Gut Microbiome in Microscopic Colitis, Boston, Case-Control
903 stool samples from patients with microscopic colitis, patients with chronic diarrhea, and matched non-diarrhea controls in Boston, Massachusetts, profiled by shotgun metagenomics in a case-control design. machine-written summary
903 samples · 903 runs · US · Age unknown · 2025 · 3.62 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,846 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 903 sample values (location site) · PMC12102337 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
96 of 332 people sampled more than once (192 samples; median 2, up to 2 per person). Schedule stated by the source: “Second stool sample collected during remission, at least 8 weeks after initial active-phase sample”.
Genera, mean relative abundance over 890 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 | 903 | 100% | ||||
| country | 903 | 100% | 903 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 428 | 47% | 428 | |||
| collection_date | 903 | 100% | 903 | |||
| detailed_location | 903 | 100% | ||||
| latitude | 903 | 100% | 903 | |||
| location_locality | 903 | 100% | 903 | |||
| location_region | 903 | 100% | 903 | |||
| location_site | 903 | 100% | 903 | |||
| longitude | 903 | 100% | 903 |
- Association of distinct microbial and metabolic signatures with microscopic colitis. 2025 PMID 40410138 PMC12102337 own_data
Archive description
Gut microbiome may be implicated with the pathogenesis of microscopic colitis (MC). To study the alterations of get microbiome in MC, we profiled stool samples from 131 patients with MC, 159 patients with chronic diarrhea, and 393 age- and sex-match controls without diarrhea with whole-genome shotgun seuqencing. Additionally, we collected one more stool sample from 66 patients with MC that experienced disease remission to compare the longitudinal change in gut microbiome related to disease activity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “profiled stool samples from 131 patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN45825032 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN45825032 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston, Massachusetts |
| SAMN45825032 | latitude | 42.3626 | R1 | 0.90 | biosample.attribute:lat_lon | 42.362567 N 71.068704 W |
| SAMN45825032 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston, Massachusetts |
| SAMN45825032 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston, Massachusetts |
| SAMN45825032 | location_site | Massachusetts General Hospital | R3 | 0.70 | paper.fulltext.methods | seen for consultation or were scheduled for a diagnostic colonoscopy at the |
| SAMN45825032 | longitude | -71.0687 | R1 | 0.90 | biosample.attribute:lat_lon | 42.362567 N 71.068704 W |
| SAMN45825032 | subject_id | MC001 | R1 | 0.70 | sample.name_rule:source_material_id | MC001A |
Sequencing
903 runs over 903 samples · mean 3.57 Gbp per run (median 3.62 Gbp, total 3,221.12 Gbp; 903 runs with a base count) · layout PAIRED 897, SINGLE 6 · platform ILLUMINA 903 · models Illumina NovaSeq 6000 (903) · 99% of runs with a Sandpiper profile · first public 2025-04-10 – 2025-04-27
Authors (14)
Chen AS first · Kim H · Nzabarushimana E · Shen J · Williams K · Gurung J · McGoldrick J · Burke KE · Yarze JC · Nguyen LH · Staller K · Chung DC · Xavier RJ · Khalili H last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1197998.csv.gz (22.2 KB) · parquet (102.4 KB) — all 903 samples, every field with route and confidence · PRJNA1197998_determinations.csv.gz (40.2 KB) — 6,749 evidence rows