Metagenome or environmental sample from human oral metagenome
BioSample: SAMN28173424 · Study: PRJNA836758 · Body site: Extracted Tooth
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 | 26.21766% |
| Lautropia mirabilis | Lautropia | Pseudomonadota | 11.37866% |
| Veillonella infantium | Veillonella | Bacillota | 5.83187% |
| Streptococcus mitis | Streptococcus | Bacillota | 5.61914% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 4.78025% |
| Streptococcus salivarius | Streptococcus | Bacillota | 4.38579% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 3.56422% |
| Veillonella dispar | Veillonella | Bacillota | 3.29640% |
| Streptococcus downei | Streptococcus | Bacillota | 2.30539% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 2.19375% |
| Streptococcus intermedius | Streptococcus | Bacillota | 1.54537% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.43590% |
| Prevotella oris | Prevotella | Bacteroidota | 1.32690% |
| Streptococcus mutans | Streptococcus | Bacillota | 1.15993% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 1.07304% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 1.04803% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.99979% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.97930% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.97227% |
| Eikenella corrodens | Eikenella | Pseudomonadota | 0.83402% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.81273% |
| Veillonella rodentium | Veillonella | Bacillota | 0.72983% |
| Prevotella multisaccharivorax | Prevotella | Bacteroidota | 0.71754% |
| Veillonella atypica | Veillonella | Bacillota | 0.68665% |
| Gemella haemolysans | Gemella | Bacillota | 0.67417% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.64906% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.63633% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.60548% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 0.54840% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 0.54109% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.53118% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.52509% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.46160% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.45747% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.43184% |
| Propionibacterium freudenreichii | Propionibacterium | Actinomycetota | 0.40184% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.38373% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.37281% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 0.36415% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.35955% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.33119% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.31530% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.31424% |
| Prevotella brevis | Prevotella | Bacteroidota | 0.31138% |
| Bradyrhizobium oligotrophicum | Bradyrhizobium | Pseudomonadota | 0.30497% |
| Leptotrichia shahii | Leptotrichia | Fusobacteriota | 0.30289% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 0.29909% |
| Gemella morbillorum | Gemella | Bacillota | 0.28979% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.28655% |
| Prevotella buccalis | Prevotella | Bacteroidota | 0.27606% |
| Selenomonas flueggei | Selenomonas | Bacillota | 0.26262% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.25178% |
| Capnocytophaga ochracea | Capnocytophaga | Bacteroidota | 0.22795% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.22704% |
| Eubacterium ramulus | Eubacterium | Bacillota | 0.22450% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.22449% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.22026% |
| Lautropia dentalis | Lautropia | Pseudomonadota | 0.21975% |
| Gemella palaticanis | Gemella | Bacillota | 0.20937% |
| Propionibacterium acidifaciens | Propionibacterium | Actinomycetota | 0.20389% |
| Capnocytophaga gingivalis | Capnocytophaga | Bacteroidota | 0.19908% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.17885% |
| Prevotella corporis | Prevotella | Bacteroidota | 0.17862% |
| Bradyrhizobium paxllaeri | Bradyrhizobium | Pseudomonadota | 0.17792% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.17664% |
| Prevotella bivia | Prevotella | Bacteroidota | 0.17261% |
| Rothia aeria | Rothia | Actinomycetota | 0.16531% |
| Rothia dentocariosa | Rothia | Actinomycetota | 0.15661% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.14778% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.14751% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 0.14471% |
| Prevotella intermedia | Prevotella | Bacteroidota | 0.13632% |
| Veillonella tobetsuensis | Veillonella | Bacillota | 0.13187% |
| Prevotella histicola | Prevotella | Bacteroidota | 0.12740% |
| Prevotella oulorum | Prevotella | Bacteroidota | 0.11835% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.10962% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.10373% |
| Prevotella copri | Prevotella | Bacteroidota | 0.09934% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 0.09743% |
| Lactobacillus psittaci | Lactobacillus | Bacillota | 0.08895% |
79 of 80 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 |
|---|---|---|
| SRR19631906_1.fastq.gz | FASTQ / 162017797 | 88da5b0a67ce740917d876a5670f9d48 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | d45cc92f0d6481656002f0d2117e0f1369e07734d6b3454342455493a0df09f0 |
| median_read_length | 1479.0 |
| reads_in_length_window | 25106 |
| 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": 6146, "elapsed_seconds": 2.4910645729999885, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 5, "fraction": 0.025, "adapters_found": {"BC_FLANK": 5}, "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 | SRR19631906 |
|---|---|
| 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 | 170786504 |
| 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 | SUB11589611 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2021-12-02 |
| collection_date_end | 2021-12-02 |
| collection_date_start | 2021-12-02 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | India: Chennai |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples |
| 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 | SRX15682443 |
| experiment_alias | TM 20 |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples |
| 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/SRR196/006/SRR19631906/SRR19631906_1.fastq.gz |
| fastq_bytes | 162017797 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/006/SRR19631906/SRR19631906_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/006/SRR19631906/SRR19631906_1.fastq.gz |
| fastq_md5 | 88da5b0a67ce740917d876a5670f9d48 |
| file_location | Not reported |
| first_created | 2023-08-27 |
| first_public | 2023-08-27 |
| 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 | GridION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Extracted Tooth |
| last_updated | 2023-08-27 |
| lat | 13.0827 |
| 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 | TM 20 |
| 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 | 13.0827 N 80.2707 E |
| location_end | 13.0827 N 80.2707 E |
| location_start | 13.0827 N 80.2707 E |
| lon | 80.2707 |
| 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 | 126796 |
| 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 | TM20.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN28173424 |
| sample_alias | TM 20 |
| 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 | SRS13380271 |
| secondary_study_accession | SRP379752 |
| 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 | PRJNA836758 |
| study_alias | PRJNA836758 |
| study_title | 16s Metagenome Sequencing and Analysis of Dental Biofilm Samples using Nanopore Sequencing Platform |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1435979 |
| 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 | TM 20 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2021-12-02 |
|---|---|
| INSDC secondary accession | SRS13380271 |
| NCBI submission package | Metagenome.environmental.1.0 |
| organism | human oral metagenome |
| host | Homo sapiens |
| geo_loc_name | India: Chennai |
| lat_lon | 13.0827 N 80.2707 E |
| isolation_source | Extracted Tooth |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2023-08-09 |
| ENA-LAST-UPDATE | 2023-08-09 |
| run | SRR19631906 |
|---|---|
| sample | SAMN28173424 |
| study | PRJNA836758 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | TM 20 |
| site | Extracted Tooth |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 80 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.