15088.MRI1948MRAP069.B.16S
BioSample: SAMEA114596688 · Study: PRJEB68381 · Body site: buccal swab
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 |
|---|---|---|---|
| Streptococcus mitis | Streptococcus | Bacillota | 19.95913% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 11.96424% |
| Streptococcus salivarius | Streptococcus | Bacillota | 11.23978% |
| Gemella haemolysans | Gemella | Bacillota | 6.95394% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 6.70679% |
| Streptococcus oralis | Streptococcus | Bacillota | 4.90250% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 4.46088% |
| Veillonella parvula | Veillonella | Bacillota | 3.83335% |
| Veillonella dispar | Veillonella | Bacillota | 3.20368% |
| Streptococcus downei | Streptococcus | Bacillota | 3.05543% |
| Gemella palaticanis | Gemella | Bacillota | 2.29663% |
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 1.40836% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 1.22653% |
| Streptococcus equinus | Streptococcus | Bacillota | 0.91277% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.90963% |
| Veillonella infantium | Veillonella | Bacillota | 0.89614% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.89526% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.76933% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.76790% |
| Gemella sanguinis | Gemella | Bacillota | 0.72134% |
| Streptococcus viridans | Streptococcus | Bacillota | 0.70233% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 0.67966% |
| Streptococcus australis | Streptococcus | Bacillota | 0.63867% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.61670% |
| Veillonella atypica | Veillonella | Bacillota | 0.61206% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.58463% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.47380% |
| Streptococcus anginosus | Streptococcus | Bacillota | 0.41619% |
| Fusobacterium periodonticum | Fusobacterium | Fusobacteriota | 0.41544% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.41417% |
| Streptococcus dysgalactiae | Streptococcus | Bacillota | 0.41134% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.39123% |
| Prevotella melaninogenica | Prevotella | Bacteroidota | 0.38362% |
| Fusobacterium nucleatum | Fusobacterium | Fusobacteriota | 0.36320% |
| Streptococcus suis | Streptococcus | Bacillota | 0.35034% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.34401% |
| Mogibacterium diversum | Mogibacterium | Bacillota | 0.34184% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.32789% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.31254% |
| Megasphaera elsdenii | Megasphaera | Bacillota | 0.26717% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.26556% |
| Gemella cuniculi | Gemella | Bacillota | 0.26497% |
| Streptococcus gordonii | Streptococcus | Bacillota | 0.26436% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.24309% |
| Peptostreptococcus stomatis | Peptostreptococcus | Bacillota | 0.20096% |
| Leptotrichia hongkongensis | Leptotrichia | Fusobacteriota | 0.19371% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.18080% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.17864% |
| Streptococcus gallolyticus | Streptococcus | Bacillota | 0.17307% |
| Streptococcus agalactiae | Streptococcus | Bacillota | 0.14775% |
| Peptostreptococcus anaerobius | Peptostreptococcus | Bacillota | 0.14468% |
| Neisseria subflava | Neisseria | Pseudomonadota | 0.14280% |
| Veillonella rodentium | Veillonella | Bacillota | 0.13625% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.12903% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.12346% |
| Streptococcus mutans | Streptococcus | Bacillota | 0.11877% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.11528% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.11380% |
| Streptococcus infantarius | Streptococcus | Bacillota | 0.11362% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.09322% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.09269% |
| Streptococcus peroris | Streptococcus | Bacillota | 0.09179% |
| Prevotella pallens | Prevotella | Bacteroidota | 0.08736% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.08549% |
| Gemella morbillorum | Gemella | Bacillota | 0.08485% |
| Schaalia odontolytica | Schaalia | Actinomycetota | 0.08356% |
66 of 66 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 |
|---|---|---|
| ERR12254123.fastq.gz | FASTQ / 346242639 | e90ab51725ffcea8481dd86158da7553 |
| 15088.MRI1948MRAP069.B.16S.R1.fastq.gz | Submitted file / 422970377 | 18a7a13f952f67f4182916cf7ddc9455 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | b6b168e9f8c97c53086eeae63931616726b4f84f0c5e5c542f64cca1d283e121 |
| median_read_length | 1452.0 |
| reads_in_length_window | 24250 |
| 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": 3447, "elapsed_seconds": 2.994712788000001, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 16, "fraction": 0.08, "adapters_found": {"BC_FLANK": 14, "27F": 2}, "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 | ERR12254123 |
