Metagenome or environmental sample from human oral metagenome
BioSample: SAMN28173407 · 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 | 13.30552% |
| Porphyromonas gingivalis | Porphyromonas | Bacteroidota | 9.00702% |
| Tannerella forsythia | Tannerella | Bacteroidota | 5.54871% |
| Veillonella parvula | Veillonella | Bacillota | 4.60340% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 4.52475% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 3.69932% |
| Eubacterium ramulus | Eubacterium | Bacillota | 3.56803% |
| Dialister invisus | Dialister | Bacillota | 3.01478% |
| Treponema denticola | Treponema | Spirochaetota | 2.97717% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 2.30227% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 2.14153% |
| Veillonella infantium | Veillonella | Bacillota | 2.13797% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 1.84075% |
| Neisseria mucosa | Neisseria | Pseudomonadota | 1.73469% |
| Selenomonas flueggei | Selenomonas | Bacillota | 1.54270% |
| Treponema putidum | Treponema | Spirochaetota | 1.48733% |
| Bradyrhizobium oligotrophicum | Bradyrhizobium | Pseudomonadota | 1.41580% |
| Prevotella ruminicola | Prevotella | Bacteroidota | 1.39809% |
| Treponema pectinovorum | Treponema | Spirochaetota | 1.33884% |
| Mogibacterium pumilum | Mogibacterium | Bacillota | 1.16450% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.08683% |
| Filifactor alocis | Filifactor | Bacillota | 1.08275% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.99540% |
| Kingella oralis | Kingella | Pseudomonadota | 0.95584% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 0.94746% |
| Bradyrhizobium denitrificans | Bradyrhizobium | Pseudomonadota | 0.88459% |
| Streptococcus downei | Streptococcus | Bacillota | 0.84111% |
| Desulfobulbus oralis | Desulfobulbus | Thermodesulfobacteriota | 0.80536% |
| Treponema succinifaciens | Treponema | Spirochaetota | 0.80117% |
| Dialister hominis | Dialister | Bacillota | 0.73784% |
| Prevotella denticola | Prevotella | Bacteroidota | 0.72400% |
| Streptococcus salivarius | Streptococcus | Bacillota | 0.70266% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.67927% |
| Bradyrhizobium paxllaeri | Bradyrhizobium | Pseudomonadota | 0.63855% |
| Treponema bryantii | Treponema | Spirochaetota | 0.63555% |
| Neisseria gonorrhoeae | Neisseria | Pseudomonadota | 0.61160% |
| Neisseria macacae | Neisseria | Pseudomonadota | 0.60188% |
| Veillonella dispar | Veillonella | Bacillota | 0.58640% |
| Neisseria canis | Neisseria | Pseudomonadota | 0.58169% |
| Porphyromonas levii | Porphyromonas | Bacteroidota | 0.55865% |
| Prevotella multisaccharivorax | Prevotella | Bacteroidota | 0.53543% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.52070% |
| Mogibacterium vescum | Mogibacterium | Bacillota | 0.51684% |
| Bradyrhizobium betae | Bradyrhizobium | Pseudomonadota | 0.50834% |
| Porphyromonas macacae | Porphyromonas | Bacteroidota | 0.48970% |
| Dialister pneumosintes | Dialister | Bacillota | 0.46506% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.38720% |
| Treponema saccharophilum | Treponema | Spirochaetota | 0.38180% |
| Prevotella brevis | Prevotella | Bacteroidota | 0.36841% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.35246% |
| Porphyromonas circumdentaria | Porphyromonas | Bacteroidota | 0.34964% |
| Mogibacterium neglectum | Mogibacterium | Bacillota | 0.33851% |
| Eubacterium ventriosum | Eubacterium | Bacillota | 0.33850% |
| Veillonella atypica | Veillonella | Bacillota | 0.33684% |
| Selenomonas noxia | Selenomonas | Bacillota | 0.33173% |
| Phocaeicola abscessus | Phocaeicola | Bacteroidota | 0.33085% |
| Neisseria meningitidis | Neisseria | Pseudomonadota | 0.32446% |
| Propionibacterium freudenreichii | Propionibacterium | Actinomycetota | 0.32110% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.31798% |
| Prevotella oris | Prevotella | Bacteroidota | 0.31487% |
| Bradyrhizobium zhanjiangense | Bradyrhizobium | Pseudomonadota | 0.30631% |
| Eubacterium multiforme | Eubacterium | Bacillota | 0.30209% |
| Neisseria sicca | Neisseria | Pseudomonadota | 0.28538% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.27431% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.27333% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.26639% |
| Neisseria elongata | Neisseria | Pseudomonadota | 0.26439% |
