Gut bacteriophages in metabolic syndrome FMT, Netherlands
46 longitudinal stool samples from adults with metabolic syndrome and healthy donors in the Netherlands, studying gut bacteriophage community dynamics before and after fecal microbiota transplant. machine-written summary
46 samples · 46 runs · NL · Adult · 2019 · 1.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 363 sample values (country, health condition, intervention, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 46 sample values (sex) · PMC8023239 |
| ○ 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 resolved
Faecal microbiota transplantation design randomized_controlled_trial · population cardiometabolic_other · Healthy-donor stool FMT vs self-stool (autologous) control transplant
“control group (self-stool transplant, n = 3) or a treatment group” — abstract:33794724 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
9 of 14 people sampled more than once (41 samples; median 5, up to 5 per person) · follow-up median 4 mo (max 4 mo) · median interval between samples 42 d (time from timepoint labels). Schedule stated by the source: “stool at week 0 (pre-FMT) and weeks 3, 6, 12, 18 post-FMT” (time origin: intervention_start); stated follow-up 4 mo.
Each row is one person (9 shown); dots are samples at days since that person's first sample.
5 healthy FMT donors, 6 donor-FMT recipients and 3 autologous-FMT controls sequenced; donor–recipient pairing not stated in text/supplement.
Genera, mean relative abundance over 38 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 | 46 | 100% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 46 | 100% | 46 | |||
| subject_id | 46 | 100% | 46 | |||
| detailed_location | 46 | 100% | ||||
| latitude | 46 | 100% | 46 | |||
| location_region | 46 | 100% | 46 | |||
| longitude | 46 | 100% | 46 | |||
| sex | 46 | 100% | 46 | |||
| timepoint_label | 46 | 100% | 46 | |||
| intervention | 41 | 89% | 41 |
- Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome. 2021 PMID 33794724 PMC8023239 own_data
Archive description
Gut bacteriophage community dynamics of subjects with metabolic syndrome before and after fecal microbial transplant was investigated.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host run.host_tax_id · “9606”
- body site study.title · “Gut bacteriophage community”
- life stage study.title · “metabolic syndrome subjects”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10342680 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN10342680 | health_condition | cardiometabolic_other | R1 | 0.70 | sample.name_rule:title | R2_1 |
| SAMN10342680 | intervention | fmt | R1 | 0.70 | sample.name_rule:title | R2_1 |
| SAMN10342680 | latitude | 51.9692 | R1 | 0.90 | biosample.attribute:lat_lon | 51.9692 N 5.6654 E |
| SAMN10342680 | location_region | Gelderland | R1 | 0.60 | biosample.attribute:lat_lon | 51.9692 N 5.6654 E |
| SAMN10342680 | longitude | 5.6654 | R1 | 0.90 | biosample.attribute:lat_lon | 51.9692 N 5.6654 E |
| SAMN10342680 | sex | male | R3 | 0.60 | paper.fulltext.results | Male, Caucasian, obese subjects with MetS were randomly |
| SAMN10342680 | subject_id | R2 | R1 | 0.70 | sample.name_rule:title | R2_1 |
| SAMN10342680 | timepoint_label | week 0 | R1 | 0.70 | sample.name_rule:title | R2_1 |
Sequencing
46 runs over 46 samples · mean 1.34 Gbp per run (median 1.30 Gbp, total 61.76 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models Illumina HiSeq 2500 (46) · 83% of runs with a Sandpiper profile · first public 2019-11-06
Authors (24)
Manrique P first · Zhu Y · van der Oost J · Herrema H · Nieuwdorp M · de Vos WM · Young M last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA499081.csv.gz (2.1 KB) · parquet (71.6 KB) — all 46 samples, every field with route and confidence · PRJNA499081_determinations.csv.gz (3.3 KB) — 409 evidence rows