Metagenome or environmental sample from human oral metagenome
BioSample: SAMN28173409 · 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 |
|---|---|---|---|
| Prevotella ruminicola | Prevotella | Bacteroidota | 9.65456% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 5.61466% |
| Selenomonas flueggei | Selenomonas | Bacillota | 4.80729% |
| Dialister pneumosintes | Dialister | Bacillota | 4.06260% |
| Megasphaera stantonii | Megasphaera | Bacillota | 3.81908% |
| Prevotella nigrescens | Prevotella | Bacteroidota | 3.73231% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 3.11750% |
| Selenomonas sputigena | Selenomonas | Bacillota | 3.07438% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 2.95176% |
| Dialister invisus | Dialister | Bacillota | 2.93680% |
| Prevotella intermedia | Prevotella | Bacteroidota | 2.63573% |
| Parvimonas micra | Parvimonas | Bacillota | 2.60220% |
| Eubacterium ramulus | Eubacterium | Bacillota | 2.57221% |
| Prevotella denticola | Prevotella | Bacteroidota | 2.55234% |
| Prevotella oris | Prevotella | Bacteroidota | 2.38965% |
| Prevotella corporis | Prevotella | Bacteroidota | 2.11067% |
| Solobacterium moorei | Solobacterium | Bacillota | 1.73682% |
| Peptostreptococcus canis | Peptostreptococcus | Bacillota | 1.68416% |
| Fusobacterium perfoetens | Fusobacterium | Fusobacteriota | 1.62630% |
| Prevotella brevis | Prevotella | Bacteroidota | 1.61739% |
| Megasphaera hexanoica | Megasphaera | Bacillota | 1.57528% |
| Mogibacterium timidum | Mogibacterium | Bacillota | 1.50532% |
| Mogibacterium pumilum | Mogibacterium | Bacillota | 1.47469% |
| Catonella morbi | Catonella | Bacillota | 1.40693% |
| Prevotella buccalis | Prevotella | Bacteroidota | 1.39279% |
| Dialister hominis | Dialister | Bacillota | 1.33552% |
| Fusobacterium simiae | Fusobacterium | Fusobacteriota | 1.29963% |
| Megasphaera coli | Megasphaera | Bacillota | 1.20490% |
| Peptostreptococcus stomatis | Peptostreptococcus | Bacillota | 1.08224% |
| Shuttleworthella satelles | Shuttleworthella | Bacillota | 1.05836% |
| Selenomonas dianae | Selenomonas | Bacillota | 0.97421% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 0.95256% |
| Mogibacterium vescum | Mogibacterium | Bacillota | 0.84151% |
| Fusobacterium russii | Fusobacterium | Fusobacteriota | 0.77493% |
| Eubacterium limosum | Eubacterium | Bacillota | 0.71529% |
| Selenomonas infelix | Selenomonas | Bacillota | 0.68464% |
| Prevotella multisaccharivorax | Prevotella | Bacteroidota | 0.67825% |
| Megasphaera massiliensis | Megasphaera | Bacillota | 0.61375% |
| Treponema pectinovorum | Treponema | Spirochaetota | 0.58577% |
| Prevotella veroralis | Prevotella | Bacteroidota | 0.55376% |
| Prevotella heparinolytica | Prevotella | Bacteroidota | 0.49723% |
| Prevotella jejuni | Prevotella | Bacteroidota | 0.46485% |
| Prevotella bivia | Prevotella | Bacteroidota | 0.46410% |
| Treponema succinifaciens | Treponema | Spirochaetota | 0.45968% |
| Pseudoramibacter alactolyticus | Pseudoramibacter | Bacillota | 0.44317% |
| Prevotella aurantiaca | Prevotella | Bacteroidota | 0.44274% |
| Prevotella loescheii | Prevotella | Bacteroidota | 0.42959% |
| Capnocytophaga sputigena | Capnocytophaga | Bacteroidota | 0.42747% |
| Treponema bryantii | Treponema | Spirochaetota | 0.42215% |
| Mogibacterium neglectum | Mogibacterium | Bacillota | 0.40923% |
| Treponema denticola | Treponema | Spirochaetota | 0.39082% |
| Megasphaera geminata | Megasphaera | Bacillota | 0.39054% |
| Selenomonas ruminantium | Selenomonas | Bacillota | 0.36035% |
| Treponema putidum | Treponema | Spirochaetota | 0.34236% |
| Prevotella pallens | Prevotella | Bacteroidota | 0.32571% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.31190% |
| Bradyrhizobium oligotrophicum | Bradyrhizobium | Pseudomonadota | 0.30209% |
| Peptostreptococcus russellii | Peptostreptococcus | Bacillota | 0.29765% |
| Megasphaera cerevisiae | Megasphaera | Bacillota | 0.29183% |
| Treponema brennaborense | Treponema | Spirochaetota | 0.29130% |
| Dialister micraerophilus | Dialister | Bacillota | 0.26646% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 0.26518% |
| Treponema medium | Treponema | Spirochaetota | 0.25158% |