| Treponema medium | Treponema | Spirochaetota | 0.26139% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.25700% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.24841% |
| Bradyrhizobium guangzhouense | Bradyrhizobium | Pseudomonadota | 0.23947% |
| Bradyrhizobium guangdongense | Bradyrhizobium | Pseudomonadota | 0.23947% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.22695% |
| Propionibacterium acidifaciens | Propionibacterium | Actinomycetota | 0.22306% |
| Bradyrhizobium pachyrhizi | Bradyrhizobium | Pseudomonadota | 0.21656% |
| Bradyrhizobium elkanii | Bradyrhizobium | Pseudomonadota | 0.20229% |
| Prevotella buccalis | Prevotella | Bacteroidota | 0.19959% |
| Capnocytophaga leadbetteri | Capnocytophaga | Bacteroidota | 0.19299% |
| Veillonella rodentium | Veillonella | Bacillota | 0.18230% |
| Eubacterium barkeri | Eubacterium | Bacillota | 0.17838% |
| Porphyromonas asaccharolytica | Porphyromonas | Bacteroidota | 0.17288% |
| Bradyrhizobium valentinum | Bradyrhizobium | Pseudomonadota | 0.16361% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.16230% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.15825% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.15013% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.14417% |
| Bradyrhizobium diazoefficiens | Bradyrhizobium | Pseudomonadota | 0.14344% |
| Bradyrhizobium cosmicum | Bradyrhizobium | Pseudomonadota | 0.13931% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.13815% |
| Capnocytophaga ochracea | Capnocytophaga | Bacteroidota | 0.13492% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 0.13389% |
| Treponema phagedenis | Treponema | Spirochaetota | 0.12852% |
| Filifactor villosus | Filifactor | Bacillota | 0.12751% |
| Selenomonas sputigena | Selenomonas | Bacillota | 0.12625% |
| Porphyromonas gingivicanis | Porphyromonas | Bacteroidota | 0.12549% |
| Neisseria dentiae | Neisseria | Pseudomonadota | 0.12334% |
| Treponema brennaborense | Treponema | Spirochaetota | 0.12209% |
| Porphyromonas endodontalis | Porphyromonas | Bacteroidota | 0.11321% |
| Prevotella oulorum | Prevotella | Bacteroidota | 0.11309% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.11279% |
| Dialister micraerophilus | Dialister | Bacillota | 0.10855% |
| Leptotrichia wadei | Leptotrichia | Fusobacteriota | 0.09929% |
| Treponema pedis | Treponema | Spirochaetota | 0.08954% |
| Sphingobium abikonense | Sphingobium | Pseudomonadota | 0.08707% |
103 of 104 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 |
|---|---|---|
| SRR19631905_1.fastq.gz | FASTQ / 63416226 | a8c1facb4c63ef0513bae94e303b9fd0 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 6339f6504ce83077ba86deee96dbaeaa5c6d190d6c36abc041297f6c87a70ae7 |
| median_read_length | 1451.0 |
| reads_in_length_window | 26999 |
| 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": 6809, "elapsed_seconds": 2.871438059999946, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 1, "fraction": 0.005, "adapters_found": {"BC_FLANK": 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 | SRR19631905 |
|---|---|
| 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 | 65411075 |
| 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 | SRX15682444 |
| experiment_alias | TM 3 |
| 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/SRR196/005/SRR19631905/SRR19631905_1.fastq.gz |
| fastq_bytes | 63416226 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/005/SRR19631905/SRR19631905_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/005/SRR19631905/SRR19631905_1.fastq.gz |
| fastq_md5 | a8c1facb4c63ef0513bae94e303b9fd0 |
| 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 3 |
| 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 | 47140 |
| 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 | TM3.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN28173407 |
| sample_alias | TM 3 |
| 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 | SRS13380272 |
| 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 3 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2021-12-02 |
|---|---|
| INSDC secondary accession | SRS13380272 |
| 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 | SRR19631905 |
|---|---|
| sample | SAMN28173407 |
| study | PRJNA836758 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | TM 3 |
| 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 | 104 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.