Gut and oral microbiome in Crohn's disease, Singapore
134 gut and oral (stool and saliva) samples from adults in Singapore, comparing Crohn's disease subjects to matched healthy controls in a case-control study using whole genome shotgun sequencing. machine-written summary
134 samples · 134 runs · SG · Adult · 2021 · 27.9 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,198 sample values (age, collection date, country, health condition, health condition detail, latitude, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 134 sample values (antibiotic exposure) · PMC7905567, PMC9624293 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
sex differs between samples of the same subject id (2 subjects, 4 samples) — sex withheld; subject ids shared by samples of both sexes (2 ids, 4 samples) — ids withheld.
The sources disagree on 4 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (8)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA7232973 | sex | male (sequence archive) | subject C0020: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA7232976 | sex | female (sequence archive) | subject C0023: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA7232997 | sex | female (sequence archive) | subject C0020: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA7233000 | sex | male (sequence archive) | subject C0023: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA7232973 | subject id | C0020 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMEA7232976 | subject id | C0023 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMEA7232997 | subject id | C0020 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMEA7233000 | subject id | C0023 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
longitudinal
65 of 65 people sampled more than once (130 samples; median 2, up to 2 per person) · follow-up median 20.0 y (max 20.0 y) · median interval between samples 20.0 y (time from age at collection).
Each row is one person (1 shown of 65); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 134 | 100% | ||||
| country | 134 | 100% | 134 | |||
| health_condition | 134 | 100% | 134 | |||
| subject_id | 130 | 97% | 130 | |||
| age_at_collection_days | 134 | 100% | 134 | |||
| antibiotic_exposure | 134 | 100% | 134 | |||
| collection_date | 134 | 100% | 134 | |||
| health_condition_detail | 134 | 100% | 134 | |||
| latitude | 134 | 100% | 134 | |||
| longitude | 134 | 100% | 134 | |||
| sex | 130 | 97% | 130 |
- Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease. 2021 PMID 33632307 PMC7905567 own_data
- Oral Microbiome of Crohn's Disease Patients With and Without Oral Manifestations. 2022 PMID 35511486 PMC9624293 own_data
Archive description
This study examined using whole genome shotgun sequencing, the oral microbiome collected from saliva as well as the gut microbiome collected from stool of subjects with well-controlled Crohn's disease (CD). The CD subjects were recruited from a mixed Asian population consisting of Han Chinese, Malay and Indian descent. Healthy controls who were age, race and gender matched were compared to the CD subjects.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “subjects with well-controlled Crohn's disease”
- body site study.title · “oral (saliva) and Gut (stool) microbiome”
- life stage sample.attr.host_age · “32 (n=122/134)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7232954 | age_at_collection_days | 20088.8 | R1 | 0.70 | sample.attr.host_age | 55 |
| SAMEA7232954 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic/probiotic/prebiotic use within a month |
| SAMEA7232954 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA7232954 | country | SG | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Singapore |
| SAMEA7232954 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Health controls |
| SAMEA7232954 | health_condition_detail | Health controls | R1 | 0.90 | sample.attr.gastrointestinal_tract_disorder | Health controls |
| SAMEA7232954 | latitude | 1.1300 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 1.13 103.59 |
| SAMEA7232954 | longitude | 103.5900 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 1.13 103.59 |
| SAMEA7232954 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA7232954 | subject_id | C0001 | R1 | 0.85 | sample.attr.host_subject_id | C0001 |
Sequencing
134 runs over 134 samples · mean 57.1 Mbp per run (median 27.9 Mbp, total 7.65 Gbp; 134 runs with a base count) · layout SINGLE 134 · platform ILLUMINA 134 · models Illumina HiSeq 4000 (134) · 0% of runs with a Sandpiper profile · first public 2021-03-03
Authors (27)
Hu S first · Png E · Gowans M · Ong DEH · de Sessions PF · Song J · Nagarajan N last · Mok J · Hartono JL · Lee JWJ last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJEB39813.csv.gz (4.4 KB) · parquet (76.2 KB) — all 134 samples, every field with route and confidence · PRJEB39813_determinations.csv.gz (8.9 KB) — 1,332 evidence rows