| Phocaeicola abscessus | Phocaeicola | Bacteroidota | 0.24495% |
| Prevotella oralis | Prevotella | Bacteroidota | 0.24132% |
| Prevotella copri | Prevotella | Bacteroidota | 0.23948% |
| Eubacterium ventriosum | Eubacterium | Bacillota | 0.23218% |
| Eubacterium xylanophilum | Eubacterium | Bacillota | 0.20817% |
| Alloprevotella tannerae | Alloprevotella | Bacteroidota | 0.20340% |
| Capnocytophaga canis | Capnocytophaga | Bacteroidota | 0.20336% |
| Campylobacter hyointestinalis | Campylobacter | Pseudomonadota | 0.20331% |
| Bradyrhizobium denitrificans | Bradyrhizobium | Pseudomonadota | 0.20009% |
| Prevotella buccae | Prevotella | Bacteroidota | 0.19520% |
| Streptococcus mitis | Streptococcus | Bacillota | 0.18743% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.18635% |
| Streptococcus downei | Streptococcus | Bacillota | 0.18274% |
| Eubacterium pyruvativorans | Eubacterium | Bacillota | 0.18198% |
| Megasphaera indica | Megasphaera | Bacillota | 0.18096% |
| Prevotella multiformis | Prevotella | Bacteroidota | 0.17889% |
| Megasphaera sueciensis | Megasphaera | Bacillota | 0.16935% |
| Eubacterium oxidoreducens | Eubacterium | Bacillota | 0.16627% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.15721% |
| Megasphaera paucivorans | Megasphaera | Bacillota | 0.15720% |
| Treponema saccharophilum | Treponema | Spirochaetota | 0.15493% |
| Eubacterium callanderi | Eubacterium | Bacillota | 0.14856% |
| Streptococcus salivarius | Streptococcus | Bacillota | 0.14517% |
| Eubacterium multiforme | Eubacterium | Bacillota | 0.13891% |
| Prevotella shahii | Prevotella | Bacteroidota | 0.13028% |
| Treponema phagedenis | Treponema | Spirochaetota | 0.12268% |
| Treponema pedis | Treponema | Spirochaetota | 0.10744% |
| Campylobacter showae | Campylobacter | Pseudomonadota | 0.10450% |
| Prevotella scopos | Prevotella | Bacteroidota | 0.10072% |
| Acidaminococcus intestini | Acidaminococcus | Bacillota | 0.09546% |
| Eubacterium ruminantium | Eubacterium | Bacillota | 0.09529% |
| Dialister propionicifaciens | Dialister | Bacillota | 0.09121% |
| Fusobacterium hwasookii | Fusobacterium | Fusobacteriota | 0.08829% |
95 of 96 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 |
|---|---|---|
| SRR19631902_1.fastq.gz | FASTQ / 122695544 | be9ceb5a2b87b75111de39e6426d1f9d |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | b6ae0b1c646930191dfa9c776c2b36047a11be6af28fd1781fe25caed9c6d273 |
| median_read_length | 1454.0 |
| reads_in_length_window | 26610 |
| 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": 5767, "elapsed_seconds": 2.623107498999957, "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 | SRR19631902 |
|---|---|
| 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 | 126574520 |
| 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 | SRX15682447 |
| experiment_alias | TM 5 |
| 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/SRR196/002/SRR19631902/SRR19631902_1.fastq.gz |
| fastq_bytes | 122695544 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/002/SRR19631902/SRR19631902_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR196/002/SRR19631902/SRR19631902_1.fastq.gz |
| fastq_md5 | be9ceb5a2b87b75111de39e6426d1f9d |
| 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 5 |
| 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 | 91613 |
| 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 | TM5.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN28173409 |
| sample_alias | TM 5 |
| 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 | SRS13380275 |
| 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 5 |
|---|---|
| title | Metagenome or environmental sample from human oral metagenome |
| description | Not reported |
| collection_date | 2021-12-02 |
|---|---|
| INSDC secondary accession | SRS13380275 |
| 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 | SRR19631902 |
|---|---|
| sample | SAMN28173409 |
| study | PRJNA836758 |
| title | Metagenome or environmental sample from human oral metagenome |
| alias | TM 5 |
| 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 | 96 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.