Gut microbiome and MPA metabolism in kidney transplant, Oslo
107 fecal metagenome samples from kidney transplant recipients (pre- and post-transplant time points) and healthy controls in Oslo, Norway, studying gut microbiome-mediated mycophenolate mofetil metabolism in a case-control design. machine-written summary
107 samples · 107 runs · NO · Adult · 2025 · 5.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,070 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12291295 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population transplant_or_immunocompromised · Kidney transplantation with post-transplant mycophenolate mofetil immunosuppression; samples pre/post-transplant
“Patient samples were collected prior to transplantation” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
34 of 36 people sampled more than once (105 samples; median 3, up to 5 per person) · follow-up median 28 d (max 56 d) · median interval between samples 14 d (time from timepoint labels). Schedule stated by the source: “patients: pre-transplant, 1 week, 3-6 weeks, 1 year post-transplant; controls: weeks 0,2,4(,8)” (time origin: transplant); stated follow-up 12 mo.
Each row is one person (15 shown of 34); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 100 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 | 107 | 100% | ||||
| country | 107 | 100% | 107 | |||
| health_condition | 107 | 100% | 107 | |||
| subject_id | 107 | 100% | 107 | |||
| collection_date | 107 | 100% | 107 | |||
| detailed_location | 107 | 100% | ||||
| health_condition_detail | 107 | 100% | 107 | |||
| latitude | 107 | 100% | 107 | |||
| location_locality | 107 | 100% | 107 | |||
| location_region | 107 | 100% | 107 | |||
| longitude | 107 | 100% | 107 | |||
| timepoint_label | 107 | 100% | 107 |
- Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients. 2025 PMID 40707990 PMC12291295 own_data
Archive description
Time series gut metagenome data from 21 kidney transplant recipients (indicated by P in sample name) and 15 healthy individuals (C in sample name), based on deep shotgun sequencing of fecal samples. Patient samples were collected prior to transplantation (indicated by Pre Feces in sample name), at one week (Week 1), between 3 and 6 weeks (PK1), and one year (PK2) after transplantation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “deep shotgun sequencing of fecal samples”
- life stage study.title · “kidney transplant patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46073655 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN46073655 | country | NO | R1 | 0.90 | sample.attr.geo_loc_name | Norway:Oslo |
| SAMN46073655 | health_condition | transplant_or_immunocompromised | R1 | 0.70 | sample.name_rule:library_names | P618_PK1 |
| SAMN46073655 | health_condition_detail | P | R1 | 0.70 | sample.name_rule:library_names | P618_PK1 |
| SAMN46073655 | latitude | 59.9100 | R1 | 0.90 | biosample.attribute:lat_lon | 59.91 N 10.75 E |
| SAMN46073655 | location_locality | Oslo | R1 | 0.85 | biosample.attribute:geo_loc_name | Norway:Oslo |
| SAMN46073655 | location_region | Oslo | R1 | 0.60 | biosample.attribute:lat_lon | 59.91 N 10.75 E |
| SAMN46073655 | longitude | 10.7500 | R1 | 0.90 | biosample.attribute:lat_lon | 59.91 N 10.75 E |
| SAMN46073655 | subject_id | P618 | R1 | 0.70 | sample.name_rule:library_names | P618_PK1 |
| SAMN46073655 | timepoint_label | PK1 | R1 | 0.70 | sample.name_rule:library_names | P618_PK1 |
Sequencing
107 runs over 107 samples · mean 6.56 Gbp per run (median 5.96 Gbp, total 701.58 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models Illumina NovaSeq 6000 (107) · 93% of runs with a Sandpiper profile · first public 2025-01-04
Authors (8)
Drevland OM first · de Muinck EJ · Trosvik P · Hammerstad M · Kvitne KE · Midtvedt K · Åsberg A · Robertsen I last
Downloads
PRJNA1206184.csv.gz (3.9 KB) · parquet (74.8 KB) — all 107 samples, every field with route and confidence · PRJNA1206184_determinations.csv.gz (8.4 KB) — 1,070 evidence rows