Metagenome or environmental sample from human oral metagenome
BioSample: SAMN28173414 · 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 |
|---|---|---|---|
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 12.98360% |
| Parvimonas micra | Parvimonas | Bacillota | 6.75858% |
| Eubacterium ramulus | Eubacterium | Bacillota | 6.73079% |
| Eubacterium limosum | Eubacterium | Bacillota | 3.44808% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 3.23762% |
| Dialister invisus | Dialister | Bacillota | 3.20025% |
| Bradyrhizobium oligotrophicum | Bradyrhizobium | Pseudomonadota | 2.64690% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 2.56014% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 1.95621% |
| Veillonella parvula | Veillonella | Bacillota | 1.80502% |
| Acidaminococcus fermentans | Acidaminococcus | Bacillota | 1.69604% |
| Treponema brennaborense | Treponema | Spirochaetota | 1.65290% |
| Pseudoramibacter alactolyticus | Pseudoramibacter | Bacillota | 1.63436% |
| Porphyromonas circumdentaria | Porphyromonas | Bacteroidota | 1.60224% |
| Prevotella multisaccharivorax | Prevotella | Bacteroidota | 1.57194% |
| Propionibacterium freudenreichii | Propionibacterium | Actinomycetota | 1.49665% |
| Megasphaera stantonii | Megasphaera | Bacillota | 1.46175% |
| Phocaeicola abscessus | Phocaeicola | Bacteroidota | 1.42559% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 1.42211% |
| Bradyrhizobium denitrificans | Bradyrhizobium | Pseudomonadota | 1.38047% |
| Porphyromonas endodontalis | Porphyromonas | Bacteroidota | 1.29498% |
| Selenomonas flueggei | Selenomonas | Bacillota | 1.28825% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 1.26945% |
| Eubacterium ventriosum | Eubacterium | Bacillota | 1.25429% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.19220% |
| Treponema lecithinolyticum | Treponema | Spirochaetota | 1.18860% |
| Treponema pectinovorum | Treponema | Spirochaetota | 1.18227% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 1.16680% |
| Propionibacterium acidifaciens | Propionibacterium | Actinomycetota | 1.15175% |
| Eubacterium multiforme | Eubacterium | Bacillota | 1.15045% |
| Treponema bryantii | Treponema | Spirochaetota | 1.07216% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 1.05724% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.97727% |
| Eubacterium barkeri | Eubacterium | Bacillota | 0.95216% |
| Bradyrhizobium elkanii | Bradyrhizobium | Pseudomonadota | 0.91776% |
| Treponema succinifaciens | Treponema | Spirochaetota | 0.87146% |
| Bradyrhizobium betae | Bradyrhizobium | Pseudomonadota | 0.80623% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.77414% |
| Tannerella forsythia | Tannerella | Bacteroidota | 0.75583% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.74594% |
| Dialister hominis | Dialister | Bacillota | 0.72634% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.72357% |
| Streptococcus salivarius | Streptococcus | Bacillota | 0.65799% |
| Bradyrhizobium paxllaeri | Bradyrhizobium | Pseudomonadota | 0.64911% |
| Streptococcus downei | Streptococcus | Bacillota | 0.64812% |
| Bradyrhizobium icense | Bradyrhizobium | Pseudomonadota | 0.64600% |
| Veillonella infantium | Veillonella | Bacillota | 0.63730% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.63298% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.57891% |
| Megasphaera hexanoica | Megasphaera | Bacillota | 0.54359% |
| Bradyrhizobium zhanjiangense | Bradyrhizobium | Pseudomonadota | 0.53099% |
| Eubacterium uniforme | Eubacterium | Bacillota | 0.49583% |
| Megasphaera cerevisiae | Megasphaera | Bacillota | 0.49285% |
| Prevotella brevis | Prevotella | Bacteroidota | 0.46191% |
| Prevotella oris | Prevotella | Bacteroidota | 0.45667% |
| Filifactor alocis | Filifactor | Bacillota | 0.42396% |
| Treponema denticola | Treponema | Spirochaetota | 0.41814% |
| Bradyrhizobium guangdongense | Bradyrhizobium | Pseudomonadota | 0.40552% |
| Bradyrhizobium guangzhouense | Bradyrhizobium | Pseudomonadota | 0.40550% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.39563% |
| Treponema putidum | Treponema | Spirochaetota | 0.39388% |
| Megasphaera coli | Megasphaera | Bacillota | 0.39029% |
| Eubacterium oxidoreducens | Eubacterium | Bacillota | 0.35381% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.34669% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 0.32648% |
| Bradyrhizobium pachyrhizi | Bradyrhizobium | Pseudomonadota | 0.32139% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.31064% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.30855% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.30712% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.30224% |
| Limosilactobacillus mucosae | Limosilactobacillus | Bacillota | 0.30110% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.29677% |
| Treponema medium | Treponema | Spirochaetota | 0.27603% |
| Limosilactobacillus fermentum | Limosilactobacillus | Bacillota | 0.27116% |
| Bradyrhizobium diazoefficiens | Bradyrhizobium | Pseudomonadota | 0.27016% |
| Prevotella buccalis | Prevotella | Bacteroidota | 0.26640% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.26078% |
| Megasphaera geminata | Megasphaera | Bacillota | 0.24739% |
| Eubacterium maltosivorans | Eubacterium | Bacillota | 0.24579% |
| Bradyrhizobium valentinum | Bradyrhizobium | Pseudomonadota | 0.22439% |
| Megasphaera massiliensis | Megasphaera | Bacillota | 0.22160% |
| Bradyrhizobium cosmicum | Bradyrhizobium | Pseudomonadota | 0.20937% |
| Treponema saccharophilum | Treponema | Spirochaetota | 0.18310% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.16109% |
| Porphyromonas asaccharolytica | Porphyromonas | Bacteroidota | 0.14848% |
| Veillonella rodentium | Veillonella | Bacillota | 0.14430% |
| Lactobacillus psittaci | Lactobacillus | Bacillota | 0.12290% |
| Stenotrophomonas maltophilia | Stenotrophomonas | Pseudomonadota | 0.11675% |
88 of 88 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 |
|---|---|---|
| SRR19631897_1.fastq.gz | FASTQ / 32562691 | 937a96dd3079af381c2417d856805e18 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | f820ceac19abf87cf2d45f79db003d0cb64f48f74a09d3c15513124e87749063 |
| median_read_length | 1402.0 |
| reads_in_length_window | 19097 |
| 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": 13479, "elapsed_seconds": 2.494078231000003, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 2, "fraction": 0.01, "adapters_found": {"BC_FLANK": 2}, "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 | SRR19631897 |
|---|---|
| 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 | 33444828 |
| 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 | SRX15682452 |
| experiment_alias | TM 10 |
| 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/SRR196/097/SRR19631897/SRR19631897_1.fastq.gz |
| fastq_bytes | 32562691 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/097/SRR19631897/SRR19631897_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/097/SRR19631897/SRR19631897_1.fastq.gz |
| fastq_md5 | 937a96dd3079af381c2417d856805e18 |
| 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 10 |
| 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 | 30154 |
| 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 | TM10.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN28173414 |
| sample_alias | TM 10 |
| 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 | SRS13380280 |
| 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 10 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2021-12-02 |
|---|---|
| INSDC secondary accession | SRS13380280 |
| 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 | SRR19631897 |
|---|---|
| sample | SAMN28173414 |
| study | PRJNA836758 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | TM 10 |
| 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 | 88 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.