Metaproteomics of gut microbiome in IBD, Israel & Germany
794 samples from Israel (696) and Germany (99), using metagenome-informed metaproteomics to study host-microbiome-dietary interactions in health and IBD; design otherwise unspecified. machine-written summary
450 samples · 795 runs · IL, DE · Age unknown · 2024 · 0.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,607 sample values (collection date, country, health condition, health condition detail, intervention, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
27 of 28 people sampled more than once (180 samples; median 7, up to 9 per person). Schedule stated by the source: “Sample names (e.g. Human_GIsamples_706.1.2/706.1.6, Human_DietaryTrial_D02_6/8/10) suggest repeated sampling per subject across timepoints, but no explicit day/week schedule or token definition is giv”.
Genera, mean relative abundance over 516 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 | 450 | 100% | 450 | |||
| health_condition | 194 | 43% | 194 | |||
| subject_id | 181 | 40% | 181 | |||
| collection_date | 450 | 100% | 450 | |||
| health_condition_detail | 194 | 43% | 194 | |||
| intervention | 138 | 31% | 138 |
- Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease. 2025 PMID 39837331 own_data
Archive description
Host-microbiome-dietary interactions play crucial roles in regulating human health, yet direct functional assessment of their interplays, cross-regulations and downstream disease impacts remains challenging. We adopted metagenome-informed metaproteomics (MIM), in both mice and humans, to simultaneously explore host, dietary, and species-level microbiome interactions across diverse scenarios, including commensal and pathogen colonization, nutritional modifications, and antibiotic-induced perturbations. Implementation of MIM in murine auto-inflammation and in human IBD characterized a ‘compositional dysbiosis’ and a concomitant, species-specific ‘functional dysbiosis’ driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutrient assessment enabled determination of IBD-related consumption patterns, dietary treatment compliance and small-intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology, while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host run.scientific_name · “mouse gut metagenome”
- body site study.title · “human gut microbiome, host and dietary exposome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117479755 | collection_date | 2024 | R1 | 0.90 | biosample.attribute:collection_date | 2024 |
| SAMEA117479755 | country | IL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Israel |
| SAMEA117480004 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:description | Human_GermanUC |
| SAMEA117480103 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | Human_ISRpCD_500_Control |
| SAMEA117480004 | health_condition_detail | Human_GermanUC | R1 | 0.85 | biosample.attribute:description | Human_GermanUC |
| SAMEA117480103 | health_condition_detail | Control | R1 | 0.70 | sample.name_rule:alias | Human_ISRpCD_500_Control |
| SAMEA117479773 | intervention | diet_intervention | R1 | 0.85 | biosample.attribute:description | Human_DietaryTrial |
| SAMEA117479864 | subject_id | GIsamples_104 | R1 | 0.70 | sample.name_rule:alias | Human_GIsamples_104.1.1 |
Sequencing
795 runs over 450 samples · mean 0.65 Gbp per run (median 0.58 Gbp, total 514.17 Gbp; 795 runs with a base count) · layout SINGLE 655, PAIRED 140 · platform ILLUMINA 795 · models Illumina NovaSeq 6000 (795) · 68% of runs with a Sandpiper profile · first public 2024-12-05
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB81106.csv.gz (10.3 KB) · parquet (85.2 KB) — all 450 samples, every field with route and confidence · PRJEB81106_determinations.csv.gz (10.7 KB) — 1,607 evidence rows