Metagenome or environmental sample from human oral metagenome
BioSample: SAMN15887590 · Study: PRJNA658726 · Body site: Subgingival
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 mitis | Streptococcus | Bacillota | 25.12228% |
| Streptococcus downei | Streptococcus | Bacillota | 13.59127% |
| Veillonella parvula | Veillonella | Bacillota | 12.34097% |
| Abiotrophia defectiva | Abiotrophia | Bacillota | 7.06306% |
| Streptococcus salivarius | Streptococcus | Bacillota | 6.65646% |
| Gemella palaticanis | Gemella | Bacillota | 3.55210% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 3.29973% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 2.78856% |
| Gemella haemolysans | Gemella | Bacillota | 2.39192% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 1.90297% |
| Streptococcus infantis | Streptococcus | Bacillota | 1.67154% |
| Veillonella infantium | Veillonella | Bacillota | 1.55257% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 1.23452% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 1.11730% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.95211% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.85133% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.76933% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.76831% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.71594% |
| Eubacterium ramulus | Eubacterium | Bacillota | 0.70634% |
| Veillonella dispar | Veillonella | Bacillota | 0.56790% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.43770% |
| Streptococcus australis | Streptococcus | Bacillota | 0.43055% |
| Filifactor alocis | Filifactor | Bacillota | 0.42058% |
| Streptococcus suis | Streptococcus | Bacillota | 0.41942% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 0.40472% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.38689% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.38246% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.36470% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.36269% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.35965% |
| Veillonella atypica | Veillonella | Bacillota | 0.33985% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.33549% |
| Veillonella rodentium | Veillonella | Bacillota | 0.33370% |
| Filifactor villosus | Filifactor | Bacillota | 0.33368% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.32167% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.31894% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 0.31736% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.30595% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.30123% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.29757% |
| Streptococcus orisratti | Streptococcus | Bacillota | 0.28597% |
| Streptococcus gallolyticus | Streptococcus | Bacillota | 0.26838% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.22914% |
| Streptococcus macacae | Streptococcus | Bacillota | 0.21987% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.21205% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 0.19335% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.18918% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.18770% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.18480% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.17407% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.17351% |
| Gemella cuniculi | Gemella | Bacillota | 0.16393% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.16266% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 0.15734% |
| Prevotella oris | Prevotella | Bacteroidota | 0.14732% |
| Streptococcus dysgalactiae | Streptococcus | Bacillota | 0.14703% |
| Veillonella denticariosi | Veillonella | Bacillota | 0.11237% |
57 of 58 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 |
|---|---|---|
| SRR12522748_1.fastq.gz | FASTQ / 364279428 | e8099bd802dc0b9de2c07300029aecfd |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | d26036ac277e004e262575954778fe43c306227efe273c18ed7f1547ce315ca0 |
| median_read_length | 1431.0 |
| reads_in_length_window | 28189 |
| 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": 9177, "elapsed_seconds": 3.025111536999999, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 4, "fraction": 0.02, "adapters_found": {"BC_FLANK": 4}, "should_trim": false}, "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 | SRR12522748 |
|---|---|
| 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 | 354700841 |
| 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 | SUB7951364 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | not applicable |
| collection_date_end | Not reported |
| collection_date_start | Not reported |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | United Arab Emirates |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: metagenomic |
| 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 | SRX9012866 |
| experiment_alias | SH61-P |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: metagenomic |
| 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/SRR125/048/SRR12522748/SRR12522748_1.fastq.gz |
| fastq_bytes | 364279428 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/048/SRR12522748/SRR12522748_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/048/SRR12522748/SRR12522748_1.fastq.gz |
| fastq_md5 | e8099bd802dc0b9de2c07300029aecfd |
| file_location | Not reported |
| first_created | 2021-10-01 |
| first_public | 2021-10-01 |
| 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 | mixed1 |
| isolation_source | oral |
| last_updated | 2021-10-01 |
| 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 | SH61-P |
| 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 | 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 | 250891 |
| 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 | SH61.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN15887590 |
| sample_alias | SH61 |
| 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 | SRS7263878 |
| secondary_study_accession | SRP278853 |
| 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 | mixed |
| study_accession | PRJNA658726 |
| study_alias | PRJNA658726 |
| study_title | The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1117712 |
| 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 | 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 | SH61 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| strain | mixed |
|---|---|
| collection_date | not applicable |
| INSDC secondary accession | SRS7263878 |
| aliquot | s7 |
| organism | human oral metagenome |
| sample_type | Subgingival |
| isolate | mixed1 |
| NCBI submission package | Metagenome.environmental.1.0 |
| periodontitis | no-mild |
| smoking | S-Shisha |
| host | Homo sapiens |
| geo_loc_name | United Arab Emirates |
| lat_lon | missing |
| isolation_source | oral |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2021-09-30 |
| ENA-LAST-UPDATE | 2021-09-30 |
| run | SRR12522748 |
|---|---|
| sample | SAMN15887590 |
| study | PRJNA658726 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | SH61 |
| site | Subgingival |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | S-Shisha |
| periodontitis | no-mild |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 58 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.