Healthy adult colon microbiome, 16S rRNA, cross-sectional
5249 samples from the mucosa and lumen of healthy adult human colon (caecum, transverse colon, sigmoid colon) and oesophagus from cadaveric donors, profiled by 16S rRNA sequencing in a cross-sectional design. machine-written summary
5,249 samples · 5,969 runs · Adult · 2018 · 45.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,750 sample values (health condition, health condition detail, sex, subject id) |
| ✓ Abstract / description | 14,731 sample values (health condition, health condition detail, location site) |
| – 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 |
Genera, mean relative abundance over 136 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 | 5,249 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 5,249 | 100% | 508 | 4,741 | ||
| subject_id | 5,207 | 99% | 5,207 | |||
| detailed_location | 5,249 | 100% | ||||
| health_condition_detail | 5,249 | 100% | 508 | 4,741 | ||
| location_site | 5,249 | 100% | 5,249 | |||
| sex | 527 | 10% | 527 |
Archive description
Cutting-edge transcriptional and bioinformatics approaches will be implemented to assess immune cells at three sites along the healthy adult human colon. Sections will be taken from four sites of the GI tract- caecum, transverse colon, sigmoid colon and oesophagus. These samples will be collected from cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM) that are representative of healthy tissues since the donors are screened for infections and disease prior to their consideration for donation. Furthermore, medical history of these donors will be available, providing unique accessory information. The sampling technique will involve incision into the wall of the colon. The mucosa will then be pull through this incision and approximately 2cm x 2cm section of the full thickness of mucosa sampled. The majority of immune cells reside in the lamina propria of the mucosa (Figure 2). Some tissue will be frozen and the remaining digested for single-cell RNA sequencing of immune cells and stromal cells. A swab of the mucosa and the luminal chyme (where appropriate) will also be collected by microbiology culture swabs (in culture gels) and with swabs in PBS. With the help from Professor Trevor Lawley, the diversity of the microbiome will be determined by 16S rRNA sequencing. From these results, changes in diversity of the microbiota and whether this correspond with changes in immune cell heterogeneity will be investigated. If I find major differences in the immune cells or bacteria at these sites than I will ask for more samples to be collect from the next individual.
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 run.scientific_name · “Homo sapiens”
- body site study.description · “healthy adult human colon”
- life stage study.description · “healthy adult human colon”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114431082 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy |
| SAMEA104369425 | health_condition | healthy_control | R4 | 0.50 | study.description | representative of healthy tissues |
| SAMEA114431082 | health_condition_detail | Healthy | R1 | 0.90 | sample.attr.arrayexpress_phenotype | Healthy |
| SAMEA104369425 | health_condition_detail | Cadaveric donors screened for infections and disease; tissues described as healthy | R4 | 0.50 | study.description | representative of healthy tissues |
| SAMEA104369425 | location_site | Cambridge Biorepository of Translational Medicine (CBTM) | R4 | 0.45 | ena.study_description | Cambridge Biorepository of Translational Medicine (CBTM) |
| SAMEA104570837 | sex | male | R1 | 0.90 | sample.attr.arrayexpress_sex | male |
| SAMEA104369425 | subject_id | Human_colon_16S7159279 | R1 | 0.85 | sample.attr.subject_id | Human_colon_16S7159279 |
Sequencing
5,969 runs over 5,249 samples · mean 0.71 Gbp per run (median 54.4 Mbp, total 4,242.82 Gbp; 5,969 runs with a base count) · layout PAIRED 5,969 · platform ILLUMINA 5,969 · models Illumina HiSeq 2500 (4,990), Illumina NovaSeq 6000 (372), Illumina HiSeq 4000 (328), Illumina MiSeq (240), HiSeq X Ten (39) · 8% of runs with a Sandpiper profile · first public 2018-11-20 – 2023-10-03
Authors (0)
No author record.
Downloads
PRJEB23147.csv.gz (120.1 KB) · parquet (288.2 KB) — all 5,249 samples, every field with route and confidence · PRJEB23147_determinations.csv.gz (118.7 KB) — 21,481 evidence rows