Patient04 saliva 16S_full-length
BioSample: SAMN47766350 · 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 |
|---|---|---|---|
| Campylobacter concisus | Campylobacter | Pseudomonadota | 32.77786% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 15.05901% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 13.01653% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 7.50756% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 6.17168% |
| Veillonella parvula | Veillonella | Bacillota | 2.84697% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 2.81369% |
| Streptococcus salivarius | Streptococcus | Bacillota | 2.07556% |
| Mycoplasma iguanae | Mycoplasma | Mycoplasmatota | 1.76161% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 1.69299% |
| Veillonella rodentium | Veillonella | Bacillota | 1.36339% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 1.27297% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.98777% |
| Veillonella dispar | Veillonella | Bacillota | 0.95868% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.77175% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.67600% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.63044% |
| Streptococcus downei | Streptococcus | Bacillota | 0.54246% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 0.48877% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 0.47379% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.47233% |
| Campylobacter ureolyticus | Campylobacter | Pseudomonadota | 0.44853% |
| Campylobacter insulaenigrae | Campylobacter | Pseudomonadota | 0.43349% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.42706% |
| Campylobacter rectus | Campylobacter | Pseudomonadota | 0.38070% |
| Campylobacter hominis | Campylobacter | Pseudomonadota | 0.37368% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.34439% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.31971% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.30900% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.29366% |
| Campylobacter lari | Campylobacter | Pseudomonadota | 0.28649% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.25162% |
| Campylobacter pinnipediorum | Campylobacter | Pseudomonadota | 0.24900% |
| Campylobacter jejuni | Campylobacter | Pseudomonadota | 0.24192% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.24065% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.23320% |
| Campylobacter fetus | Campylobacter | Pseudomonadota | 0.23018% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.21293% |
| Veillonella seminalis | Veillonella | Bacillota | 0.19307% |
| Campylobacter coli | Campylobacter | Pseudomonadota | 0.16891% |
40 of 40 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 |
|---|---|---|
| SRR33005021_1.fastq.gz | FASTQ / 36580868 | af5c7c26876e627702eef6a8344cdfb1 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 5a27ae7d6d62238c2c69e8c5d1c9f886a80659697e2b9aee722d79cc4e1a5d6c |
| median_read_length | 649.0 |
| reads_in_length_window | 12791 |
| 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": 16574, "elapsed_seconds": 2.2394750890000523, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 30, "fraction": 0.15, "adapters_found": {"27F": 30}, "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 | SRR33005021 |
|---|---|
| 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 | 39635302 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Human unstimulated saliva patient04 |
| 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 | 2021 |
| collection_date_end | 2021-12-31 |
| collection_date_start | 2021-01-01 |
| 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 patient04 |
| environment_feature | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| environment_material | Unstimulated saliva |
| environmental_medium | Unstimulated saliva |
| environmental_sample | Not reported |
| experiment_accession | SRX28271103 |
| experiment_alias | pt04 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/SRR330/021/SRR33005021/SRR33005021_1.fastq.gz |
| fastq_bytes | 36580868 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/021/SRR33005021/SRR33005021_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/021/SRR33005021/SRR33005021_1.fastq.gz |
| fastq_md5 | af5c7c26876e627702eef6a8344cdfb1 |
| 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 | pt04 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 | 46363 |
| 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 | patient04.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN47766350 |
| sample_alias | Patient04 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 | SRS24617233 |
| 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 | Patient04 saliva 16S_full-length |
|---|---|
| title | Not reported |
| description | Not reported |
| collection_date | 2021 |
|---|---|
| ENA-FIRST-PUBLIC | 2025-04-08 |
| organism | human oral metagenome |
| ENA-LAST-UPDATE | 2025-04-08 |
| env_broad_scale | Human unstimulated saliva patient04 |
| 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 | SRR33005021 |
|---|---|
| sample | SAMN47766350 |
| study | PRJNA1243403 |
| title | Not reported |
| alias | Patient04 saliva 16S_full-length |
| site | Saliva |
| subject | Patient04 |
| 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 | 40 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.