Metagenome or environmental sample from human oral metagenome
BioSample: SAMN17774973 · 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 |
|---|---|---|---|
| Streptococcus salivarius | Streptococcus | Bacillota | 21.64404% |
| Streptococcus anginosus | Streptococcus | Bacillota | 9.54432% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 7.52028% |
| Streptococcus downei | Streptococcus | Bacillota | 6.32221% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 5.82102% |
| Streptococcus gordonii | Streptococcus | Bacillota | 5.35924% |
| Veillonella parvula | Veillonella | Bacillota | 4.68456% |
| Streptococcus mitis | Streptococcus | Bacillota | 3.93510% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 3.89629% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 2.77438% |
| Veillonella dispar | Veillonella | Bacillota | 2.57369% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 2.00065% |
| Gemella palaticanis | Gemella | Bacillota | 1.68869% |
| Streptococcus oralis | Streptococcus | Bacillota | 1.63761% |
| Veillonella rodentium | Veillonella | Bacillota | 1.54183% |
| Gemella haemolysans | Gemella | Bacillota | 1.43299% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 1.23884% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 1.17754% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.89590% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.70224% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.69982% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.66990% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.60723% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.59515% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.59107% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.56298% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.52973% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.52894% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.50126% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.49475% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.47129% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.46873% |
| Veillonella infantium | Veillonella | Bacillota | 0.44287% |
| Veillonella seminalis | Veillonella | Bacillota | 0.41447% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.30995% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.28969% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.28477% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 0.26938% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.26888% |
| Gemella morbillorum | Gemella | Bacillota | 0.26429% |
| Streptococcus sinensis | Streptococcus | Bacillota | 0.26299% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.25465% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.25400% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.25004% |
| Gemella asaccharolytica | Gemella | Bacillota | 0.23033% |
| Streptococcus suis | Streptococcus | Bacillota | 0.21570% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.19609% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.17669% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.17494% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.16231% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.15273% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.14729% |
| Streptococcus dysgalactiae | Streptococcus | Bacillota | 0.14481% |
| Gemella taiwanensis | Gemella | Bacillota | 0.14470% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.14007% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.13794% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 0.13020% |
| Gemella cuniculi | Gemella | Bacillota | 0.12953% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.12950% |
| Streptococcus acidominimus | Streptococcus | Bacillota | 0.12494% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.12300% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.11673% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.11643% |
| Streptococcus macacae | Streptococcus | Bacillota | 0.11622% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.10465% |
| Streptococcus milleri | Streptococcus | Bacillota | 0.10368% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.10326% |
67 of 67 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 |
|---|---|---|
| SRR13679670_1.fastq.gz | FASTQ / 145328807 | f99bf27c110c3477c45908696d970b98 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | d13490b2172b6560dc165824427b60f2ed1768fe3de44b82d6ba74637d9289c5 |
| median_read_length | 1584.0 |
| reads_in_length_window | 28322 |
| 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": 7487, "elapsed_seconds": 2.82854888199995, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 18, "fraction": 0.09, "adapters_found": {"27F": 18}, "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 | SRR13679670 |
|---|---|
| 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 | 147479293 |
| 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: mid 23 |
| 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 | SRX10069035 |
| experiment_alias | saliva_mid_23 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: 16s RNA of human oral metagenome: mid 23 |
| 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/SRR136/070/SRR13679670/SRR13679670_1.fastq.gz |
| fastq_bytes | 145328807 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR136/070/SRR13679670/SRR13679670_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR136/070/SRR13679670/SRR13679670_1.fastq.gz |
| fastq_md5 | f99bf27c110c3477c45908696d970b98 |
| 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_mid_23 |
| 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 | 96000 |
| 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_mid_23.fq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN17774973 |
| sample_alias | football19_saliva_mid_23 |
| 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 | SRS8230796 |
| 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_mid_23 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2019-10 |
|---|---|
| INSDC secondary accession | SRS8230796 |
| NCBI submission package | Metagenome.environmental.1.0 |
| player_id | 23 |
| organism | human oral metagenome |
| post-concussion | no |
| 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 | SRR13679670 |
|---|---|
| sample | SAMN17774973 |
| study | PRJNA699316 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | football19_saliva_mid_23 |
| site | saliva |
| subject | 23 |
| 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 | 30000 |
| species_reported | 67 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.