SWS3 PD05
BioSample: SAMN48098220 · 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 |
|---|---|---|---|
| Veillonella dispar | Veillonella | Bacillota | 10.35992% |
| Prevotella jejuni | Prevotella | Bacteroidota | 7.19668% |
| Lancefieldella parvula | Lancefieldella | Actinomycetota | 7.13289% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 6.34696% |
| Veillonella parvula | Veillonella | Bacillota | 5.36486% |
| Prevotella pallens | Prevotella | Bacteroidota | 5.03889% |
| Prevotella salivae | Prevotella | Bacteroidota | 4.61238% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 3.45676% |
| Selenomonas infelix | Selenomonas | Bacillota | 3.42290% |
| Schaalia odontolytica | Schaalia | Actinomycetota | 2.88219% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 2.72383% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 2.45297% |
| Streptococcus oralis | Streptococcus | Bacillota | 2.35047% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 2.12058% |
| Neisseria subflava | Neisseria | Pseudomonadota | 1.95975% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 1.88910% |
| Iodobacter arcticus | Iodobacter | Pseudomonadota | 1.80150% |
| Solobacterium moorei | Solobacterium | Bacillota | 1.79485% |
| Prevotella veroralis | Prevotella | Bacteroidota | 1.78521% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 1.57548% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.45873% |
| Streptococcus salivarius | Streptococcus | Bacillota | 1.36276% |
| Actinomyces pacaensis | Actinomyces | Actinomycetota | 1.35233% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 1.17664% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 1.03703% |
| Prevotella oris | Prevotella | Bacteroidota | 0.96380% |
| Campylobacter cuniculorum | Campylobacter | Pseudomonadota | 0.95964% |
| Prevotella oulorum | Prevotella | Bacteroidota | 0.95167% |
| Streptococcus viridans | Streptococcus | Bacillota | 0.79759% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.74312% |
| Rothia dentocariosa | Rothia | Actinomycetota | 0.64481% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.62488% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.59828% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 0.54483% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.53846% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.51490% |
| Helcococcus seattlensis | Helcococcus | Bacillota | 0.47955% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.47327% |
| Rothia mucilaginosa | Rothia | Actinomycetota | 0.45870% |
| Helcococcus ovis | Helcococcus | Bacillota | 0.44823% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.44539% |
| Campylobacter avium | Campylobacter | Pseudomonadota | 0.43406% |
| Helcococcus kunzii | Helcococcus | Bacillota | 0.40842% |
| Campylobacter insulaenigrae | Campylobacter | Pseudomonadota | 0.38356% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.37237% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.35526% |
| Veillonella rodentium | Veillonella | Bacillota | 0.35011% |
| Rothia aeria | Rothia | Actinomycetota | 0.33238% |
| Gemella haemolysans | Gemella | Bacillota | 0.33238% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.31909% |
| Prevotella histicola | Prevotella | Bacteroidota | 0.30633% |
| Actinomyces oris | Actinomyces | Actinomycetota | 0.29659% |
| Actinomyces israelii | Actinomyces | Actinomycetota | 0.28366% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.27948% |
| Actinomyces naeslundii | Actinomyces | Actinomycetota | 0.25516% |
| Actinomyces radicidentis | Actinomyces | Actinomycetota | 0.24815% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.24765% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.21558% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.20084% |
| Campylobacter coli | Campylobacter | Pseudomonadota | 0.19014% |
| Campylobacter peloridis | Campylobacter | Pseudomonadota | 0.18827% |
| Iodobacter fluviatilis | Iodobacter | Pseudomonadota | 0.17949% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.17589% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.16681% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.16619% |
| Campylobacter helveticus | Campylobacter | Pseudomonadota | 0.16455% |
| Lancefieldella rimae | Lancefieldella | Actinomycetota | 0.15290% |
| Veillonella atypica | Veillonella | Bacillota | 0.15193% |
68 of 68 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 |
|---|---|---|
| SRR33251601_1.fastq.gz | FASTQ / 154485869 | c187f8bad7ef4ae3fd0d5c918710fbc5 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | a5dd517ff1eb56e76d541b38adf0c50bf63f96a4e144c579039d5c8ee2972346 |
| median_read_length | 1397.0 |
| reads_in_length_window | 19736 |
| 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": 20000, "reads_skipped": 4740, "elapsed_seconds": 2.048626143999968, "reads_submitted": 20000, "reads_after_filter": 20000, "adapter_scan": {"sampled": 200, "matched": 5, "fraction": 0.025, "adapters_found": {"27F": 5}, "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 | SRR33251601 |
|---|---|
| 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 | 176917973 |
| 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 | 2021-05 |
| collection_date_end | 2021-05-31 |
| collection_date_start | 2021-04-30 |
| 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 | SRX28497613 |
| experiment_alias | SWS3 PD05 |
| 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/SRR332/001/SRR33251601/SRR33251601_1.fastq.gz |
| fastq_bytes | 154485869 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/001/SRR33251601/SRR33251601_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/001/SRR33251601/SRR33251601_1.fastq.gz |
| fastq_md5 | c187f8bad7ef4ae3fd0d5c918710fbc5 |
| 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 | PD |
| host_scientific_name | Homo sapiens |
| host_sex | male |
| 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 | 2026-06-16 |
| 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 PD05 |
| 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 | DS05NBD94.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN48098220 |
| sample_alias | DS05NBD94 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | SWS3 PD05 |
| 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 PD05 |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS24814999 |
| 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 | DS05NBD94 |
|---|---|
| title | SWS3 PD05 |
| description | SWS3 PD05 |
| collection_date | 2021-05 |
|---|---|
| INSDC secondary accession | SRS24814999 |
| organism | human oral metagenome |
| env_broad_scale | human oral cavity |
| env_local_scale | Stimulated whole saliva |
| host_subject_id | PD05 |
| host_phenotype | PD |
| NCBI submission package | MIMARKS.survey.human-oral.6.0 |
| host_sex | male |
| 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 | SRR33251601 |
|---|---|
| sample | SAMN48098220 |
| study | PRJNA1242173 |
| title | SWS3 PD05 |
| alias | DS05NBD94 |
| site | Saliva |
| subject | PD05 |
| phenotype | PD |
| sex | male |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 20000 |
| species_reported | 68 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.