Stool vs swab vs mucosal tissue microbiome comparison, USA
1,397 shotgun metagenomes from matched stool, rectal swab and mucosal tissue samples from 240 USA participants at two time points, comparing taxonomic and functional profiles and their associations with age, sex, BMI, NSAID and antibiotic use. machine-written summary
1,397 samples · 1,397 runs · US · Age unknown · 2021 · 4.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,985 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 5,588 sample values (health condition, health condition detail, location locality, location site) · PMC12799418 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Stool, rectal swab, mucosal tissue at beginning (baseline) and end of trial” (time origin: intervention_start).
Genera, mean relative abundance over 836 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 | 0 | 0% | ||||
| country | 1,397 | 100% | 1,397 | |||
| health_condition | 1,397 | 100% | 1,397 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 1,397 | 100% | 1,397 | |||
| detailed_location | 1,397 | 100% | ||||
| health_condition_detail | 1,397 | 100% | 1,397 | |||
| latitude | 1,397 | 100% | 1,397 | |||
| location_locality | 1,397 | 100% | 1,397 | |||
| location_region | 1,397 | 100% | 1,397 | |||
| location_site | 1,397 | 100% | 1,397 | |||
| longitude | 1,397 | 100% | 1,397 |
- On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples. 2021 PMID 34290321 PMC8295290 own_data
- The Association of Gut Microbiota With TRPM7 Genotype, Colorectal Polyps, and Magnesium. 2025 PMID 40750038 PMC12799418 own_data
Archive description
In this study, we collected matched stool, rectal swab and mucosal tissue samples from 240 study participants at two time points, which resulted in 1,397 shotgun metagenomes. We estimated the biospecimen type variation of both metagenome taxonomy and functional pathways. We also assessed whether the associations between taxa/pathways and age, sex, body mass index (BMI), non-steroidal anti-inflammatory drugs (NSAIDs) use and antibiotics use were consistent across the different sample types.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome(1397)”
- body site study.description · “collected matched stool, rectal swab and mucosal tissue samples”
- body site sample.attr.isolation_source · “tissue (n=466/1397)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17485572 | collection_date | 2011-04 | R1 | 0.90 | biosample.attribute:collection_date | 2011-04 |
| SAMN17485572 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN17485572 | health_condition | intervention_cohort | R3 | 0.70 | paper.fulltext.methods | double-blind 2 × 2 factorial randomized controlled trial |
| SAMN17485572 | health_condition_detail | double-blind 2x2 factorial randomized controlled trial of Ca:Mg intake ratios and Mg supplementation | R3 | 0.70 | paper.fulltext.methods | double-blind 2 × 2 factorial randomized controlled trial |
| SAMN17485572 | latitude | 36.1600 | R1 | 0.90 | biosample.attribute:lat_lon | 36.16 N 86.78 W |
| SAMN17485572 | location_locality | Nashville | R3 | 0.70 | paper.fulltext.methods | Vanderbilt University Medical Center (VUMC), Nashville, Tennessee |
| SAMN17485572 | location_region | Tennessee | R1 | 0.60 | biosample.attribute:lat_lon | 36.16 N 86.78 W |
| SAMN17485572 | location_site | Vanderbilt University Medical Center | R3 | 0.70 | paper.fulltext.methods | randomized controlled trial conducted at Vanderbilt University Medical Center (VUMC) |
| SAMN17485572 | longitude | -86.7800 | R1 | 0.90 | biosample.attribute:lat_lon | 36.16 N 86.78 W |
Sequencing
1,397 runs over 1,397 samples · mean 4.49 Gbp per run (median 4.36 Gbp, total 6,268.00 Gbp; 1,397 runs with a base count) · layout PAIRED 1,397 · platform ILLUMINA 1,397 · models Illumina HiSeq 4000 (1,397) · 90% of runs with a Sandpiper profile · first public 2021-02-09
Authors (14)
Sun S first · Zhu X · Huang X · Murff HJ · Ness RM · Seidner DL · Sorgen AA · Blakley IC · Yu C · Dai Q · Azcarate-Peril MA · Shrubsole MJ · Fodor AA last · Su T
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA693850.csv.gz (33.7 KB) · parquet (121.1 KB) — all 1,397 samples, every field with route and confidence · PRJNA693850_determinations.csv.gz (65.9 KB) — 12,573 evidence rows