Gut metagenomics in slow transit constipation, China
Case-control study of 118 gut metagenome samples from adults in China comparing slow transit constipation patients and healthy individuals, examining microbiome differences at phylum, genus, and species level. machine-written summary
118 samples · 118 runs · CN · Adult · 2021 · 10.83 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 590 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 236 sample values (location site, subject id) · PMC8862142 |
| ✓ Supplementary tables | 236 sample values (health condition, health condition detail) |
| – 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 |
Genera, mean relative abundance over 108 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 | 118 | 100% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 118 | 100% | 118 | |||
| subject_id | 118 | 100% | 118 | |||
| collection_date | 118 | 100% | 118 | |||
| detailed_location | 118 | 100% | ||||
| health_condition_detail | 118 | 100% | 118 | |||
| latitude | 118 | 100% | 118 | |||
| location_region | 118 | 100% | 118 | |||
| location_site | 118 | 100% | 118 | |||
| longitude | 118 | 100% | 118 |
- Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation. 2021 PMID 35211481 PMC8862142 own_data
Archive description
Slow transit constipation (STC) is one of the most frequent gastrointestinal diagnoses. We found that the intestinal microbiome of STC patients was significantly different from that of healthy individuals at the phylum, genus, and species level. Our findings suggest that alteration of the microbiome may lead to constipation by changing the levels of microbial-derived metabolites in the gut.
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 metagenomics in slow”
- body site study.description · “the most frequent gastrointestinal diagnoses. We found”
- 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 |
|---|---|---|---|---|---|---|
| SAMN23227415 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN23227415 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN23227415 | health_condition | ibd_or_gi_disease | R2 | 0.85 | paper.supp.Data_Sheet_1.xlsx[Table S1!Group] | t_stc03: STC |
| SAMN23227415 | health_condition_detail | STC | R2 | 0.85 | paper.supp.Data_Sheet_1.xlsx[Table S1!Group] | t_stc03: STC |
| SAMN23227415 | latitude | 31.2700 | R1 | 0.90 | biosample.attribute:lat_lon | 31.27 N 121.45 E |
| SAMN23227415 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.27 N 121.45 E |
| SAMN23227415 | location_site | Shanghai Tenth People's Hospital | R3 | 0.70 | paper.fulltext.methods_results | were enrolled in this study from the Shanghai Tenth People's Hospital |
| SAMN23227415 | longitude | 121.4500 | R1 | 0.90 | biosample.attribute:lat_lon | 31.27 N 121.45 E |
| SAMN23227415 | subject_id | SAMN23227415 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal samples were collected from the recruited subjects from these 118 participants. |
Sequencing
118 runs over 118 samples · mean 11.18 Gbp per run (median 10.83 Gbp, total 1,319.07 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models Illumina HiSeq 2500 (118) · 92% of runs with a Sandpiper profile · first public 2021-11-18
Authors (0)
No author record.
Downloads
PRJNA781055.csv.gz (4.2 KB) · parquet (75.7 KB) — all 118 samples, every field with route and confidence · PRJNA781055_determinations.csv.gz (7.5 KB) — 1,062 evidence rows