Ileostomy metagenome from a Swedish adult with ulcerative colitis
Cross-sectional study of 5 ileostomy content samples from one adult in Sweden with ulcerative colitis, collected on different occasions and processed with different DNA extraction methods, characterised by 16S and metagenomic sequencing. machine-written summary
5 samples · 5 runs · SE · Adult · 2019 · 0.91 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 23 sample values (collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7474095 |
| ○ 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 |
country: sequence archive and microbeatlas disagree for 2 samples (e.g. SE vs NO) — withheld.
The sources disagree on 2 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 (2)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA6265412 | country | SE (sequence archive) | NO (microbeatlas) | withheld: neither value published |
| SAMEA6265413 | country | SE (sequence archive) | NO (microbeatlas) | withheld: neither value published |
Genera, mean relative abundance over 5 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 | 5 | 100% | ||||
| country | 3 | 60% | 3 | |||
| health_condition | 5 | 100% | 5 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 5 | 100% | 5 | |||
| health_condition_detail | 5 | 100% | 5 | |||
| sex | 5 | 100% | 5 |
- Genome sequence of segmented filamentous bacteria present in the human intestine. 2020 PMID 32887924 PMC7474095 unsure
Archive description
Ileostomy bag content was collected on different occasions and submitted to different DNA extraction methods, before being characterised by both 16S and metagenomic sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Ileostomy content from a colectomised”
- life stage study.title · “Swedish adult individual”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6265410 | collection_date | 2002 | R1 | 0.90 | biosample.attribute:collection_date | 2002 |
| SAMEA6265410 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA6265410 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | Ulcerative colitis leading to proctocolectomy |
| SAMEA6265410 | health_condition_detail | Ulcerative colitis leading to proctocolectomy | R1 | 0.90 | sample.attr.gastrointestinal_tract_disorder | Ulcerative colitis leading to proctocolectomy |
| SAMEA6265410 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
Sequencing
5 runs over 5 samples · mean 0.92 Gbp per run (median 0.91 Gbp, total 4.61 Gbp; 5 runs with a base count) · layout PAIRED 5 · platform ILLUMINA 5 · models Illumina NovaSeq 6000 (5) · 100% of runs with a Sandpiper profile · first public 2019-12-03
Authors (5)
Jonsson H first · Hugerth LW · Sundh J · Lundin E · Andersson AF last
Downloads
PRJEB34939.csv.gz (1.0 KB) · parquet (69.4 KB) — all 5 samples, every field with route and confidence · PRJEB34939_determinations.csv.gz (635 B) — 23 evidence rows