetota | 0.20864% |
| Treponema denticola | Treponema | Spirochaetota | 0.19733% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.17481% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.17481% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.16353% |
| Prevotella oulorum | Prevotella | Bacteroidota | 0.16350% |
| Gemella morbillorum | Gemella | Bacillota | 0.15305% |
| Porphyromonas catoniae | Porphyromonas | Bacteroidota | 0.13546% |
| Peptostreptococcus stomatis | Peptostreptococcus | Bacillota | 0.13513% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.12403% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.11842% |
61 of 61 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 |
|---|---|---|
| SRR33251605_1.fastq.gz | FASTQ / 147844477 | 542c72053514e8097415c5b5da52ce64 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 859eb7bb3dc9a8d404bf54b6fedf3027768c17cf1eb39f36dfd89e24cd124475 |
| median_read_length | 1399.0 |
| reads_in_length_window | 29660 |
| 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": 11998, "elapsed_seconds": 2.260439235000149, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 8, "fraction": 0.04, "adapters_found": {"27F": 8}, "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 | SRR33251605 |
|---|---|
| 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 | 177045651 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | human oral cavity |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB15259383 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2022-09 |
| collection_date_end | 2022-09-30 |
| collection_date_start | 2022-08-31 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Denmark:Copenhagen |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | PromethION sequencing: 16S V1-V8 Sequencing of the Human oral Microbiome in Adults : Stimulated Whole Saliva |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | human oral cavity |
| environment_feature | Stimulated whole saliva |
| environment_material | Saliva |
| environmental_medium | Saliva |
| environmental_sample | Not reported |
| experiment_accession | SRX28497609 |
| experiment_alias | SWS3 PD58 |
| experiment_target | Not reported |
| experiment_title | PromethION sequencing: 16S V1-V8 Sequencing of the Human oral Microbiome in Adults : Stimulated Whole Saliva |
| 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/SRR332/005/SRR33251605/SRR33251605_1.fastq.gz |
| fastq_bytes | 147844477 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/005/SRR33251605/SRR33251605_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/005/SRR33251605/SRR33251605_1.fastq.gz |
| fastq_md5 | 542c72053514e8097415c5b5da52ce64 |
| file_location | Not reported |
| first_created | 2026-05-03 |
| first_public | 2026-05-03 |
| 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 | nonPD |
| host_scientific_name | Homo sapiens |
| host_sex | female |
| host_status | Not reported |
| host_tax_id | 9606 |
| identified_by | Not reported |
| instrument_model | PromethION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Not reported |
| last_updated | 2026-06-17 |
| lat | 55.694 |
| 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 | SWS3 PD58 |
| 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 | Stimulated whole saliva |
| location | 55.694 N 12.563 E |
| location_end | 55.694 N 12.563 E |
| location_start | 55.694 N 12.563 E |
| lon | 12.563 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | MIMARKS.survey;MIGS/MIMS/MIMARKS.human-oral |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | human oral microbiome |
| protocol_label | Not reported |
| read_count | 128000 |
| 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 | DS38NBD94.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN48098252 |
| sample_alias | DS38NBD94 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | SWS3 PD58 |
| 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 | SWS3 PD58 |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS24814995 |
| secondary_study_accession | SRP580494 |
| 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 | PRJNA1242173 |
| study_alias | PRJNA1242173 |
| study_title | 16S rRNA gene amplicon sequencing of whole saliva and supragingival plaque microbiota in Parkinson's disease |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA2116554 |
| 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 | DS38NBD94 |
|---|---|
| title | SWS3 PD58 |
| description | SWS3 PD58 |
| collection_date | 2022-09 |
|---|---|
| INSDC secondary accession | SRS24814995 |
| organism | human oral metagenome |
| env_broad_scale | human oral cavity |
| env_local_scale | Stimulated whole saliva |
| host_subject_id | PD58 |
| host_phenotype | nonPD |
| NCBI submission package | MIMARKS.survey.human-oral.6.0 |
| host_sex | female |
| host | Homo sapiens |
| geo_loc_name | Denmark:Copenhagen |
| env_medium | Saliva |
| lat_lon | 55.694 N 12.563 E |
| BioSampleModel | MIGS/MIMS/MIMARKS.human-oral |
| ENA-FIRST-PUBLIC | 2026-04-30 |
| ENA-LAST-UPDATE | 2026-04-30 |
| run | SRR33251605 |
|---|---|
| sample | SAMN48098252 |
| study | PRJNA1242173 |
| title | SWS3 PD58 |
| alias | DS38NBD94 |
| site | Saliva |
| subject | PD58 |
| phenotype | nonPD |
| sex | female |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 61 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.