Gut metagenomes, post-infection IBS, Minnesota
27 adult gut metagenome samples from Minnesota, USA, studying post-infection irritable bowel syndrome and fecal proteolytic activity, using a case-control design. machine-written summary
27 samples · 207 runs · US · Adult · 2022 · 1.63 Gbp / sample
One study deposited as 2 BioProjects (77 catalog samples together): PRJNA705217 · PRJNA705695 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 87 sample values (country, location region, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9081267 |
| ✓ Supplementary tables | 42 sample values (health condition, health condition detail, sex) |
| – 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
2 of 19 people sampled more than once (9 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 177 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 | 27 | 100% | ||||
| country | 27 | 100% | 27 | |||
| health_condition | 16 | 59% | 16 | |||
| subject_id | 26 | 96% | 26 | |||
| detailed_location | 27 | 100% | ||||
| location_region | 27 | 100% | 27 | |||
| health_condition_detail | 16 | 59% | 16 | |||
| sex | 10 | 37% | 10 | |||
| timepoint_label | 7 | 26% | 7 |
- Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome. 2022 PMID 35484230 PMC9081267 unsure
Archive description
The objective of this study was to determine microbial regulation of proteolytic activity in intestinal tract using phenotype of post-infection irritable bowel syndrome, a condition characterized by high fecal proteolytic activity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut metagenomes of patients”
- body site study.description · “proteolytic activity in intestinal tract using phenotype”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18096303 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Minnesota |
| SAMN18096303 | health_condition | ibs | R2 | 0.80 | paper.supp.NIHMS1787854-supplement-Source_Data_Fig_4.xlsx[Fig4c!PAStatus_] | 1 | PAStatus_: PI-IBS (High PA) |
| SAMN18096303 | health_condition_detail | PI-IBS (High PA) | R2 | 0.80 | paper.supp.NIHMS1787854-supplement-Source_Data_Fig_4.xlsx[Fig4c!PAStatus_] | 1 | PAStatus_: PI-IBS (High PA) |
| SAMN18096303 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota |
| SAMN18096303 | sex | female | R2 | 0.80 | paper.supp.NIHMS1787854-supplement-Source_Data_Extended_Data_Fig_1.xlsx[Extended Data 1a!Gender] | 1 | Gender: F |
| SAMN18096303 | subject_id | 001 | R1 | 0.70 | sample.name_rule:alias | Patient_Stool_001 |
| SAMN18096306 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | Patient_Stool_011_FMT_Rd_1 |
Sequencing
207 runs over 27 samples · mean 1.62 Gbp per run (median 1.63 Gbp, total 335.20 Gbp; 207 runs with a base count) · layout PAIRED 207 · platform ILLUMINA 207 · models Illumina HiSeq 4000 (207) · 86% of runs with a Sandpiper profile · first public 2022-02-24 – 2022-02-25
Authors (23)
Edwinson AL first · Yang L · Peters S · Hanning N · Jeraldo P · Jagtap P · Simpson JB · Yang TY · Kumar P · Mehta S · Nair A · Breen-Lyles M · Chikkamenahalli L · Graham RP · De Winter B · Patel R · Dasari S · Kashyap P · Griffin T · Chen J · Farrugia G · Redinbo MR · Grover M last
Downloads
PRJNA705695.csv.gz (1.6 KB) · parquet (70.5 KB) — all 27 samples, every field with route and confidence · PRJNA705695_determinations.csv.gz (1.9 KB) — 129 evidence rows