Terminal ileum metagenomes in healthy adults, Chicago
13 small intestinal samples (biopsies, mucosal brushes, luminal aspirate) from healthy adults without intestinal inflammation in Chicago, USA, in a cross-sectional pilot study on segmented filamentous bacteria. machine-written summary
13 samples · 13 runs · US · Adult · 2021 · 17.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 117 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex) |
| ✓ Abstract / description | 26 sample values (health condition, health condition detail) |
| – 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
5 of 5 people sampled more than once (13 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 3 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 | 13 | 100% | ||||
| country | 13 | 100% | 13 | |||
| health_condition | 13 | 100% | 13 | |||
| subject_id | 13 | 100% | 13 | |||
| age_at_collection_days | 13 | 100% | 13 | |||
| collection_date | 13 | 100% | 13 | |||
| detailed_location | 13 | 100% | ||||
| health_condition_detail | 13 | 100% | 13 | |||
| latitude | 13 | 100% | 13 | |||
| location_locality | 13 | 100% | 13 | |||
| location_region | 13 | 100% | 13 | |||
| longitude | 13 | 100% | 13 | |||
| sex | 13 | 100% | 13 |
Archive description
Human small intestine metagenomes from 5 healthy adults without intestinal inflammation. Samples were taken from the terminal ileum and include 9 biopsies, 3 mucosal brushes, and 1 luminal aspirate.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “terminal ileum and include 9 biopsies”
- life stage study.description · “5 healthy adults without intestinal inflammation”
- life stage sample.attr.host_age · “66 (n=3/13)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21897446 | age_at_collection_days | 22280.2 | R1 | 0.70 | sample.attr.host_age | 61 |
| SAMN21897446 | collection_date | 2019-10-29 | R1 | 0.90 | biosample.attribute:collection_date | 2019-10-29 |
| SAMN21897446 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Chicago |
| SAMN21897446 | health_condition | healthy_control | R4 | 0.50 | study.description | healthy adults without intestinal inflammation |
| SAMN21897446 | health_condition_detail | All subjects are healthy without intestinal inflammation. | R4 | 0.50 | study.description | healthy adults without intestinal inflammation |
| SAMN21897446 | latitude | 41.7886 | R1 | 0.90 | biosample.attribute:lat_lon | 41.7886 N 87.5987 W |
| SAMN21897446 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Chicago |
| SAMN21897446 | location_region | Illinois | R1 | 0.60 | biosample.attribute:lat_lon | 41.7886 N 87.5987 W |
| SAMN21897446 | longitude | -87.5987 | R1 | 0.90 | biosample.attribute:lat_lon | 41.7886 N 87.5987 W |
| SAMN21897446 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN21897446 | subject_id | SFB01 | R1 | 0.70 | sample.name_rule:sample_alias | SFB01-BIO-01_S6 |
Sequencing
13 runs over 13 samples · mean 16.28 Gbp per run (median 17.19 Gbp, total 211.63 Gbp; 13 runs with a base count) · layout PAIRED 13 · platform ILLUMINA 13 · models NextSeq 500 (13) · 23% of runs with a Sandpiper profile · first public 2021-11-16
Authors (0)
No author record.
Downloads
PRJNA767321.csv.gz (1.4 KB) · parquet (71.2 KB) — all 13 samples, every field with route and confidence · PRJNA767321_determinations.csv.gz (1.8 KB) — 143 evidence rows