Metagenomes in acute cholecystitis, Japan, cross-sectional
16 samples from acute cholecystitis patients in Japan, analyzed by metagenome sequencing to assess pathogen detection and rapid diagnostics; cross-sectional study design. machine-written summary
16 samples · 16 runs · JP · Age unknown · 2017 · 4.7 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 80 sample values (collection date, country, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 61 sample values (age, antibiotic exposure, location site, sex) · PMC5397476 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 3 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 16 | 100% | ||||
| country | 16 | 100% | 16 | |||
| health_condition | 16 | 100% | 16 | |||
| subject_id | 16 | 100% | 16 | |||
| age_at_collection_days | 16 | 100% | 16 | |||
| collection_date | 16 | 100% | 16 | |||
| detailed_location | 16 | 100% | ||||
| health_condition_detail | 16 | 100% | 16 | |||
| location_site | 16 | 100% | 16 | |||
| sex | 16 | 100% | 16 | |||
| antibiotic_exposure | 13 | 81% | 13 |
- Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach. 2017 PMID 28473817 PMC5397476 own_data
Archive description
Acute cholecystitis (AC) is a benign inflammatory disease that can be fatal if treated inappropriately. In this study, metagenome analysis was performed to evaluate the characteristics of AC patients and usefulness of rapid diagnostics.
How this project entered the registry
Classified as human gut / stool / oral cavity / other human site / multiple sites / blood / tissue / internal fluids shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human bile metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human saliva metagenome”
- body site sample.attr.env_medium · “Bile (n=6/16)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00063086 | age_at_collection_days | 31046.0 | R3 | 0.80 | paper.body.Table 1[Age (years)] | P1 Age (years): 85 |
| SAMD00063086 | antibiotic_exposure | yes | R3 | 0.80 | paper.body.Table 1[Antimicrobial agents] | P1 Antimicrobial agents: CTRX |
| SAMD00063086 | collection_date | 2015-09 | R1 | 0.90 | biosample.attribute:collection_date | 2015-09 |
| SAMD00063086 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00063086 | health_condition | liver_disease | R1 | 0.90 | biosample_attr | cholecystitis |
| SAMD00063086 | health_condition_detail | cholecystitis | R1 | 0.90 | sample.attr.host_disease_stat | cholecystitis |
| SAMD00063086 | location_site | Toho University Ohashi Medical Center | R3 | 0.70 | paper.body.methods | six patients (P1–P6) who underwent cholecystectomy for AC at the Department of Surgery, Toho University Ohashi Medical Center |
| SAMD00063086 | sex | female | R3 | 0.80 | paper.body.Table 1[Sex (M/F)] | P1 Sex (M/F): F |
| SAMD00063086 | subject_id | P1 | R1 | 0.85 | sample.attr.host_subject_id | P1 |
Sequencing
16 runs over 16 samples · mean 43.2 Mbp per run (median 4.7 Mbp, total 0.69 Gbp; 16 runs with a base count) · layout SINGLE 16 · platform ILLUMINA 16 · models Illumina MiSeq (16) · 19% of runs with a Sandpiper profile · first public 2017-03-24
Authors (0)
No author record.
Downloads
PRJDB5180.csv.gz (1.4 KB) · parquet (70.8 KB) — all 16 samples, every field with route and confidence · PRJDB5180_determinations.csv.gz (1.8 KB) — 141 evidence rows