Patient23 saliva 16S_full-length
BioSample: SAMN47766388 · Study: PRJNA1243403 · 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 |
|---|---|---|---|
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 10.63929% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 7.50125% |
| Streptococcus salivarius | Streptococcus | Bacillota | 6.35308% |
| Streptococcus anginosus | Streptococcus | Bacillota | 4.92641% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 4.58481% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 3.12273% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 3.12263% |
| Neisseria elongata | Neisseria | Pseudomonadota | 3.04560% |
| Veillonella dispar | Veillonella | Bacillota | 2.46623% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 2.23751% |
| Prevotella intermedia | Prevotella | Bacteroidota | 2.06978% |
| Veillonella parvula | Veillonella | Bacillota | 1.99855% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 1.68303% |
| Neisseria animalis | Neisseria | Pseudomonadota | 1.60041% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 1.59466% |
| Veillonella rodentium | Veillonella | Bacillota | 1.42769% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 1.42181% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 1.37795% |
| Parvimonas micra | Parvimonas | Bacillota | 1.31046% |
| Selenomonas sputigena | Selenomonas | Bacillota | 1.28412% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 1.07575% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.02706% |
| Prevotella denticola | Prevotella | Bacteroidota | 1.02664% |
| Neisseria subflava | Neisseria | Pseudomonadota | 1.01655% |
| Streptococcus downei | Streptococcus | Bacillota | 0.99493% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.98738% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.98142% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.94697% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.94376% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.92804% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.88111% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.76396% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.76195% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.74778% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.72315% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.67979% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.65468% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.60750% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.60159% |
| Parvularcula bermudensis | Parvularcula | Pseudomonadota | 0.57644% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.51198% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.51139% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.51134% |
| Neisseria cinerea | Neisseria | Pseudomonadota | 0.50695% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.48246% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.47949% |
| Prevotella oris | Prevotella | Bacteroidota | 0.47095% |
| Dialister hominis | Dialister | Bacillota | 0.46653% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.44840% |
| Veillonella seminalis | Veillonella | Bacillota | 0.44404% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.43422% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.42088% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.42082% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.41881% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 0.41725% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.40559% |
| Parvularcula lutaonensis | Parvularcula | Pseudomonadota | 0.35013% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.34702% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.33493% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.33357% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.32303% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.31363% |
| Neisseria perflava | Neisseria | Pseudomonadota | 0.30230% |
| Gemella palaticanis | Gemella | Bacillota | 0.30069% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.28203% |
| Neisseria weaveri | Neisseria | Pseudomonadota | 0.27446% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.27281% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.26992% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.26385% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.24390% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.22715% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.22238% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.21948% |
| Neisseria dumasiana | Neisseria | Pseudomonadota | 0.21661% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 0.21254% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.20913% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.20119% |
| Streptococcus equinus | Streptococcus | Bacillota | 0.20047% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.19151% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.18894% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.18861% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.18174% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.17969% |
| Fusobacterium necrophorum | Fusobacterium | Fusobacteriota | 0.17591% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.17248% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 0.16935% |
| Neisseria iguanae | Neisseria | Pseudomonadota | 0.16832% |
| Neisseria chenwenguii | Neisseria | Pseudomonadota | 0.16760% |
| Leptotrichia shahii | Leptotrichia | Fusobacteriota | 0.16626% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.16297% |
| Prevotella bryantii | Prevotella | Bacteroidota | 0.16203% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 0.16056% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.15541% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.15541% |
