Patient25 saliva 16S_full-length
BioSample: SAMN47766392 · 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 | 13.43277% |
| Streptococcus anginosus | Streptococcus | Bacillota | 13.01836% |
| Streptococcus salivarius | Streptococcus | Bacillota | 11.36519% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 3.75134% |
| Veillonella parvula | Veillonella | Bacillota | 3.47361% |
| Streptococcus mitis | Streptococcus | Bacillota | 2.86676% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 2.81354% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 2.76951% |
| Actinobacillus delphinicola | Actinobacillus | Pseudomonadota | 2.30324% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 2.24007% |
| Actinobacillus equuli | Actinobacillus | Pseudomonadota | 2.18318% |
| Streptococcus oralis | Streptococcus | Bacillota | 1.85482% |
| Streptococcus gordonii | Streptococcus | Bacillota | 1.82463% |
| Streptococcus downei | Streptococcus | Bacillota | 1.80837% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 1.74797% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 1.74367% |
| Actinobacillus porcinus | Actinobacillus | Pseudomonadota | 1.46587% |
| Veillonella rodentium | Veillonella | Bacillota | 1.39464% |
| Prevotella intermedia | Prevotella | Bacteroidota | 1.36291% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.99233% |
| Actinobacillus suis | Actinobacillus | Pseudomonadota | 0.97365% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.84228% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.79372% |
| Parvimonas micra | Parvimonas | Bacillota | 0.72253% |
| Rothia aeria | Rothia | Actinomycetota | 0.71271% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 0.66831% |
| Actinobacillus lignieresii | Actinobacillus | Pseudomonadota | 0.64304% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.53853% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.53126% |
| Treponema brennaborense | Treponema | Spirochaetota | 0.48092% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.46999% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.46467% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.46393% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.46364% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.45709% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.45295% |
| Actinobacillus indolicus | Actinobacillus | Pseudomonadota | 0.43489% |
| Veillonella dispar | Veillonella | Bacillota | 0.42785% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.42149% |
| Neisseria animalis | Neisseria | Pseudomonadota | 0.38512% |
| Veillonella seminalis | Veillonella | Bacillota | 0.37909% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.37156% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.36920% |
| Parvularcula bermudensis | Parvularcula | Pseudomonadota | 0.34555% |
| Actinobacillus porcitonsillarum | Actinobacillus | Pseudomonadota | 0.33906% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.33060% |
| Gemella palaticanis | Gemella | Bacillota | 0.32595% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.31241% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.30138% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.25434% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.25417% |
| Dialister hominis | Dialister | Bacillota | 0.25365% |
| Parvularcula lutaonensis | Parvularcula | Pseudomonadota | 0.25336% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.25152% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.24683% |
| Rothia amarae | Rothia | Actinomycetota | 0.24682% |
| Actinobacillus succinogenes | Actinobacillus | Pseudomonadota | 0.24572% |
| Treponema succinifaciens | Treponema | Spirochaetota | 0.24319% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.24138% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.23950% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.23547% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.22840% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.22255% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.21664% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.21522% |
| Actinobacillus pleuropneumoniae | Actinobacillus | Pseudomonadota | 0.20418% |
| Actinobacillus hominis | Actinobacillus | Pseudomonadota | 0.20012% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.19788% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.19647% |
| Gemella haemolysans | Gemella | Bacillota | 0.19366% |
| Treponema bryantii | Treponema | Spirochaetota | 0.18701% |
| Streptococcus equinus | Streptococcus | Bacillota | 0.18500% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 0.18336% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.18227% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.18118% |
| Streptococcus milleri | Streptococcus | Bacillota | 0.17807% |
| Actinobacillus capsulatus | Actinobacillus | Pseudomonadota | 0.17619% |
| Dialister pneumosintes | Dialister | Bacillota | 0.17485% |
| Actinobacillus minor | Actinobacillus | Pseudomonadota | 0.17462% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.17258% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.17201% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.17057% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.16861% |
| Treponema putidum | Treponema | Spirochaetota | 0.16330% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.15630% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.15477% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.15215% |
