rCDI patients and FMT donors, Netherlands, case-control
156 fecal metagenome samples from rCDI patients and their fecal microbiota transplantation donors in the Netherlands, studied in a case-control design to assess pks+ E coli presence and transmission via FMT. machine-written summary
156 samples · 156 runs · NL · Age unknown · 2022 · 5.50 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 | 1,224 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 156 sample values (location site) |
| ○ Full text | read; no usable statement or table · PMC10902993, PMC11782615, PMC12180181, PMC12547691 |
| ✓ Supplementary tables | 76 sample values (subject id) |
| – 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 observational_with_procedure · population gi_infection_or_diarrhoea · FMT for recurrent C. difficile infection, donor vs recipient samples
“treated by fecal microbiota transplantation” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient — not resolved
49 of 49 people sampled more than once (154 samples; median 2, up to 17 per person). Schedule stated by the source: “Patients sampled pre-FMT and post-FMT at multiple timepoints (15 distinct timepoint labels); donors sampled once or more as donor samples.”.
49 rCDI patients each paired with an FMT donor from NDFB; 56 donor samples, 50 pre-FMT and 50 post-FMT patient samples..
Genera, mean relative abundance over 138 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 | 156 | 100% | 156 | |||
| health_condition | 156 | 100% | 156 | |||
| subject_id | 154 | 99% | 78 | 76 | ||
| collection_date | 156 | 100% | 156 | |||
| detailed_location | 156 | 100% | ||||
| health_condition_detail | 156 | 100% | 156 | |||
| latitude | 156 | 100% | 156 | |||
| location_region | 156 | 100% | 156 | |||
| location_site | 156 | 100% | 156 | |||
| longitude | 156 | 100% | 156 | |||
| timepoint_label | 54 | 35% | 54 |
- Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients. 2021 PMID 34126062 own_data
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status. 2025 PMID 39885121 PMC11782615 own_data
- 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
- Gut microbiota strain richness is species specific and affects engraftment. 2025 PMID 39604726 PMC12547691 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Archive description
Fecal shotgun metagenomes of healthy donors from the Netherlands Donor Feces bank and of multiple recurrent Clostridioides infected patients treated by fecal microbiota transplantation. 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. This publication first described the dataset: https://doi.org/10.1053/j.gastro.2021.06.009 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 0.75. Assay shotgun_dna.
- host study.description · “human-derived reads have been removed”
- host run.scientific_name · “human gut metagenome”
- body site study.description · “Fecal shotgun metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114243028 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA114243028 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA114243028 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | description: Gut microbiota of healthy NDFB donor |
| SAMEA8683853 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample_attr | pre-FMT |
| SAMEA114243028 | health_condition_detail | Gut microbiota of healthy NDFB donor | R1 | 0.85 | biosample.attribute:description | description: Gut microbiota of healthy NDFB donor |
| SAMEA114243028 | latitude | 52.1520 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243028 | location_region | South Holland | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243028 | location_site | Netherlands Donor Feces Bank | R4 | 0.40 | ena.study_title | Netherlands Donor Feces Bank |
| SAMEA114243028 | longitude | 4.4810 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.152 4.481 |
| SAMEA114243028 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | alias: D1-8 |
| SAMEA8683862 | subject_id | LUMC_Rgna_QRD010 | R2 | 0.75 | paper.supp.figure2b.tsv[full_new_ID] | full_new_ID: LUMC_Rgna_QRD010 |
| SAMEA114243028 | timepoint_label | 8 | R1 | 0.70 | sample.name_rule:alias | alias: D1-8 |
Sequencing
156 runs over 156 samples · mean 6.21 Gbp per run (median 5.50 Gbp, total 969.39 Gbp; 156 runs with a base count) · layout PAIRED 156 · platform ILLUMINA 156 · models NextSeq 550 (156) · 88% of runs with a Sandpiper profile · first public 2022-01-05 – 2023-08-10
Authors (72)
Nooij S first · Ducarmon QR · Laros JFJ · Zwittink RD · Norman JM · Smits WK · Verspaget HW · Keller JJ · Terveer EM · Kuijper EJ · Working Group of the Netherlands Donor Feces Bank last · Vendrik KEW · Netherlands Donor Feces Bank study group 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 · Chen-Liaw A first · Aggarwala V · Mogno I · Haifer C · Li Z · Eggers J · Helmus D · Hart A · Wehkamp J · Lamousé-Smith ESN · Kerby RL · Rey FE · Colombel JF · Kamm MA · Olle B · Menon R · Watson AR · Crossette E · Borody TJ · Grinspan A · Paramsothy S · Kaakoush NO · Dubinsky MC · Faith JJ last · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Karcher N · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last
Downloads
PRJEB44737.csv.gz (5.1 KB) · parquet (76.8 KB) — all 156 samples, every field with route and confidence · PRJEB44737_determinations.csv.gz (11.2 KB) — 1,456 evidence rows