| Prevotella dentalis | Prevotella | Bacteroidota | 0.14882% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.14761% |
| Dialister pneumosintes | Dialister | Bacillota | 0.14723% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.14385% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.14136% |
| Prevotella corporis | Prevotella | Bacteroidota | 0.13764% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.13741% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 0.13606% |
| Gemella haemolysans | Gemella | Bacillota | 0.13087% |
| Rothia aeria | Rothia | Actinomycetota | 0.13087% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.13015% |
| Veillonella infantium | Veillonella | Bacillota | 0.12491% |
| Neisseria shayeganii | Neisseria | Pseudomonadota | 0.12390% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.12242% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.12226% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.12026% |
| Neisseria arctica | Neisseria | Pseudomonadota | 0.11660% |
| Campylobacter rectus | Campylobacter | Pseudomonadota | 0.11557% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.11353% |
| Prevotella enoeca | Prevotella | Bacteroidota | 0.10812% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.10479% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.10297% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.10097% |
| Lachnoanaerobaculum gingivalis | Lachnoanaerobaculum | Bacillota | 0.09887% |
| Veillonella atypica | Veillonella | Bacillota | 0.09721% |
| Megasphaera cerevisiae | Megasphaera | Bacillota | 0.09201% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.09023% |
120 of 121 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 |
|---|---|---|
| SRR33005028_1.fastq.gz | FASTQ / 171607448 | 3ff6af293126599489f8812fcdef6b91 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 238712228b6e2d9f260b9e866239a8fbbb0b17cccb95632720ba34cabe7d72e3 |
| median_read_length | 1588.0 |
| reads_in_length_window | 26760 |
| 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": 5374, "elapsed_seconds": 2.7957741689999693, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 35, "fraction": 0.175, "adapters_found": {"27F": 35}, "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 | SRR33005028 |
|---|---|
| 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 | 192966498 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Human unstimulated saliva patient23 |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB15232072 |
| 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 | Germany: Dsseldorf |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: Full-Length 16S sequencing of saliva from Alzheimer patients and healthy controls |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Human unstimulated saliva patient23 |
| environment_feature | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| environment_material | Unstimulated saliva |
| environmental_medium | Unstimulated saliva |
| environmental_sample | Not reported |
| experiment_accession | SRX28271096 |
| experiment_alias | pt23 sa 16S full-length |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: Full-Length 16S sequencing of saliva from Alzheimer patients and healthy controls |
| 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/SRR330/028/SRR33005028/SRR33005028_1.fastq.gz |
| fastq_bytes | 171607448 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/028/SRR33005028/SRR33005028_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/028/SRR33005028/SRR33005028_1.fastq.gz |
| fastq_md5 | 3ff6af293126599489f8812fcdef6b91 |
| file_location | Not reported |
| first_created | 2025-04-08 |
| first_public | 2025-04-08 |
| 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 | Not reported |
| last_updated | 2025-04-08 |
| lat | 51.2277 |
| 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 | pt23 sa 16S full-length |
| 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 | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| location | 51.2277 N 6.7735 E |
| location_end | 51.2277 N 6.7735 E |
| location_start | 51.2277 N 6.7735 E |
| lon | 6.7735 |
| 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 | Not reported |
| protocol_label | Not reported |
| read_count | 131044 |
| 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 | patient23.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN47766388 |
| sample_alias | Patient23 saliva 16S_full-length |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Not reported |
| 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 | Not reported |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS24617226 |
| secondary_study_accession | SRP573912 |
| 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 | PRJNA1243403 |
| study_alias | PRJNA1243403 |
| study_title | Oral microbiota of patients with Alzheimer's disease and healthy controls |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA2107592 |
| 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 | Patient23 saliva 16S_full-length |
|---|---|
| title | Not reported |
| description | Not reported |
| collection_date | 2022 |
|---|---|
| ENA-FIRST-PUBLIC | 2025-04-08 |
| organism | human oral metagenome |
| ENA-LAST-UPDATE | 2025-04-08 |
| env_broad_scale | Human unstimulated saliva patient23 |
| host | Homo sapiens |
| BioSampleModel | MIGS/MIMS/MIMARKS.human-oral |
| geo_loc_name | Germany: Dsseldorf |
| scientific_name | human oral metagenome |
| env_medium | Unstimulated saliva |
| lat_lon | 51.227700 N 6.77350 E |
| env_local_scale | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| run | SRR33005028 |
|---|---|
| sample | SAMN47766388 |
| study | PRJNA1243403 |
| title | Not reported |
| alias | Patient23 saliva 16S_full-length |
| site | Saliva |
| subject | Patient23 |
| phenotype | Patient |
| 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 | 121 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.