Study of an Oxford Nanopore sequenced Plaque Microbiome Community
BioSample: SAMEA120314438 · Study: PRJEB98716 · Body site: unknown
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 |
|---|---|---|---|
| Staphylococcus aureus | Staphylococcus | Bacillota | 16.68573% |
| Listeria monocytogenes | Listeria | Bacillota | 11.64981% |
| Bacillus subtilis | Bacillus | Bacillota | 10.57685% |
| Salmonella enterica | Salmonella | Pseudomonadota | 9.42268% |
| Enterococcus faecalis | Enterococcus | Bacillota | 8.88783% |
| Bacillus amyloliquefaciens | Bacillus | Bacillota | 6.97994% |
| Escherichia coli | Escherichia | Pseudomonadota | 6.23906% |
| Limosilactobacillus fermentum | Limosilactobacillus | Bacillota | 5.78384% |
| Bacillus velezensis | Bacillus | Bacillota | 4.47466% |
| Enterococcus faecium | Enterococcus | Bacillota | 3.52450% |
| Listeria ivanovii | Listeria | Bacillota | 2.80373% |
| Listeria welshimeri | Listeria | Bacillota | 2.22525% |
| Bacillus halotolerans | Bacillus | Bacillota | 1.23057% |
| Bacillus licheniformis | Bacillus | Bacillota | 1.13450% |
| Pseudomonas aeruginosa | Pseudomonas | Pseudomonadota | 1.11863% |
| Staphylococcus pseudintermedius | Staphylococcus | Bacillota | 1.07226% |
| Enterococcus columbae | Enterococcus | Bacillota | 0.75632% |
| Bacillus cereus | Bacillus | Bacillota | 0.59750% |
| Shigella sonnei | Shigella | Pseudomonadota | 0.58167% |
| Shigella dysenteriae | Shigella | Pseudomonadota | 0.44592% |
| Listeria innocua | Listeria | Bacillota | 0.40936% |
| Listeria seeligeri | Listeria | Bacillota | 0.34556% |
| Shigella flexneri | Shigella | Pseudomonadota | 0.32621% |
| Limosilactobacillus mucosae | Limosilactobacillus | Bacillota | 0.27355% |
| Limosilactobacillus reuteri | Limosilactobacillus | Bacillota | 0.25612% |
| Bacillus coagulans | Bacillus | Bacillota | 0.24035% |
| Bacillus circulans | Bacillus | Bacillota | 0.23097% |
| Escherichia fergusonii | Escherichia | Pseudomonadota | 0.22869% |
| Bacillus thuringiensis | Bacillus | Bacillota | 0.22834% |
| Lactobacillus psittaci | Lactobacillus | Bacillota | 0.20736% |
| Limosilactobacillus gorillae | Limosilactobacillus | Bacillota | 0.20183% |
| Bacillus pumilus | Bacillus | Bacillota | 0.19557% |
| Staphylococcus argensis | Staphylococcus | Bacillota | 0.19130% |
| Staphylococcus lugdunensis | Staphylococcus | Bacillota | 0.15238% |
| Shigella boydii | Shigella | Pseudomonadota | 0.14637% |
| Listeria cornellensis | Listeria | Bacillota | 0.11476% |
| Limosilactobacillus oris | Limosilactobacillus | Bacillota | 0.06002% |
35 of 37 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 |
|---|---|---|
| ERR15751974.fastq.gz | FASTQ / 25622831 | 97f4c2111d6fced913c4c8ea25d6a6c3 |
| Zymobiomics_DNA_mix.fastq.gz | Submitted file / 25557229 | 45a273e4cbfe4240d740a63ddd991efa |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 2a37236c9988f2f6df5586d57c6518d37bdd6a54c3b965ca8ecbc8b480ad2b02 |
| median_read_length | 1493 |
| reads_in_length_window | 19268 |
| 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": 20195, "reads_skipped": 1819, "elapsed_seconds": 5.01230846, "reads_submitted": 20195, "reads_after_filter": 20195, "adapter_scan": {"sampled": 200, "matched": 24, "fraction": 0.12, "adapters_found": {"BC_FLANK": 20, "27F": 4}, "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 | ERR15751974 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | fasp.sra.ebi.ac.uk:/vol1/err/ERR157/074/ERR15751974/ERR15751974.bam |
| bam_bytes | 26510893 |
| bam_file_role | ARCHIVAL_FILE |
| bam_ftp | ftp.sra.ebi.ac.uk/vol1/err/ERR157/074/ERR15751974/ERR15751974.bam |
| bam_galaxy | ftp.sra.ebi.ac.uk/vol1/err/ERR157/074/ERR15751974/ERR15751974.bam |
| bam_md5 | 37c80ad14c66ea6b26277ed902a05a18 |
| base_count | 29793436 |
| 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 | University of Sheffield, School of Clinical Dentistry |
| checklist | ERC000011:1.3 |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2018 |
| collection_date_end | 2018-12-31 |
| collection_date_start | 2018-01-01 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | United Kingdom |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing |
