Patient12 saliva 16S_full-length
BioSample: SAMN47766366 · 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 |
|---|---|---|---|
| Streptococcus salivarius | Streptococcus | Bacillota | 13.85990% |
| Veillonella parvula | Veillonella | Bacillota | 7.84268% |
| Streptococcus anginosus | Streptococcus | Bacillota | 5.82163% |
| Streptococcus downei | Streptococcus | Bacillota | 4.50107% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 4.29237% |
| Streptococcus gordonii | Streptococcus | Bacillota | 3.26630% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 2.56200% |
| Veillonella rodentium | Veillonella | Bacillota | 2.44306% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 2.43494% |
| Streptococcus mitis | Streptococcus | Bacillota | 2.34952% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 2.31679% |
| Veillonella dispar | Veillonella | Bacillota | 2.09245% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 2.03116% |
| Gemella palaticanis | Gemella | Bacillota | 1.93877% |
| Gemella haemolysans | Gemella | Bacillota | 1.80069% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 1.76914% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 1.61910% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 1.38723% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 1.31611% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 1.20898% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 1.15395% |
| Catonella morbi | Catonella | Bacillota | 1.10153% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 1.06887% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 1.00488% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.97442% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.94608% |
| Leptotrichia shahii | Leptotrichia | Fusobacteriota | 0.93164% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.90001% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.83755% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.83392% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.72579% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.72000% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.68044% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.67422% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 0.64396% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.57672% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.55954% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.51573% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.50624% |
| Veillonella seminalis | Veillonella | Bacillota | 0.49172% |
| Gemella morbillorum | Gemella | Bacillota | 0.48663% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 0.48161% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.46252% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.45613% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.45094% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.44156% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.38971% |
| Veillonella infantium | Veillonella | Bacillota | 0.38546% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.38284% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.37535% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.37366% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.36619% |
| Gemella asaccharolytica | Gemella | Bacillota | 0.36358% |
| Leptotrichia hofstadii | Leptotrichia | Fusobacteriota | 0.35744% |
| Abiotrophia defectiva | Abiotrophia | Bacillota | 0.35037% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.34650% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.34547% |
| Porphyromonas pasteri | Porphyromonas | Bacteroidota | 0.33374% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.31224% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.29413% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 0.28540% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 0.27516% |
| Leptotrichia trevisanii | Leptotrichia | Fusobacteriota | 0.27129% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.26468% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.26397% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.24910% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.23420% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.23134% |
| Porphyromonas catoniae | Porphyromonas | Bacteroidota | 0.22725% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.21043% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.20792% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 0.20600% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.20383% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.20249% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.19967% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.19326% |
| Neisseria animalis | Neisseria | Pseudomonadota | 0.19211% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.18808% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.17787% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 0.17630% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.17531% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.17521% |
| Prevotella corporis | Prevotella | Bacteroidota | 0.17168% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.16993% |
| Streptococcus sinensis | Streptococcus | Bacillota | 0.16618% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.16497% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.16463% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 0.16033% |
| Prevotella oris | Prevotella | Bacteroidota | 0.15651% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.15572% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.15428% |
| Schaalia cardiffensis | Schaalia | Actinomycetota | 0.15265% |
| Schaalia funkei | Schaalia | Actinomycetota | 0.15018% |
| Streptococcus suis | Streptococcus | Bacillota | 0.14515% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.14293% |
| Gemella cuniculi | Gemella | Bacillota | 0.14249% |
| Prevotella bryantii | Prevotella | Bacteroidota | 0.14100% |
| Lachnoanaerobaculum saburreum | Lachnoanaerobaculum | Bacillota | 0.13981% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.13771% |
| Gemella sanguinis | Gemella | Bacillota | 0.13640% |
| Schaalia odontolytica | Schaalia | Actinomycetota | 0.13449% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.13254% |
| Veillonella tobetsuensis | Veillonella | Bacillota | 0.12176% |
| Porphyromonas cangingivalis | Porphyromonas | Bacteroidota | 0.12097% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 0.12029% |
| Peptostreptococcus canis | Peptostreptococcus | Bacillota | 0.11927% |
| Gemella taiwanensis | Gemella | Bacillota | 0.11752% |
| Streptococcus equinus | Streptococcus | Bacillota | 0.11420% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.11321% |
| Streptococcus acidominimus | Streptococcus | Bacillota | 0.11040% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.10948% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.10856% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.09823% |
| Veillonella atypica | Veillonella | Bacillota | 0.09693% |
| Porphyromonas crevioricanis | Porphyromonas | Bacteroidota | 0.09609% |
| Megasphaera cerevisiae | Megasphaera | Bacillota | 0.09053% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.09012% |
| Lachnoanaerobaculum gingivalis | Lachnoanaerobaculum | Bacillota | 0.08488% |
118 of 118 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 |
|---|---|---|
| SRR33005052_1.fastq.gz | FASTQ / 152868617 | aa6e22c07de4f81dee4feb787f423501 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 7ca67259833be01fb26acb148ceaa3d3589e94ac45b39ef4655e4139f729faf7 |
| median_read_length | 1572.0 |
| reads_in_length_window | 29017 |
| 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": 5558, "elapsed_seconds": 2.725326196000026, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 29, "fraction": 0.145, "adapters_found": {"27F": 29}, "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 | SRR33005052 |
|---|---|
| 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 | 167416375 |
| 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 | SRX28271072 |
| experiment_alias | pt12 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/SRR330/052/SRR33005052/SRR33005052_1.fastq.gz |
| fastq_bytes | 152868617 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/052/SRR33005052/SRR33005052_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/052/SRR33005052/SRR33005052_1.fastq.gz |
| fastq_md5 | aa6e22c07de4f81dee4feb787f423501 |
| 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 | pt12 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 | 108372 |
| 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 | patient12.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN47766366 |
| 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 | SRS24617202 |
| 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 | Patient12 saliva 16S_full-length |
|---|---|
| title | MIMARKS Survey related sample from human oral metagenome |
| description | Not reported |
| source | NCBI BioSample |
| collection_date | 2021 |
|---|---|
| env_broad_scale | Human unstimulated saliva patient12 |
| 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 | SRR33005052 |
|---|---|
| sample | SAMN47766366 |
| study | PRJNA1243403 |
| title | Not reported |
| alias | Patient12 saliva 16S_full-length |
| site | Saliva |
| subject | Patient12 |
| 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 | 118 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.