Metagenome or environmental sample from human oral metagenome
BioSample: SAMN15887572 · 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 |
|---|---|---|---|
| Veillonella parvula | Veillonella | Bacillota | 27.02497% |
| Streptococcus mitis | Streptococcus | Bacillota | 16.72193% |
| Streptococcus downei | Streptococcus | Bacillota | 13.12811% |
| Streptococcus salivarius | Streptococcus | Bacillota | 7.72876% |
| Streptococcus gordonii | Streptococcus | Bacillota | 3.59194% |
| Veillonella infantium | Veillonella | Bacillota | 3.53268% |
| Streptococcus mutans | Streptococcus | Bacillota | 2.27111% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 1.97102% |
| Veillonella dispar | Veillonella | Bacillota | 1.74985% |
| Selenomonas flueggei | Selenomonas | Bacillota | 1.69055% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.56978% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 1.52645% |
| Limosilactobacillus vaginalis | Limosilactobacillus | Bacillota | 1.51915% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 1.18197% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 1.10052% |
| Streptococcus anginosus | Streptococcus | Bacillota | 1.01750% |
| Veillonella atypica | Veillonella | Bacillota | 1.00466% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.95128% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.94345% |
| Limosilactobacillus reuteri | Limosilactobacillus | Bacillota | 0.82911% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.78403% |
| Streptococcus gallolyticus | Streptococcus | Bacillota | 0.63803% |
| Veillonella rodentium | Veillonella | Bacillota | 0.61354% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.59461% |
| Lactobacillus psittaci | Lactobacillus | Bacillota | 0.59165% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.55309% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.53249% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.52947% |
| Limosilactobacillus frumenti | Limosilactobacillus | Bacillota | 0.51531% |
| Veillonella denticariosi | Veillonella | Bacillota | 0.47259% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.46148% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 0.43238% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.39048% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.35817% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.35211% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.34543% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.31808% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.28477% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.17749% |
38 of 39 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 |
|---|---|---|
| SRR12522729_1.fastq.gz | FASTQ / 680227915 | c99e549ab7d007a904ec79f5306fbb22 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 7ed5abe1bc9dc58ba239663b52309b7e8006d3504623c2e57cb50d569f46ed05 |
| median_read_length | 1439.0 |
| reads_in_length_window | 9562 |
| 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": 10000, "reads_skipped": 1321, "elapsed_seconds": 1.1066475240000102, "reads_submitted": 10000, "reads_after_filter": 10000, "adapter_scan": {"sampled": 200, "matched": 0, "fraction": 0.0, "adapters_found": {}, "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 | SRR12522729 |
|---|---|
| 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 | 666237131 |
| 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 | SRX9012885 |
| experiment_alias | C75-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/SRR125/029/SRR12522729/SRR12522729_1.fastq.gz |
| fastq_bytes | 680227915 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/029/SRR12522729/SRR12522729_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/029/SRR12522729/SRR12522729_1.fastq.gz |
| fastq_md5 | c99e549ab7d007a904ec79f5306fbb22 |
| 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 | C75-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 | 471501 |
| 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 | C75.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN15887572 |
| sample_alias | C75 |
| 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 | SRS7263897 |
| 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 | C75 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| strain | mixed |
|---|---|
| collection_date | not applicable |
| INSDC secondary accession | SRS7263897 |
| aliquot | cig9 |
| organism | human oral metagenome |
| sample_type | Subgingival |
| isolate | mixed1 |
| NCBI submission package | Metagenome.environmental.1.0 |
| periodontitis | no-mild |
| smoking | S-Cigarettes |
| 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 | SRR12522729 |
|---|---|
| sample | SAMN15887572 |
| study | PRJNA658726 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | C75 |
| site | Subgingival |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | S-Cigarettes |
| periodontitis | no-mild |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 10000 |
| species_reported | 39 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.