FMT for recurrent C. difficile infection, Netherlands, long.
83 faecal metagenome samples from the Netherlands, from multiple recurrent C. difficile infection patients and their stool donors, collected before and after faecal microbiota transplantation (FMT) in a longitudinal design. machine-written summary
83 samples · 83 runs · NL · Age unknown · 2023 · 12.65 Gbp / sample · cohort Long-term beneficial effect of faecal microbiota t
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 729 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10902993 |
| ○ 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
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · FMT in recurrent C. difficile infection patients, before/after, with donor samples
“effect of FMT in patients with multiple recurrent” — abstract:38419010 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
28 of 29 people sampled more than once (82 samples; median 3, up to 4 per person) · follow-up median 2.2 y (max 2.2 y) · median interval between samples 13 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “stool pre-FMT, ~27 days post-FMT (short-term), and ~801 days post-FMT (long-term follow-up)”.
Each row is one person (21 shown of 28); dots are samples at days since that person's first sample.
NDFB donors (D01–D11) and rCDI recipients pre/post/long-term; donor-recipient links not published.
Genera, mean relative abundance over 73 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 | 83 | 100% | 83 | |||
| health_condition | 63 | 76% | 63 | |||
| subject_id | 83 | 100% | 83 | |||
| collection_date | 83 | 100% | 83 | |||
| detailed_location | 83 | 100% | ||||
| latitude | 83 | 100% | 83 | |||
| location_region | 83 | 100% | 83 | |||
| longitude | 83 | 100% | 83 | |||
| health_condition_detail | 63 | 76% | 63 | |||
| timepoint_label | 63 | 76% | 63 | |||
| intervention | 42 | 51% | 42 |
- Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. 2024 PMID 38419010 PMC10902993 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Archive description
A batch of faecal metagenomes of stool samples from multiple recurrent Clostridioides difficile infected patients collected before, shortly after and at a long-term after faecal microbiota transplantation, and stool samples of their respective donors. Note that for privacy reasons, human-derived reads have been removed from these files by mapping raw reads to the human reference genome (GRCh38.p7 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.33/)) using bowtie2 (version 2.4.2) with the '--very-sensitive-local' parameter. Non-mapping reads are selected with samtools (version 1.11) using the parameters ' -f 1 -f 4 -f 8'. The resulting paired-end raw read files are deposited here. The human read removal workflow is based on: https://git.lumc.nl/snooij/metagenomics-preprocessing
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host study.description · “multiple recurrent Clostridioides difficile infected patients”
- body site study.title · “Faecal shotgun metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114243814 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA114243814 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA114243834 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:description | Gut microbiota of recurrent Clostridioides difficile patient |
| SAMEA114243835 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample_attr | post-FMT |
| SAMEA114243834 | health_condition_detail | Gut microbiota of recurrent Clostridioides difficile patient | R1 | 0.85 | biosample.attribute:description | Gut microbiota of recurrent Clostridioides difficile patient |
| SAMEA114243834 | intervention | fmt | R1 | 0.85 | biosample.attribute:category | LTFU |
| SAMEA114243814 | latitude | 52.1520 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243814 | location_region | South Holland | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243814 | longitude | 4.4810 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243814 | subject_id | D01 | R1 | 0.70 | sample.name_rule:alias | D01-09 |
| SAMEA114243834 | timepoint_label | long-term follow-up | R1 | 0.70 | sample.name_rule:alias | P27-LTFUP |
Sequencing
83 runs over 83 samples · mean 16.85 Gbp per run (median 12.65 Gbp, total 1,398.67 Gbp; 83 runs with a base count) · layout PAIRED 83 · platform ILLUMINA 83 · models Illumina NovaSeq 6000 (83) · 88% of runs with a Sandpiper profile · first public 2023-09-08
Authors (15)
Nooij S first · Vendrik KEW · Zwittink RD · Ducarmon QR · Keller JJ · Kuijper EJ · Terveer EM · Netherlands Donor Feces Bank study group last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last
Downloads
PRJEB64621.csv.gz (3.3 KB) · parquet (74.2 KB) — all 83 samples, every field with route and confidence · PRJEB64621_determinations.csv.gz (7.0 KB) — 729 evidence rows