| 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 | ERX15157072 |
| experiment_alias | ena-EXPERIMENT-TAB-22-10-2025-11:46:53:210-14644 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing |
| 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/ERR157/074/ERR15751974/ERR15751974.fastq.gz |
| fastq_bytes | 25622831 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/ERR157/074/ERR15751974/ERR15751974.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/ERR157/074/ERR15751974/ERR15751974.fastq.gz |
| fastq_md5 | 97f4c2111d6fced913c4c8ea25d6a6c3 |
| file_location | Not reported |
| first_created | 2025-10-22 |
| first_public | 2025-10-27 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Not reported |
| 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 | Not reported |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | Not reported |
| identified_by | Not reported |
| instrument_model | MinION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Not reported |
| last_updated | 2025-10-27 |
| lat | Not reported |
| 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 | LIB005 |
| 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 | Not reported |
| location_end | Not reported |
| location_start | Not reported |
| lon | Not reported |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Not reported |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | Study of an Oxford Nanopore sequenced Plaque Microbiome Community |
| protocol_label | Not reported |
| read_count | 20195 |
| 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 | ena-RUN-TAB-22-10-2025-11:46:53:210-14645 |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMEA120314438 |
| sample_alias | ena-SAMPLE-TAB-09-10-2025-12:17:51:474-13501 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Development and use of Oral microbiome optimised Oxford Nanopore 16S primers and their use to elucidate the effect of sialidase inhibitors on a plaque community biofilm model |
| 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 | Study of an Oxford Nanopore sequenced Plaque Microbiome Community |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | ERS26976425 |
| secondary_study_accession | ERP181091 |
| 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 | PRJEB98716 |
| study_alias | 08303eff-6b47-4418-8c2a-498b21188afc |
| study_title | Development and Use of Oral Microbiome Optimised Oxford Nanopore 16S Primers to Elucidate the Effect of Sialidase Inhibitors on a Plaque Community Biofilm Model |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | ERA35069360 |
| submission_tool | Not reported |
| submitted_aspera | fasp.sra.ebi.ac.uk:/vol1/run/ERR157/ERR15751974/Zymobiomics_DNA_mix.fastq.gz |
| submitted_bytes | 25557229 |
| submitted_file_role | SUBMISSION_FILE |
| submitted_format | FASTQ |
| submitted_ftp | ftp.sra.ebi.ac.uk/vol1/run/ERR157/ERR15751974/Zymobiomics_DNA_mix.fastq.gz |
| submitted_galaxy | ftp.sra.ebi.ac.uk/vol1/run/ERR157/ERR15751974/Zymobiomics_DNA_mix.fastq.gz |
| submitted_host_sex | Not reported |
| submitted_md5 | 45a273e4cbfe4240d740a63ddd991efa |
| submitted_read_type | SINGLE |
| surveillance_target | Not reported |
| tag | Not reported |
| 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 | ena-SAMPLE-TAB-09-10-2025-12:17:51:474-13501 |
|---|---|
| title | Study of an Oxford Nanopore sequenced Plaque Microbiome Community |
| description | Development and use of Oral microbiome optimised Oxford Nanopore 16S primers and their use to elucidate the effect of sialidase inhibitors on a plaque community biofilm model |
| ENA-CHECKLIST | ERC000011:1.3 |
|---|---|
| organism | human oral metagenome |
| collection date | 2018 |
| scientific_name | human oral metagenome |
| geographic location (country and/or sea) | United Kingdom |
| run | ERR15751974 |
|---|---|
| sample | SAMEA120314438 |
| study | PRJEB98716 |
| title | Study of an Oxford Nanopore sequenced Plaque Microbiome Community |
| alias | ena-SAMPLE-TAB-09-10-2025-12:17:51:474-13501 |
| site | unknown |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | True |
| state | complete |
| reads_input | 20195 |
| species_reported | 37 |
| human_primary | False |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.