| Treponema pedis | Treponema | Spirochaetota | 0.15190% |
| Rothia dentocariosa | Rothia | Actinomycetota | 0.14926% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.14486% |
| Prevotella oris | Prevotella | Bacteroidota | 0.14380% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.13695% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.13505% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.12847% |
| Schaalia funkei | Schaalia | Actinomycetota | 0.12531% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.12104% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.11614% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.11568% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.11251% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.11236% |
| Streptococcus dysgalactiae | Streptococcus | Bacillota | 0.11217% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.11012% |
| Treponema pectinovorum | Treponema | Spirochaetota | 0.10897% |
| Prevotella dentalis | Prevotella | Bacteroidota | 0.10621% |
| Treponema primitia | Treponema | Spirochaetota | 0.10387% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.10253% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.10242% |
| Porphyromonas cangingivalis | Porphyromonas | Bacteroidota | 0.10215% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.10143% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.09915% |
| Schaalia cardiffensis | Schaalia | Actinomycetota | 0.09873% |
| Actinobacillus seminis | Actinobacillus | Pseudomonadota | 0.09867% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.09563% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.09215% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.09159% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.08734% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.08354% |
117 of 117 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 |
|---|---|---|
| SRR33005024_1.fastq.gz | FASTQ / 194509953 | 58d9884d7af1b09cbad71a4689d5ca07 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 5a3d9c1f1487fa5e1c77e27e2b87be11b44241930cf7a6802548bddc68227b79 |
| median_read_length | 1594.0 |
| reads_in_length_window | 28009 |
| 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": 3392, "elapsed_seconds": 2.590312363999999, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 33, "fraction": 0.165, "adapters_found": {"27F": 33}, "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 | SRR33005024 |
|---|---|
| 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 | 223671131 |
| 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 | SUB15232072 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | Not reported |
| collection_date_end | Not reported |
| collection_date_start | Not reported |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Not reported |
| 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 | Not reported |
| environment_feature | Not reported |
| environment_material | Not reported |
| environmental_medium | Not reported |
| environmental_sample | Not reported |
| experiment_accession | SRX28271100 |
| experiment_alias | pt25 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/SRR330/024/SRR33005024/SRR33005024_1.fastq.gz |
| fastq_bytes | 194509953 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/024/SRR33005024/SRR33005024_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/024/SRR33005024/SRR33005024_1.fastq.gz |
| fastq_md5 | 58d9884d7af1b09cbad71a4689d5ca07 |
| file_location | Not reported |
| first_created | 2025-04-08 |
| first_public | 2025-04-08 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Not reported |
| 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 | Not reported |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | Not reported |
| 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 | Not reported |
| 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 | pt25 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 | 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 | Not reported |
| 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 | 146943 |
| 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 | patient25.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN47766392 |
| sample_alias | Not reported |
| 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 | Not reported |
| secondary_project | Not reported |
| secondary_sample_accession | SRS24617230 |
| 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 | Not reported |
| target_gene | Not reported |
| tax_id | Not reported |
| tax_lineage | Not reported |
| 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 | Patient25 saliva 16S_full-length |
|---|---|
| title | MIMARKS Survey related sample from human oral metagenome |
| description | Not reported |
| source | NCBI BioSample |
| collection_date | 2023 |
|---|---|
| env_broad_scale | Human unstimulated saliva patient25 |
| env_local_scale | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| env_medium | Unstimulated saliva |
| geo_loc_name | Germany: Dsseldorf |
| host | Homo sapiens |
| lat_lon | 51.227700 N 6.77350 E |
| run | SRR33005024 |
|---|---|
| sample | SAMN47766392 |
| study | PRJNA1243403 |
| title | Not reported |
| alias | Patient25 saliva 16S_full-length |
| site | Saliva |
| subject | Patient25 |
| 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 | 117 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.