Metagenome or environmental sample from human oral metagenome
BioSample: SAMN17774961 · Study: PRJNA699316 · 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 | 11.11710% |
| Veillonella parvula | Veillonella | Bacillota | 7.64141% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 6.59778% |
| Streptococcus salivarius | Streptococcus | Bacillota | 6.53570% |
| Veillonella dispar | Veillonella | Bacillota | 4.19919% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 3.27088% |
| Streptococcus anginosus | Streptococcus | Bacillota | 3.25310% |
| Actinobacillus equuli | Actinobacillus | Pseudomonadota | 3.08434% |
| Veillonella rodentium | Veillonella | Bacillota | 3.04719% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 2.79819% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 2.78087% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 2.54536% |
| Streptococcus downei | Streptococcus | Bacillota | 2.39028% |
| Neisseria elongata | Neisseria | Pseudomonadota | 2.05154% |
| Actinobacillus lignieresii | Actinobacillus | Pseudomonadota | 1.83206% |
| Streptococcus gordonii | Streptococcus | Bacillota | 1.68337% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.55691% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.51890% |
| Neisseria subflava | Neisseria | Pseudomonadota | 1.47506% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 1.46674% |
| Neisseria canis | Neisseria | Pseudomonadota | 1.29336% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 1.24045% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 1.19154% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 1.15773% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 1.14591% |
| Neisseria polysaccharea | Neisseria | Pseudomonadota | 1.10883% |
| Actinobacillus capsulatus | Actinobacillus | Pseudomonadota | 0.99359% |
| Veillonella infantium | Veillonella | Bacillota | 0.96746% |
| Gemella palaticanis | Gemella | Bacillota | 0.95715% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.90886% |
| Neisseria lactamica | Neisseria | Pseudomonadota | 0.89183% |
| Neisseria animaloris | Neisseria | Pseudomonadota | 0.85412% |
| Neisseria zoodegmatis | Neisseria | Pseudomonadota | 0.84034% |
| Gemella haemolysans | Gemella | Bacillota | 0.82037% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.80515% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.79261% |
| Actinobacillus pleuropneumoniae | Actinobacillus | Pseudomonadota | 0.75088% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.73333% |
| Actinobacillus delphinicola | Actinobacillus | Pseudomonadota | 0.70504% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.63436% |
| Neisseria animalis | Neisseria | Pseudomonadota | 0.63274% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.62203% |
| Veillonella seminalis | Veillonella | Bacillota | 0.57964% |
| Neisseria iguanae | Neisseria | Pseudomonadota | 0.48082% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.46225% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.43622% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.42715% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.42213% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.37600% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 0.37451% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.37061% |
| Neisseria cinerea | Neisseria | Pseudomonadota | 0.34899% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.34178% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.33982% |
| Actinobacillus suis | Actinobacillus | Pseudomonadota | 0.29274% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.29194% |
| Actinobacillus indolicus | Actinobacillus | Pseudomonadota | 0.29188% |
| Actinobacillus porcinus | Actinobacillus | Pseudomonadota | 0.28729% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.27711% |
| Actinobacillus porcitonsillarum | Actinobacillus | Pseudomonadota | 0.25982% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.25531% |
| Veillonella criceti | Veillonella | Bacillota | 0.24448% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.23773% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.23497% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.22961% |
| Veillonella ratti | Veillonella | Bacillota | 0.22203% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.21225% |
| Neisseria chenwenguii | Neisseria | Pseudomonadota | 0.21089% |
| Gemella morbillorum | Gemella | Bacillota | 0.20510% |
| Megasphaera stantonii | Megasphaera | Bacillota | 0.19672% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.19655% |
71 of 71 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 |
|---|---|---|
| SRR13679642_1.fastq.gz | FASTQ / 356147245 | 63944a67040ea3a5550d28afad7753cc |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 291e7ac4deaed7a0573abd6d68a01ef878ce36629e9baf595262693f155f2995 |
| median_read_length | 1579.0 |
| reads_in_length_window | 14180 |
| 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": 15000, "reads_skipped": 3204, "elapsed_seconds": 1.509995181999983, "reads_submitted": 15000, "reads_after_filter": 15000, "adapter_scan": {"sampled": 200, "matched": 42, "fraction": 0.21, "adapters_found": {"1492R_rc": 24, "27F": 17, "BC_FLANK": 1}, "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 | SRR13679642 |
|---|---|
| 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 | 356092381 |
| 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 | SUB9029329 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2019-10 |
| collection_date_end | 2019-10-31 |
| collection_date_start | 2019-09-30 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | USA: Texas |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: 16s RNA of human oral metagenome: conc 10 |
| 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 | SRX10069063 |
| experiment_alias | saliva_conc_10 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: 16s RNA of human oral metagenome: conc 10 |
| 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/SRR136/042/SRR13679642/SRR13679642_1.fastq.gz |
| fastq_bytes | 356147245 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR136/042/SRR13679642/SRR13679642_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR136/042/SRR13679642/SRR13679642_1.fastq.gz |
| fastq_md5 | 63944a67040ea3a5550d28afad7753cc |
| file_location | Not reported |
| first_created | 2022-03-03 |
| first_public | 2022-03-03 |
| 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 | 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 | saliva |
| last_updated | 2022-03-03 |
| lat | 29.76 |
| 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 | saliva_conc_10 |
| 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 | 29.76 N 95.37 W |
| location_end | 29.76 N 95.37 W |
| location_start | 29.76 N 95.37 W |
| lon | -95.37 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Metagenome or environmental |
| 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 | 232000 |
| 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 | saliva_conc_10.fq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN17774961 |
| sample_alias | football19_saliva_conc_10 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Metagenome or environmental sample from human oral metagenome |
| 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 | Metagenome or environmental sample from human oral metagenome |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS8230824 |
| secondary_study_accession | SRP305684 |
| 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 | PRJNA699316 |
| study_alias | PRJNA699316 |
| study_title | Gut and saliva microbiome in collegiate football athletes |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1194482 |
| 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 | football19_saliva_conc_10 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2019-10 |
|---|---|
| INSDC secondary accession | SRS8230824 |
| NCBI submission package | Metagenome.environmental.1.0 |
| player_id | 10 |
| organism | human oral metagenome |
| post-concussion | yes |
| time_point | mid-season |
| host | Homo sapiens |
| geo_loc_name | USA: Texas |
| samp_mat_process | Norgen Saliva DNA Isolation Reagent Kit, MinION nanopore sequencer |
| lat_lon | 29.76 N 95.37 W |
| isolation_source | saliva |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2021-02-03 |
| ENA-LAST-UPDATE | 2021-02-28 |
| run | SRR13679642 |
|---|---|
| sample | SAMN17774961 |
| study | PRJNA699316 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | football19_saliva_conc_10 |
| site | saliva |
| subject | 10 |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | mid-season |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 15000 |
| species_reported | 71 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.