Gut microbiome by sample type in healthy adults, Nashville
143 samples (stool, rectal swab, mucosa) from healthy adult and elderly participants in Nashville, Tennessee, USA, comparing bacterial community composition across sample types in a cross-sectional design. machine-written summary
143 samples · 143 runs · US · Age unknown · 2017 · 0.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,859 sample values (age, bmi, collection date, country, intervention, intervention detail, latitude, location locality) |
| ✓ Abstract / description | 143 sample values (health condition) |
| ✓ Full text | 143 sample values (antibiotic exposure) · PMC5841359 |
| ○ 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
49 of 50 people sampled more than once (142 samples; median 2, up to 6 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 3 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “stool and swab samples collected at two time points, approximately three months apart” (time origin: enrolment); stated follow-up 3 mo.
Each row is one person (36 shown of 49); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 143 | 100% | ||||
| country | 143 | 100% | 143 | |||
| health_condition | 143 | 100% | 143 | |||
| subject_id | 143 | 100% | 143 | |||
| age_at_collection_days | 143 | 100% | 143 | |||
| antibiotic_exposure | 143 | 100% | 143 | |||
| bmi | 143 | 100% | 143 | |||
| collection_date | 143 | 100% | 143 | |||
| detailed_location | 143 | 100% | ||||
| intervention | 143 | 100% | 143 | |||
| intervention_detail | 143 | 100% | 143 | |||
| latitude | 143 | 100% | 143 | |||
| location_locality | 143 | 100% | 143 | |||
| location_region | 143 | 100% | 143 | |||
| longitude | 143 | 100% | 143 | |||
| sex | 143 | 100% | 143 | |||
| timepoint_label | 143 | 100% | 143 |
- Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. 2018 PMID 29515151 PMC5841359 own_data
- Proportion-based normalizations outperform compositional data transformations in machine learning applications 2024 PMC10913632 unsure
Archive description
The purpose of this study is to evaluate similarities and differences in gut bacterial measurements and stability in the microbial communities of three different types of samples that could be used to assess different niches of the human gut microbiome: rectal swab, stool, and normal rectal mucosa samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “stool, rectal swab, and mucosal samples”
- life stage sample.attr.age · “61 (n=82/143)”
- life stage sample.attr.age · “74 (n=61/143)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07457498 | age_at_collection_days | 20454.0 | R1 | 0.70 | sample.attr.age | 56 |
| SAMN07457498 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | used oral or injected antibiotics in the past 12 months |
| SAMN07457498 | bmi | 22.4 | R1 | 0.90 | sample.attr.bmi | 22.4 |
| SAMN07457498 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN07457498 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Tennessee,Nashville |
| SAMN07457498 | health_condition | healthy_control | R4 | 0.50 | study.description | normal rectal mucosa samples |
| SAMN07457498 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:visit | visit: Pre |
| SAMN07457504 | intervention | placebo | R1 | 0.90 | biosample.attribute:treatment | treatment: Placebo |
| SAMN07457498 | intervention_detail | pre-intervention visit; assigned arm: magnesium citrate bowel preparation for mucosal sampling | R1 | 0.90 | biosample.attribute:visit | visit: Pre |
| SAMN07457504 | intervention_detail | placebo/sham bowel prep arm | R1 | 0.90 | biosample.attribute:treatment | treatment: Placebo |
| SAMN07457498 | latitude | 36.1417 | R1 | 0.90 | biosample.attribute:lat_lon | 36.1417 N 86.8021 W |
| SAMN07457498 | location_locality | Nashville | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Tennessee,Nashville |
| SAMN07457498 | location_region | Tennessee | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Tennessee,Nashville |
| SAMN07457498 | longitude | -86.8021 | R1 | 0.90 | biosample.attribute:lat_lon | 36.1417 N 86.8021 W |
| SAMN07457498 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN07457498 | subject_id | PP00740 | R1 | 0.85 | biosample.attribute:study_id | PP00740 |
| SAMN07457498 | timepoint_label | Pre | R1 | 0.85 | sample.attr.visit | Pre |
Sequencing
143 runs over 143 samples · mean 0.13 Gbp per run (median 0.12 Gbp, total 18.34 Gbp; 143 runs with a base count) · layout PAIRED 143 · platform ILLUMINA 143 · models Illumina MiSeq (143) · 0% of runs with a Sandpiper profile · first public 2017-08-08
Authors (15)
Jones RB first · Zhu X · Moan E · Murff HJ · Ness RM · Seidner DL · Sun S · Yu C · Dai Q · Fodor AA · Azcarate-Peril MA · Shrubsole MJ last · Yerke A first · Fry Brumit D · Fodor A last
Downloads
PRJNA397450.csv.gz (5.0 KB) · parquet (78.0 KB) — all 143 samples, every field with route and confidence · PRJNA397450_determinations.csv.gz (15.3 KB) — 2,145 evidence rows