|---|---|
| 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/ERR122/023/ERR12254123/ERR12254123.bam |
| bam_bytes | 356805268 |
| bam_file_role | ARCHIVAL_FILE |
| bam_ftp | ftp.sra.ebi.ac.uk/vol1/err/ERR122/023/ERR12254123/ERR12254123.bam |
| bam_galaxy | ftp.sra.ebi.ac.uk/vol1/err/ERR122/023/ERR12254123/ERR12254123.bam |
| bam_md5 | 013551f311e9ef634036eaa5088f8342 |
| base_count | 395934545 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | urban biome |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | University of California San Diego Microbiome Initiative;UCSDMI |
| checklist | ERC000011 |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2021 |
| collection_date_end | 2021-12-31 |
| collection_date_start | 2021-01-01 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Germany:Gottingen;Germany |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: qiita_ptid_15275:15088.MRI1948MRAP069.B.16S |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | 150.0 |
| environment_biome | urban biome |
| environment_feature | human-associated habitat |
| environment_material | saliva |
| environmental_medium | saliva |
| environmental_sample | Not reported |
| experiment_accession | ERX11665023 |
| experiment_alias | qiita_ptid_15275:15088.MRI1948MRAP069.B.16S |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: qiita_ptid_15275:15088.MRI1948MRAP069.B.16S |
| 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/ERR122/023/ERR12254123/ERR12254123.fastq.gz |
| fastq_bytes | 346242639 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/023/ERR12254123/ERR12254123.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/023/ERR12254123/ERR12254123.fastq.gz |
| fastq_md5 | e90ab51725ffcea8481dd86158da7553 |
| file_location | Not reported |
| first_created | 2023-11-09 |
| first_public | 2023-11-10 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Homo sapiens |
| host_body_site | UBERON:buccal mucosa |
| 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 | Not reported |
| last_updated | 2023-11-10 |
| lat | 51.53 |
| library_construction_protocol | 16S_pcr/adapter_ligation |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | 15088.MRI1948MRAP069.B.16S |
| 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 | human-associated habitat |
| location | 51.53 N 9.93 E |
| location_end | 51.53 N 9.93 E |
| location_start | 51.53 N 9.93 E |
| lon | 9.93 |
| 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 | Not reported |
| protocol_label | Not reported |
| read_count | 303767 |
| 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 | qiita_ppdid_178493:15088.MRI1948MRAP069.B.16S |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMEA114596688 |
| sample_alias | qiita_sid_15088:15088.MRI1948MRAP069.B.16S |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | P-MAPS |
| 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 | 15088.MRI1948MRAP069.B.16S |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | ERS16773687 |
| secondary_study_accession | ERP153335 |
| 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 | male |
| 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 | PRJEB68381 |
| study_alias | qiita_sid_15088 |
| study_title | Pancreatitis - Microbiome As Predictor of Severity P-MAPS |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | ERA27376419 |
| submission_tool | Not reported |
| submitted_aspera | fasp.sra.ebi.ac.uk:/vol1/run/ERR122/ERR12254123/15088.MRI1948MRAP069.B.16S.R1.fastq.gz |
| submitted_bytes | 422970377 |
| submitted_file_role | SUBMISSION_FILE |
| submitted_format | FASTQ |
| submitted_ftp | ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12254123/15088.MRI1948MRAP069.B.16S.R1.fastq.gz |
| submitted_galaxy | ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12254123/15088.MRI1948MRAP069.B.16S.R1.fastq.gz |
| submitted_host_sex | Not reported |
| submitted_md5 | 18a7a13f952f67f4182916cf7ddc9455 |
| submitted_read_type | SINGLE |
| 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 | qiita_sid_15088:15088.MRI1948MRAP069.B.16S |
|---|---|
| title | 15088.MRI1948MRAP069.B.16S |
| description | P-MAPS |
| host_height_units | cm |
|---|---|
| year | 2021 |
| host_taxid | 9606 |
| infected_collection | no |
| opioid_name | not collected |
| cardiovascular_disease_in_past | no |
| sequencing | not collected |
| empo_4 | Animal secretion (non-saline) |
| pm_none | yes |
| cholestasis_at_time_of_enrollment | yes |
| empo_2 | Host-associated (non-saline) |
| nsaid | no |
| empo_3 | Animal (non-saline) |
| grade_of_stool | not collected |
| kidney_injury_akin1 | no |
| acute_fluid_collection | no |
| kidney_injury_akin2 | no |
| empo_1 | Host-associated |
| kidney_injury_akin3 | no |
| respiratory_failure_grade_1 | no |
| host_body_habitat | UBERON:oral cavity |
