Metagenome or environmental sample from human oral metagenome
BioSample: SAMN15887593 · 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 |
|---|---|---|---|
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 9.88306% |
| Streptococcus mitis | Streptococcus | Bacillota | 9.01272% |
| Filifactor alocis | Filifactor | Bacillota | 8.30485% |
| Eubacterium ramulus | Eubacterium | Bacillota | 7.27138% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 6.22400% |
| Veillonella parvula | Veillonella | Bacillota | 4.84650% |
| Selenomonas flueggei | Selenomonas | Bacillota | 4.11734% |
| Streptococcus downei | Streptococcus | Bacillota | 4.10956% |
| Filifactor villosus | Filifactor | Bacillota | 3.95344% |
| Dialister invisus | Dialister | Bacillota | 3.14456% |
| Parvimonas micra | Parvimonas | Bacillota | 2.92503% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 2.80343% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 2.74791% |
| Selenomonas sputigena | Selenomonas | Bacillota | 2.39399% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 2.24799% |
| Streptococcus salivarius | Streptococcus | Bacillota | 1.70959% |
| Gemella palaticanis | Gemella | Bacillota | 1.31804% |
| Eubacterium limosum | Eubacterium | Bacillota | 1.25961% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.24207% |
| Mogibacterium pumilum | Mogibacterium | Bacillota | 1.16883% |
| Tannerella forsythia | Tannerella | Bacteroidota | 1.04187% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.93865% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.87017% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.77118% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.68312% |
| Dialister hominis | Dialister | Bacillota | 0.66628% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.66437% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.61602% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.60580% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.57919% |
| Gemella haemolysans | Gemella | Bacillota | 0.55754% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 0.55128% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.53806% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.53658% |
| Mogibacterium vescum | Mogibacterium | Bacillota | 0.47225% |
| Veillonella infantium | Veillonella | Bacillota | 0.46074% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 0.45579% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.42227% |
| Aggregatibacter segnis | Aggregatibacter | Pseudomonadota | 0.40894% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.40630% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 0.38935% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.36137% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.34474% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.33815% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.31901% |
| Peptostreptococcus stomatis | Peptostreptococcus | Bacillota | 0.29862% |
| Prevotella oris | Prevotella | Bacteroidota | 0.28567% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.26943% |
| Eubacterium multiforme | Eubacterium | Bacillota | 0.26533% |
| Aggregatibacter aphrophilus | Aggregatibacter | Pseudomonadota | 0.25629% |
| Gemella morbillorum | Gemella | Bacillota | 0.25229% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.24950% |
| Selenomonas infelix | Selenomonas | Bacillota | 0.24275% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.23138% |
| Leptotrichia shahii | Leptotrichia | Fusobacteriota | 0.22818% |
| Eubacterium barkeri | Eubacterium | Bacillota | 0.20423% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.20046% |
| Veillonella dispar | Veillonella | Bacillota | 0.19687% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.18801% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.18171% |
| Streptococcus suis | Streptococcus | Bacillota | 0.17015% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.16921% |
| Mogibacterium neglectum | Mogibacterium | Bacillota | 0.16169% |
| Dialister pneumosintes | Dialister | Bacillota | 0.15277% |
| Veillonella atypica | Veillonella | Bacillota | 0.15162% |
| Streptococcus australis | Streptococcus | Bacillota | 0.15132% |
| Eubacterium ventriosum | Eubacterium | Bacillota | 0.15011% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.14191% |
| Dialister propionicifaciens | Dialister | Bacillota | 0.13652% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.13194% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.12523% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.12392% |
71 of 72 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 |
|---|---|---|
| SRR12522745_1.fastq.gz | FASTQ / 577180324 | 4540ebcec74bb0d395ad3e76aa15e0d3 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 71be0589bd9622e5e10dde816c03baf8a0644f869b5ae6914c570d22d5c2eed2 |
| median_read_length | 1411.0 |
| reads_in_length_window | 27950 |
| 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": 9397, "elapsed_seconds": 2.7552555510000047, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 3, "fraction": 0.015, "adapters_found": {"BC_FLANK": 2, "27F": 1}, "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 | SRR12522745 |
|---|---|
| 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 | 549808255 |
| 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 | SRX9012869 |
| experiment_alias | SH70-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/SRR125/045/SRR12522745/SRR12522745_1.fastq.gz |
| fastq_bytes | 577180324 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/045/SRR12522745/SRR12522745_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/045/SRR12522745/SRR12522745_1.fastq.gz |
| fastq_md5 | 4540ebcec74bb0d395ad3e76aa15e0d3 |
| 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 | SH70-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 | 394405 |
| 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 | SH70.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN15887593 |
| sample_alias | SH70 |
| 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 | SRS7263881 |
| 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 | SH70 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| strain | mixed |
|---|---|
| collection_date | not applicable |
| INSDC secondary accession | SRS7263881 |
| aliquot | s10 |
| 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 | SRR12522745 |
|---|---|
| sample | SAMN15887593 |
| study | PRJNA658726 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | SH70 |
| 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 | 72 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.