Small intestine microbiome/metabolome in healthy London adults
242 longitudinal samples from stomach, duodenum, and ileum of healthy adult participants in London, UK, collected after consuming legume-based meals, profiling metabolites and microbial strains across the gut. machine-written summary
242 samples · 242 runs · GB · Adult · 2026 · 10.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,936 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| – Abstract / description | no abstract or project description |
| ✓ Full text | 242 sample values (location site) |
| – 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 |
intervention — arms not resolved
design single_arm_before_after · Structurally varied legume-based test meals consumed by participants
longitudinal — not resolved
Schedule stated by the source: “Baseline then postprandial samples per participant: gastric/duodenal up to 3h post-meal, ileal up to 8h post-meal; aliases encode visit/day/timepoint (e.g. UGIV1D4-150, LGIV1D3, Oral-Baseline, Oral-af” (time origin: meal consumption (postprandial)); stated follow-up 0 d.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 242 | 100% | ||||
| country | 242 | 100% | 242 | |||
| health_condition | 242 | 100% | 242 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 242 | 100% | 242 | |||
| detailed_location | 242 | 100% | ||||
| health_condition_detail | 242 | 100% | 242 | |||
| latitude | 242 | 100% | 242 | |||
| location_locality | 242 | 100% | 242 | |||
| location_region | 242 | 100% | 242 | |||
| location_site | 242 | 100% | 242 | |||
| longitude | 242 | 100% | 242 |
- Dietary Modulation of The Human Small Intestine Metabolome and Microbiome 2025 own_data
- Dietary Modulation of The Human Small Intestine Metabolome and Microbiome 2026 own_data
Archive description
The gastrointestinal tract is a dynamic system where different anatomical regions interact to regulate whole-body physiology. Diet-derived and microbially linked metabolites contribute significantly to inter-individual variation, but spatially and temporally resolved data on human dietary metabolism across the small intestine remain limited. Here, we use naso-enteral intubation to collect longitudinal samples from the stomach, duodenum, and ileum of 10 healthy participants consuming structurally varied legume-based meals. Gastric and duodenal samples were collected up to 3 hours postprandially and ileal samples up to 8 hours. Metabolite profiling was performed using NMR spectroscopy, and shotgun metagenomic sequencing enabled microbial strain tracking from the oral cavity to the ileum. We find that metabolite profiles and microbial communities exhibit rapid spatial and temporal dynamics, with oral bacterial strains detected in the ileum. The structural properties of food influence metabolite composition and microbial populations, correlating with gut hormone responses (GLP-1 and PYY). These findings reveal greater small intestinal metabolic and microbial plasticity during food ingestion than previously appreciated and suggest a route for oral bacteria, including potential pathogens and pathobionts, to reach the ileum via the food bolus. This study highlights the interplay between diet, microbiota, and host physiology, with implications for metabolic health.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “stomach, duodenum, and ileum of 10 healthy participants”
- life stage study.description · “10 healthy participants consuming structurally varied legume-based meals”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47543142 | collection_date | 2016-01-27 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-27 |
| SAMN47543142 | country | GB | R1 | 0.90 | sample.attr.geo_loc_name | United Kingdom: London |
| SAMN47543142 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: Healthy |
| SAMN47543142 | health_condition_detail | Healthy | R1 | 0.90 | sample.attr.gastrointest_disord | Healthy |
| SAMN47543142 | latitude | 51.5072 | R1 | 0.90 | biosample.attribute:lat_lon | 51.5072 N 0.1276 W |
| SAMN47543142 | location_locality | London | R1 | 0.85 | biosample.attribute:geo_loc_name | United Kingdom: London |
| SAMN47543142 | location_region | England | R1 | 0.60 | biosample.attribute:lat_lon | 51.5072 N 0.1276 W |
| SAMN47543142 | location_site | NIHR Imperial Clinical Research Facility, Hammersmith Hospital | R3 | 0.70 | paper.fulltext.methods | NIHR Imperial Clinical Research Facility (CRF) at Hammersmith Hospital |
| SAMN47543142 | longitude | -0.1276 | R1 | 0.90 | biosample.attribute:lat_lon | 51.5072 N 0.1276 W |
Sequencing
242 runs over 242 samples · mean 11.76 Gbp per run (median 10.99 Gbp, total 2,845.55 Gbp; 242 runs with a base count) · layout PAIRED 242 · platform ILLUMINA 242 · models Illumina NovaSeq 6000 (189), Illumina NovaSeq X (53) · 0% of runs with a Sandpiper profile · first public 2026-08-13
Authors (20)
Fernandes N first · Cai M · Warren FJ · Duncan A · Warren F · Harris H · Serrano Contreras JI · Sidorczuk K · Contreras JIS · Bernal A · Castillo A · Petropoulou K · Blunt D · Perez-Moral N · Garcia-Perez I · Edwards C · Hildebrand F · Holmes E · Wist J · Frost G last
Downloads
PRJNA1240928.csv.gz (7.1 KB) · parquet (81.0 KB) — all 242 samples, every field with route and confidence · PRJNA1240928_determinations.csv.gz (14.7 KB) — 2,178 evidence rows