Mucosal and faecal metagenomics in healthy adults, ileum/colon
20 samples (mucosal biopsies from terminal ileum, transverse colon, rectum, plus faeces) from 5 healthy adult subjects, cross-sectional shotgun metagenomics study of gut mucosa-associated microbiota. machine-written summary
20 samples · 89 runs · Adult · 2019 · 12.68 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 60 sample values (health condition, health condition detail, location locality) · PMC7486370 |
| ○ 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 |
longitudinal — not resolved
5 of 5 people sampled more than once (20 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 19 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 | 20 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 20 | 100% | 20 | |||
| subject_id | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| health_condition_detail | 20 | 100% | 20 | |||
| location_locality | 20 | 100% | 20 |
- Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals. 2020 PMID 32917913 PMC7486370 own_data
Archive description
Gut mucosa microbes evolved in closest proximity with the host, developing unique phenotypes and specialized local communities. The main technology for studying the gut microbiota is currently 16S rRNA sequencing, which provides moderate-throughput data that cannot reliably resolve taxonomy beyond genus level. This study aimed at employing shotgun metagenomics to investigate biopsy-derived microbial species in healthy individuals, to explore the composition of the local microbial communities of terminal ileum and large intestine. Therefore, mucosal biopsies were collected from terminal ileum, transverse colon and rectum of 5 healthy subjects, as well as faeces samples, and shotgun metagenomics sequencing were applied for each sample.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.title · “healthy individuals from a population-based study”
- body site study.description · “biopsies were collected from terminal ileum”
- body site study.description · “as well as faeces samples”
- life stage study.title · “healthy individuals from a population-based study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5740753 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | All subjects were free from any objective finding |
| SAMEA5740753 | health_condition_detail | healthy individuals, free from any objective finding at colonoscopy | R3 | 0.70 | paper.fulltext.methods | All subjects were free from any objective finding |
| SAMEA5740753 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | Five healthy adult volunteers from Stockholm |
| SAMEA5740753 | subject_id | 1 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: Fecal sample from P1 |
Sequencing
89 runs over 20 samples · mean 3.20 Gbp per run (median 3.19 Gbp, total 284.41 Gbp; 89 runs with a base count) · layout PAIRED 89 · platform ILLUMINA 89 · models Illumina HiSeq 2000 (89) · 90% of runs with a Sandpiper profile · first public 2019-09-30
Authors (15)
Vaga S first · Lee S · Ji B · Andreasson A · Talley NJ · Agréus L · Bidkhori G · Kovatcheva-Datchary P · Park J · Lee D · Proctor G · Ehrlich SD · Nielsen J · Engstrand L · Shoaie S last
Downloads
PRJEB33194.csv.gz (1.4 KB) · parquet (69.7 KB) — all 20 samples, every field with route and confidence · PRJEB33194_determinations.csv.gz (1.1 KB) — 80 evidence rows