Gut microbial calprotectin metabolism in IBD patients
22 fecal samples from an academic IBD clinic cohort, studying gut microbial degradation of fecal calprotectin in ulcerative colitis versus Crohn's disease; case-control design. machine-written summary
22 samples · 22 runs · US · Age unknown · 2022 · 0.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| – Abstract / description | no abstract or project description |
| ✓ Full text | 22 sample values (subject id) · PMC9494624 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 66 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 22 | |||
| subject_id | 22 | 100% | 22 | |||
| health_condition_detail | 22 | 100% | 22 |
- Interpersonal Variability in Gut Microbial Calprotectin Metabolism. 2022 PMID 36160305 PMC9494624 own_data
Archive description
Background: The gold standard for staging (i.e. defining severity and distribution of inflammation) in patients with inflammatory bowel diseases (IBD) is endoscopy with biopsies. However, it is not feasible to obtain endoscopic and histologic data frequently. Therefore, there is a clinical need for reliable non-invasive testing to monitor IBD patients. Fecal calprotectin is a promising but imperfect biomarker for disease activity, as it can be deceptively low despite active inflammation. We hypothesized that the gut microbiome can metabolize calprotectin and thereby alter its fecal measurements. Methods: We recruited 22 individuals from an academic IBD clinic. We collected clinical data and fecal samples. Using ELISA, we quantified fecal calprotectin. Using a novel ex vivo functional assay, we characterized gut microbial calprotectin degradation in each patient microbiome. We performed this assay in two different bacterial growth media containing high or low levels of free amino acids. Results: We found that the gut microbiome can modulate calprotectin levels in a manner dependent upon free amino acid levels in growth media, typically reducing calprotectin to a significantly greater extent in the low amino acid environments. Microbiome-mediated calprotectin degradation varied between individuals and was significantly greater in ulcerative colitis than Crohn's disease. Subdoligranulum abundance was correlated with observed reduction in measured calprotectin. We demonstrate in vitro that Subdoligranulum variabile degrades calprotectin to a significantly greater degree than a control strain. Conclusions: The gut microbiome may alter measured fecal calprotectin levels in IBD patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “fecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA14410995 | country | US | R2 | 0.75 | external.gmrepo source | country: United States of America |
| SAMEA14410995 | health_condition | ibd_unspecified | R2 | 0.75 | external.gmrepo source | phenotype: Inflammatory Bowel Diseases |
| SAMEA14410995 | health_condition_detail | Inflammatory Bowel Diseases | R2 | 0.75 | external.gmrepo source | phenotype: Inflammatory Bowel Diseases |
| SAMEA14410995 | subject_id | SAMEA14410995 | R3 | 0.70 | design.one_sample_per_subject:fulltext | We recruited 22 individuals with IBD (64% female; 73% with colonic disease; Table ), who provided stool samples |
Sequencing
22 runs over 22 samples · mean 0.12 Gbp per run (median 0.13 Gbp, total 2.65 Gbp; 22 runs with a base count) · layout SINGLE 22 · platform ILLUMINA 22 · models Illumina MiniSeq (22) · 0% of runs with a Sandpiper profile · first public 2022-05-20
Authors (0)
No author record.
Downloads
PRJEB52930.csv.gz (1.4 KB) · parquet (69.8 KB) — all 22 samples, every field with route and confidence · PRJEB52930_determinations.csv.gz (1.3 KB) — 88 evidence rows