In vitro small intestinal microbiota model from 4 donors
36 samples from an in vitro model of the terminal ileum representing four donors, used to study interindividual variability in small intestinal microbiota structure and function via shotgun metagenomics and metabolomics. machine-written summary
36 samples · 36 runs · US · Age unknown · 2026 · 0.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 252 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| ○ 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
4 of 4 people sampled more than once (36 samples; median 9, up to 9 per person) · follow-up median 31 d (max 31 d) · median interval between samples 31 d (time from collection months (month precision)). Schedule stated by the source: “Repeated sampling of 4 in vitro reactor units (one per donor) over 9 distinct days (0 through 10).”.
Each row is one person (4 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 36 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 | 36 | 100% | 36 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 36 | 100% | 36 | |||
| collection_date | 36 | 100% | 36 | |||
| detailed_location | 36 | 100% | ||||
| latitude | 36 | 100% | 36 | |||
| location_region | 36 | 100% | 36 | |||
| longitude | 36 | 100% | 36 | |||
| timepoint_label | 36 | 100% | 36 |
- An <i>in vitro</i> model of the small intestinal microbiota provides key insights into interindividual variability in structure and function. 2026 PMID 41744504 PMC13011344 own_data
Archive description
Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing was used to evaluate the in vitro community structure and untargeted metabolomics used to examine community function.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host study.title · “small intestinal microbiota in vitro using 4 donors”
- body site study.title · “small intestinal microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN53270662 | collection_date | 2023-01 | R1 | 0.90 | biosample.attribute:collection_date | 2023-01 |
| SAMN53270662 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Pennsylvania |
| SAMN53270662 | latitude | 39.9523 | R1 | 0.90 | biosample.attribute:lat_lon | 39.952305 N 75.193703 W |
| SAMN53270662 | location_region | Pennsylvania | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Pennsylvania |
| SAMN53270662 | longitude | -75.1937 | R1 | 0.90 | biosample.attribute:lat_lon | 39.952305 N 75.193703 W |
| SAMN53270662 | subject_id | SIM1 | R1 | 0.85 | biosample.attribute:unit | SIM1 |
| SAMN53270662 | timepoint_label | 0 | R1 | 0.85 | sample.attr.day | 0 |
Sequencing
36 runs over 36 samples · mean 0.88 Gbp per run (median 0.88 Gbp, total 31.73 Gbp; 36 runs with a base count) · layout PAIRED 36 · platform ILLUMINA 36 · models HiSeq X Five (36) · 100% of runs with a Sandpiper profile · first public 2026-01-23
Authors (8)
Firrman J first · Liu L · Mahalak K · Lemons JMS · Narrowe A · Friedman ES · Wu GD · Van de Weile T last
Downloads
PRJNA1365125.csv.gz (1.7 KB) · parquet (70.8 KB) — all 36 samples, every field with route and confidence · PRJNA1365125_determinations.csv.gz (2.0 KB) — 252 evidence rows