Ex vivo synthetic glycan fermentation of US stool samples
154 stool samples from healthy individuals in the USA were treated ex vivo with 3 glycans for 45 hours under anaerobic conditions in Mega Medium, in an intervention study. machine-written summary
154 samples · 154 runs · US · Age unknown · 2022 · 0.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 984 sample values (collection date, country, health condition, intervention, latitude, longitude, medication, medication detail) |
| ✓ Abstract / description | 278 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC8913648 |
| ○ 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 — not resolved
26 of 26 people sampled more than once (154 samples; median 6, up to 6 per person).
Genera, mean relative abundance over 118 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 | 154 | 100% | 154 | |||
| health_condition | 154 | 100% | 30 | 124 | ||
| subject_id | 154 | 100% | 154 | |||
| collection_date | 154 | 100% | 154 | |||
| health_condition_detail | 154 | 100% | 154 | |||
| intervention | 154 | 100% | 154 | |||
| latitude | 154 | 100% | 154 | |||
| longitude | 154 | 100% | 154 | |||
| medication | 15 | 10% | 15 | |||
| medication_detail | 15 | 10% | 15 |
- Synthetic glycans control gut microbiome structure and mitigate colitis in mice. 2022 PMID 35273143 PMC8913648 own_data
Archive description
3 glycans across multiple healthy human stool samples treated ex vivo for 45 hours under anaerobic conditions in Mega Medium and sequenced
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “healthy human stool samples treated ex vivo”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25283235 | collection_date | 2018-07-07 | R1 | 0.90 | biosample.attribute:collection_date | 2018-07-07 |
| SAMN25283235 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN25283259 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Lactulose |
| SAMN25283235 | health_condition | healthy_control | R4 | 0.50 | study.description | healthy human stool samples |
| SAMN25283235 | health_condition_detail | Healthy individuals; ex vivo screening study | R4 | 0.50 | study.description | healthy human stool samples |
| SAMN25283235 | intervention | prebiotic_or_fibre | R1 | 0.85 | biosample.attribute:treatment | BQM |
| SAMN25283235 | latitude | 38.0400 | R1 | 0.90 | biosample.attribute:lat_lon | 38.04 N 84.50 W |
| SAMN25283235 | longitude | -84.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 38.04 N 84.50 W |
| SAMN25283259 | medication | laxative | R1 | 0.90 | biosample.attribute:treatment | Lactulose |
| SAMN25283259 | medication_detail | Lactulose | R1 | 0.90 | biosample.attribute:treatment | Lactulose |
| SAMN25283235 | subject_id | 801-003 | R1 | 0.85 | sample.attr.subject_id | 801-003 |
Sequencing
154 runs over 154 samples · mean 0.23 Gbp per run (median 0.23 Gbp, total 35.35 Gbp; 154 runs with a base count) · layout SINGLE 154 · platform ILLUMINA 154 · models HiSeq X Ten (154) · 77% of runs with a Sandpiper profile · first public 2022-02-02
Authors (17)
Tolonen AC first · Beauchemin N · Bayne C · Li L · Tan J · Lee J · Meehan BM · Meisner J · Millet Y · LeBlanc G · Kottler R · Rapp E · Murphy C · Turnbaugh PJ · von Maltzahn G · Liu CM · van Hylckama Vlieg JET last
Downloads
PRJNA800792.csv.gz (4.2 KB) · parquet (75.8 KB) — all 154 samples, every field with route and confidence · PRJNA800792_determinations.csv.gz (7.6 KB) — 1,262 evidence rows