S-Medwakh SAMP4
BioSample: SAMN20606010 · Study: PRJNA752710 · Body site: Supragingival
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 | 12.41871% |
| Streptococcus mitis | Streptococcus | Bacillota | 7.54309% |
| Streptococcus salivarius | Streptococcus | Bacillota | 6.84545% |
| Selenomonas flueggei | Selenomonas | Bacillota | 5.42153% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 4.84755% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 4.81589% |
| Streptococcus downei | Streptococcus | Bacillota | 4.44638% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 2.79239% |
| Gemella palaticanis | Gemella | Bacillota | 2.77692% |
| Streptococcus cristatus | Streptococcus | Bacillota | 2.68019% |
| Lachnoanaerobaculum saburreum | Lachnoanaerobaculum | Bacillota | 2.52829% |
| Selenomonas sputigena | Selenomonas | Bacillota | 2.04592% |
| Gemella haemolysans | Gemella | Bacillota | 1.96923% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.67332% |
| Lachnoanaerobaculum umeaense | Lachnoanaerobaculum | Bacillota | 1.65983% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 1.62007% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 1.60587% |
| Lachnoanaerobaculum orale | Lachnoanaerobaculum | Bacillota | 1.52318% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 1.42994% |
| Veillonella dispar | Veillonella | Bacillota | 1.42622% |
| Selenomonas noxia | Selenomonas | Bacillota | 1.34366% |
| Veillonella rodentium | Veillonella | Bacillota | 1.30048% |
| Veillonella infantium | Veillonella | Bacillota | 1.23054% |
| Gemella morbillorum | Gemella | Bacillota | 1.09504% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 1.06677% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.98375% |
| Tannerella forsythia | Tannerella | Bacteroidota | 0.95006% |
| Aggregatibacter segnis | Aggregatibacter | Pseudomonadota | 0.82607% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.80536% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.79850% |
| Leptotrichia shahii | Leptotrichia | Fusobacteriota | 0.73295% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.70584% |
| Aggregatibacter aphrophilus | Aggregatibacter | Pseudomonadota | 0.65857% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.65075% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.63034% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.62379% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.59596% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 0.49106% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 0.47341% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.44789% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.40003% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.38949% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.35605% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.35035% |
| Corynebacterium matruchotii | Corynebacterium | Actinomycetota | 0.34175% |
| Porphyromonas pasteri | Porphyromonas | Bacteroidota | 0.33873% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.33426% |
| Corynebacterium camporealense | Corynebacterium | Actinomycetota | 0.33354% |
| Leptotrichia buccalis | Leptotrichia | Fusobacteriota | 0.31530% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.30504% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.29669% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.29224% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.29039% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.26995% |
| Veillonella atypica | Veillonella | Bacillota | 0.25944% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.25786% |
| Porphyromonas macacae | Porphyromonas | Bacteroidota | 0.25387% |
| Leptotrichia hofstadii | Leptotrichia | Fusobacteriota | 0.25290% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.24543% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.23068% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.22777% |
| Prevotella loescheii | Prevotella | Bacteroidota | 0.21962% |
| Porphyromonas catoniae | Porphyromonas | Bacteroidota | 0.20637% |
| Capnocytophaga ochracea | Capnocytophaga | Bacteroidota | 0.20309% |
| Lachnoanaerobaculum gingivalis | Lachnoanaerobaculum | Bacillota | 0.20259% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.20021% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.19847% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.19522% |
| Veillonella seminalis | Veillonella | Bacillota | 0.19361% |
| Selenomonas infelix | Selenomonas | Bacillota | 0.18039% |
| Prevotella oris | Prevotella | Bacteroidota | 0.15898% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.15682% |
| Gemella taiwanensis | Gemella | Bacillota | 0.15605% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 0.15312% |
| Leptotrichia trevisanii | Leptotrichia | Fusobacteriota | 0.14318% |
| Streptococcus suis | Streptococcus | Bacillota | 0.14252% |
| Prevotella buccalis | Prevotella | Bacteroidota | 0.14148% |
