Gut metagenomes in quiescent Crohn's Disease flare prediction
138 longitudinal gut metagenome samples from adults, part of a prospective study of quiescent Crohn's Disease patients tracked over time to identify fecal/serum metabolome and microbiome signals preceding clinical flares. machine-written summary
138 samples · 138 runs · IL · Adult · 2026 · 6.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,242 sample values (age, country, health condition, health condition detail, latitude, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 138 sample values (collection date) · PMC12920629 |
| ✓ Supplementary tables | 136 sample values (timepoint) |
| – 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
34 of 55 people sampled more than once (117 samples; median 3, up to 7 per person). Schedule stated by the source: “serial stool/serum samples per subject over up to 2 years or until clinical flare, no fixed visit schedule stated” (time origin: enrolment); stated follow-up 2.0 y.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 138 | 100% | ||||
| country | 138 | 100% | 138 | |||
| health_condition | 138 | 100% | 138 | |||
| subject_id | 138 | 100% | 138 | |||
| age_at_collection_days | 138 | 100% | 138 | |||
| collection_date | 138 | 100% | 138 | |||
| detailed_location | 138 | 100% | ||||
| health_condition_detail | 138 | 100% | 138 | |||
| latitude | 138 | 100% | 138 | |||
| location_region | 138 | 100% | 138 | |||
| longitude | 138 | 100% | 138 | |||
| sex | 138 | 100% | 138 | |||
| timepoint_label | 136 | 99% | 136 |
- Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease. 2026 PMID 41629500 PMC12920629 own_data
Archive description
We analyzed the dynamics of serum and fecal metabolites in a prospective cohort of quiescent CD patients over 2 years or until the occurrence of a clinical flare, aiming to identify whether changes precede and predict relapse. We further defined complex interactions between serum and fecal metabolites and the gut microbiome, and signals linked with CD. Here are 138 metagenome gut microbiome samples from this study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.description · “quiescent CD patients over 2 years”
- body site study.description · “fecal metabolites”
- body site study.description · “metagenome gut microbiome samples”
- life stage study.description · “quiescent CD patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39139535 | age_at_collection_days | 13879.5 | R1 | 0.70 | sample.attr.age | 38 |
| SAMN39139535 | collection_date | 2014/2019 | R3 | 0.70 | paper.fulltext.methods | Samples were collected during the years 2014 and 2019 |
| SAMN39139535 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel |
| SAMN39139535 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:dx | dx: CD |
| SAMN39139535 | health_condition_detail | CD | R1 | 0.85 | biosample.attribute:dx | dx: CD |
| SAMN39139535 | latitude | 31.0460 | R1 | 0.90 | biosample.attribute:lat_lon | 31.046 N 34.8516 E |
| SAMN39139535 | location_region | Southern District | R1 | 0.60 | biosample.attribute:lat_lon | 31.046 N 34.8516 E |
| SAMN39139535 | longitude | 34.8516 | R1 | 0.90 | biosample.attribute:lat_lon | 31.046 N 34.8516 E |
| SAMN39139535 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN39139535 | subject_id | p26 | R1 | 0.85 | biosample.attribute:pn_id | pn_id: p26 |
| SAMN39139535 | timepoint_label | 1 | R2 | 0.85 | paper.supp.41598_2026_38558_MOESM1_ESM.zip/Metabolomics_supp_materials_R3/R3_Supp_Dataset_1.xlsx[Fecal_metabolomics_metadata!Visit] | SampleID_298: Visit=1 |
Sequencing
138 runs over 138 samples · mean 7.04 Gbp per run (median 6.33 Gbp, total 971.38 Gbp; 138 runs with a base count) · layout SINGLE 138 · platform ILLUMINA 138 · models Illumina NovaSeq 6000 (138) · 0% of runs with a Sandpiper profile · first public 2026-05-20
Authors (21)
Levhar N first · Hadar R · Braun T · Shacham H · Algavi Y · Naamneh R · Efroni G · Agranovich B · Abramovich I · Talan Asher A · Picard O · Yavzori M · Lahat A · Yablecovitch D · Kopylov U · Denson L · Borenstein E · Eliakim R · Ben-Horin S · Amir A · Haberman Y last
Downloads
PRJNA1057679.csv.gz (4.7 KB) · parquet (76.3 KB) — all 138 samples, every field with route and confidence · PRJNA1057679_determinations.csv.gz (11.2 KB) — 1,516 evidence rows