Fecal microbiome in long COVID patients, Netherlands
Cross-sectional study of 115 fecal samples from adult and elderly long COVID patients in the Netherlands, sampled 3-6 months post-infection to relate gut microbiome composition to clinical characteristics. machine-written summary
115 samples · 115 runs · NL · Adult · 2026 · 7.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,025 sample values (age, country, health condition detail, latitude, location region, longitude, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 115 sample values (health condition) · PMC11855614 |
| ○ 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 |
longitudinal — not resolved
28 of 87 people sampled more than once (56 samples; median 2, up to 2 per person).
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 | 115 | 100% | ||||
| country | 115 | 100% | 115 | |||
| health_condition | 115 | 100% | 115 | |||
| subject_id | 115 | 100% | 115 | |||
| detailed_location | 115 | 100% | ||||
| health_condition_detail | 115 | 100% | 115 | |||
| latitude | 115 | 100% | 115 | |||
| location_region | 115 | 100% | 115 | |||
| longitude | 115 | 100% | 115 | |||
| timepoint_label | 115 | 100% | 115 | |||
| age_at_collection_days | 110 | 96% | 110 | |||
| sex | 110 | 96% | 110 |
- Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection. 2025 PMID 40004244 PMC11855614 own_data
Archive description
This data describes the fecal microbiome of long COVID-19 patients 3-6 months after infection with the SARS-CoV-2 virus. There is no treatment group, and microbial characteristics were related to clinical variables obtained in other parts of the P4O2 COVID-19 study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
- life stage sample.attr.host_age · “51 (n=94/115)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44567586 | age_at_collection_days | 18262.5 | R1 | 0.70 | sample.attr.host_age | 50 |
| SAMN44567581 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN44567581 | health_condition | other_infection | R3 | 0.70 | paper.fulltext.abstract | patients with long COVID evaluated at 3 to 6 months |
| SAMN44567581 | health_condition_detail | Timepoint: N/A | R1 | 0.90 | sample.attr.host_phenotype | Timepoint: N/A |
| SAMN44567581 | latitude | 52.3462 | R1 | 0.90 | biosample.attribute:lat_lon | 52.34616254 N 4.92180056 E |
| SAMN44567581 | location_region | North Holland | R1 | 0.60 | biosample.attribute:lat_lon | 52.34616254 N 4.92180056 E |
| SAMN44567581 | longitude | 4.9218 | R1 | 0.90 | biosample.attribute:lat_lon | 52.34616254 N 4.92180056 E |
| SAMN44567586 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN44567581 | subject_id | NEG_CON_1 | R1 | 0.85 | sample.attr.host_subject_id | NEG_CON_1 |
| SAMN44567581 | timepoint_label | Timepoint: N/A | R1 | 0.85 | biosample.attribute:host_phenotype | Timepoint: N/A |
Sequencing
115 runs over 115 samples · mean 7.56 Gbp per run (median 7.47 Gbp, total 869.52 Gbp; 115 runs with a base count) · layout PAIRED 115 · platform ILLUMINA 115 · models Illumina NovaSeq 6000 (115) · 88% of runs with a Sandpiper profile · first public 2026-01-01
Authors (8)
Blankestijn JM first · Baalbaki N · Beijers RJHCG · Cornelissen MEB · Wiersinga WJ · Abdel-Aziz MI · Maitland-van der Zee AH · P4O2 Consortium last
Downloads
PRJNA1181655.csv.gz (6.3 KB) · parquet (81.3 KB) — all 115 samples, every field with route and confidence · PRJNA1181655_determinations.csv.gz (10.1 KB) — 1,140 evidence rows