Gut microbiome in peritoneal dialysis peritonitis, case-control
75 samples (anal swabs and peritoneal dialysis fluid) from peritoneal dialysis patients with kidney disease, used to study peritonitis risk factors and gut microbiota via mNGS in a case-control design. machine-written summary
75 samples · 75 runs · CN · Age unknown · 2024 · 31.5 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 185 sample values (health condition, health condition detail, subject id) |
| ✓ Full text | 150 sample values (collection date, country) · PMC11602453 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 17 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 | 0 | 0% | ||||
| country | 75 | 100% | 75 | |||
| health_condition | 75 | 100% | 75 | |||
| subject_id | 35 | 47% | 35 | |||
| collection_date | 75 | 100% | 75 | |||
| health_condition_detail | 75 | 100% | 75 |
- Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics. 2024 PMID 39611142 PMC11602453 own_data
Archive description
Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality. In this study, mNGS was performed on peritoneal dialysis fluid and anal swabs of 41 PD patients to evaluate the detection performance of mNGS in PDRP patients and the intestinal microecological characteristics of PD patients.
How this project entered the registry
Classified as human gut / stool / other human site / blood / tissue / internal fluids shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “peritoneal dialysis fluid and anal swabs”
- body site sample.attr.isolation_source · “dialysis effluent (n=40/75)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40181175 | collection_date | 2015-08/2022-08 | R3 | 0.70 | paper.fulltext.methods | From 01/08/2015 to 31/08/2022 |
| SAMN40181175 | country | CN | R3 | 0.70 | paper.fulltext.methods | The First Hospital of Jilin University |
| SAMN40181175 | health_condition | kidney_disease | R4 | 0.50 | study.description | PD patients |
| SAMN40181175 | health_condition_detail | peritoneal dialysis patients (kidney disease requiring dialysis) | R4 | 0.50 | study.description | PD patients |
| SAMN40181175 | subject_id | SAMN40181175 | R4 | 0.60 | design.one_sample_per_subject:abstract | Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data. |
Sequencing
75 runs over 75 samples · mean 0.12 Gbp per run (median 31.5 Mbp, total 8.90 Gbp; 75 runs with a base count) · layout SINGLE 75 · platform ILLUMINA 75 · models NextSeq 550 (75) · 24% of runs with a Sandpiper profile · first public 2024-03-03
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1081608.csv.gz (2.7 KB) · parquet (72.9 KB) — all 75 samples, every field with route and confidence · PRJNA1081608_determinations.csv.gz (2.1 KB) — 335 evidence rows