| antibiotic_treatment_before_enrollment | More than 1 month no antibiotics |
| gastrointestinal_cancer_in_past | no |
| heart_failure_in_past | no |
| env_feature | human-associated habitat |
| hepatic_failure | no |
| sirs | 1 |
| host_weight | 61 |
| respiratory_failure_grade_2 | no |
| respiratory_failure_grade_3 | no |
| respiratory_failure_grade_4 | no |
| tag_mg_dl | 67 |
| drainage_required | no |
| inflammatory_bowel_disease | no |
| glc_mg_dl | 141 |
| ercp_with_papillotomy | yes |
| hematologic_failure | no |
| rheumatic_disease_in_past | no |
| tube_id | P-MAPS_MRI1948MRAP069_B_16S |
| atlanta | 1 |
| clostridioides_diff_infection_in_past | no |
| duodenal_obstruction | no |
| env_package | human-oral |
| length_of_hospital_stay | 11 |
| insulin | no |
| ca_mmol_l | 2,38 |
| collection date | 2021 |
| latitude | 51.53 |
| other_antidiabetics | no |
| host_subject_id | 816 |
| no_food_intake_possible_for_24h | no |
| env_material | saliva |
| length_of_hospital_stay_binned | short |
| etiology_drugs | not collected |
| time_pain_hosp | <12h |
| diat | vegetarian |
| confusion_ad_admission | not collected |
| irb_protocol_id | 02807 |
| pleural_effusion | not collected |
| env_biome | urban biome |
| mestenterial_thrombosis | no |
| acute_necrotic_collection | no |
| opioid_dose | not collected |
| crea_mg_dl | 0.8 |
| sex | male |
| collection_device | eSwab |
| ct_or_sonographic_drainage | no |
| irritable_stomach_bowel_disease_in_past | no |
| ppi | no |
| metformin | no |
| immunosuppressant | no |
| hematologic_cancer_in_past | no |
| qiita_sample_type | buccal swab |
| extra_gastrointestinal_cancer_in_past | no |
| statines | no |
| non_invasive_ventilation | no |
| necrosis | no |
| collection_method | buccal |
| geo_loc_name | Germany:Gottingen |
| irb_institute | University medical center Goettingen |
| parkinson_in_past | no |
| specific_current_antibiotics | not collected |
| country | Germany |
| crp_mg_l | 8 |
| true_control | TRUE |
| ercp_with_stent_implantation | yes |
| host scientific name | Homo sapiens |
| laxatives | no |
| haps | 1 |
| sample_type | buccal swab |
| eus_drainage_with_pigtails | no |
| collection_timestamp | 2021 |
| ENA-FIRST-PUBLIC | 2023-11-10 |
| hiv | no |
| ENA-LAST-UPDATE | 2023-11-10 |
| walled_off_necrosis | no |
| neuroleptics | no |
| invasive_ventilation | no |
| longitude | 9.93 |
| perotinitis | no |
| host_body_mass_index | 21.61281179 |
| comment4 | not collected |
| comment3 | not collected |
| comment2 | not collected |
| organism | human oral metagenome |
| physical_specimen_remaining | FALSE |
| comment1 | not collected |
| host_body_site | UBERON:buccal mucosa |
| ercp_yes | yes |
| scientific_name | human oral metagenome |
| bisap | not collected |
| abdominal_pain_vas | 7 |
| chronic_constipation_in_past | no |
| ca_mg_dl | not collected |
| host_height | 168 |
| dementia_in_past | no |
| ethic | Caucasian |
| hepatitis_in_past | no |
| life_stage | adult |
| etiology_other | not collected |
| icu_admission | no |
| other_abdominal_surgery | no |
| confusion_at_admission | not collected |
| chronic_alcohol_consumption | Never chronic alcohol consumption |
| eus_drainage_with_lams | no |
| death | no |
| chronic_diarrhea_in_past | no |
| origin | not collected |
| physical_specimen_location | U Gottingen |
| host_body_product | UBERON:saliva |
| pseudocyst | no |
| antidiabetics | no |
| other_neurological_disease | no |
| alcohol_units | not collected |
| hkt | 44.3 |
| liver_cirrhosis_in_past | no |
| number_of_opioid_application | not collected |
| paracetamol | no |
| host_common_name | human |
| nicotine_consumption | No |
| bun_mg_dl | 9 |
| geographic location (country and/or sea) | Germany |
| neurologic_failure | no |
| elevation | 150 |
| severity | mild |
| ENA-CHECKLIST | ERC000011 |
| dna_extracted | TRUE |
| diabetes_mellitus_in_past | no |
| center | MRI |
| host_weight_units | kg |
| bowel_intestinal_surgery_in_past | no |
| no_previous_medication | yes |
| autism | no |
| cardiovascular_failure_grade_1 | no |
| host_age_units | years |
| other_organ_failure | no |
| cardiovascular_failure_grade_2 | no |
| etiology | biliary |
| leuk_10_3_ml | 10.93 |
| cardiovascular_failure_grade_3 | no |
| nafld | no |
| cardiovascular_failure_grade_4 | no |
| ldh | 427 |
| no_complication | yes |
| host_age | 73 |
| depression_in_past | no |
| other_gastrointestinal_diseases_in_past | no |
| specific_previous_week_antibiotics | not collected |
| opioid_intake | no |
| eus_drainage | no |
| run | ERR12254123 |
|---|---|
| sample | SAMEA114596688 |
| study | PRJEB68381 |
| title | 15088.MRI1948MRAP069.B.16S |
| alias | qiita_sid_15088:15088.MRI1948MRAP069.B.16S |
| site | buccal swab |
| subject | 816 |
| phenotype | Not reported |
| sex | male |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 30000 |
| species_reported | 66 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.