| Gemella cuniculi | Gemella | Bacillota | 0.14065% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.14005% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.12718% |
| Porphyromonas levii | Porphyromonas | Bacteroidota | 0.12707% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 0.12426% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.12250% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.12200% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.12077% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.11491% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.11088% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.11028% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.10640% |
| Campylobacter ureolyticus | Campylobacter | Pseudomonadota | 0.10181% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.10036% |
| Aggregatibacter actinomycetemcomitans | Aggregatibacter | Pseudomonadota | 0.09921% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.09825% |
| Capnocytophaga granulosa | Capnocytophaga | Bacteroidota | 0.09519% |
| Veillonella denticariosi | Veillonella | Bacillota | 0.09414% |
| Selenomonas artemidis | Selenomonas | Bacillota | 0.09058% |
| Streptococcus gallolyticus | Streptococcus | Bacillota | 0.08981% |
| Gemella asaccharolytica | Gemella | Bacillota | 0.08947% |
97 of 98 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 |
|---|---|---|
| SRR15373519_1.fastq.gz | FASTQ / 637453135 | f33c814fa58ee00817147821cf2054cb |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 5e15a7f5bd02775ecc0abcbb7b60f24ece70dc5ac68062a9fcc84f66a224f642 |
| median_read_length | 1459.0 |
| reads_in_length_window | 28256 |
| 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": 5394, "elapsed_seconds": 2.7384114159999626, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 14, "fraction": 0.07, "adapters_found": {"BC_FLANK": 2, "27F": 12}, "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 | SRR15373519 |
|---|---|
| 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 | 610306254 |
| 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 | SUB10164078 |
| 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: 16srRNA |
| 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 | SRX11676042 |
| experiment_alias | SM29 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: 16srRNA |
| 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/SRR153/019/SRR15373519/SRR15373519_1.fastq.gz |
| fastq_bytes | 637453135 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/019/SRR15373519/SRR15373519_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/019/SRR15373519/SRR15373519_1.fastq.gz |
| fastq_md5 | f33c814fa58ee00817147821cf2054cb |
| file_location | Not reported |
| first_created | 2022-10-01 |
| first_public | 2022-10-01 |
| 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 | 2022-10-01 |
| lat | 23.4241 |
| 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 | SM29 |
| 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 | METAGENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | 23.4241 N 53.8478 E |
| location_end | 23.4241 N 53.8478 E |
| location_start | 23.4241 N 53.8478 E |
| lon | 53.8478 |
| 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 | 426224 |
| 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 | M29.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN20606010 |
| sample_alias | SM29 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | S-Medwakh SAMP4 |
| 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 | S-Medwakh SAMP4 |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS9708025 |
| secondary_study_accession | SRP331639 |
| 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 | PRJNA752710 |
| study_alias | PRJNA752710 |
| study_title | Supragingival microbiome alternations as a consequence of smoking different tobacco types and its relation to dental caries |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1273766 |
| 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 | SM29 |
|---|---|
| title | S-Medwakh SAMP4 |
| description | Not reported |
| strain | mixed |
|---|---|
| collection_date | not applicable |
| INSDC secondary accession | SRS9708025 |
| aliquot | S-Medwakh SAMP4 |
| organism | human oral metagenome |
| sample_type | Supragingival |
| isolate | mixed1 |
| NCBI submission package | Metagenome.environmental.1.0 |
| smoking | S-Medwakh |
| host | Homo sapiens |
| geo_loc_name | United Arab Emirates |
| lat_lon | 23.4241 N 53.8478 E |
| isolation_source | oral |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2022-09-30 |
| ENA-LAST-UPDATE | 2022-09-30 |
| run | SRR15373519 |
|---|---|
| sample | SAMN20606010 |
| study | PRJNA752710 |
| title | S-Medwakh SAMP4 |
| alias | SM29 |
| site | Supragingival |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | S-Medwakh |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 98 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.