Gut microbiome in African migrants' colonic biopsies
Cross-sectional study of 40 colonic biopsy samples from recent and long-term African migrants, comparing gut microbiota in healthy controls, colorectal adenoma, and other cancer samples (20, 10, and 10 samples respectively; 31 adult, 9 elderly). machine-written summary
40 samples · 40 runs · Adult · 2016 · 0.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 200 sample values (age, health condition, health condition detail, sex, subject id) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
10 of 30 people sampled more than once (20 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 17 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 | 40 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 40 | 100% | 40 | |||
| subject_id | 40 | 100% | 40 | |||
| age_at_collection_days | 40 | 100% | 40 | |||
| health_condition_detail | 40 | 100% | 40 | |||
| sex | 40 | 100% | 40 |
Archive description
A metagenomic analysis of the gut flora in recent (<1 year) and old African migrants’ (>5 years) colonic biopsies’ microenvironment.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host study.title · “Bacteria and human colon samples”
- host run.scientific_name · “Homo sapiens”
- body site study.description · “African migrants’ (>5 years) colonic biopsies’ microenvironment”
- life stage sample.attr.age · “53 (n=29/40)”
- life stage sample.attr.age · “73 (n=11/40)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04535553 | age_at_collection_days | 23376.0 | R1 | 0.70 | sample.attr.age | 64 |
| SAMN04535553 | health_condition | colorectal_adenoma | R1 | 0.90 | biosample_attr | Adenoma |
| SAMN04535553 | health_condition_detail | Adenoma | R1 | 0.90 | sample.attr.disease | Adenoma |
| SAMN04535553 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN04535553 | subject_id | 839 | R1 | 0.85 | biosample.attribute:isolate | isolate: 839 |
| SAMN04535573 | subject_id | 1024 | R1 | 0.70 | sample.name_rule:alias | 1024N |
Sequencing
40 runs over 40 samples · mean 1.19 Gbp per run (median 0.71 Gbp, total 47.45 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina MiSeq (40) · 45% of runs with a Sandpiper profile · first public 2016-03-15
Authors (0)
No author record.
Downloads
PRJNA314481.csv.gz (2.1 KB) · parquet (70.8 KB) — all 40 samples, every field with route and confidence · PRJNA314481_determinations.csv.gz (2.2 KB) — 200 evidence rows