Elderberry extract effect on gut microbiome via SHIME model
48 samples from an in vitro SHIME gut model inoculated with fecal material from donors in South Tyrol, Italy, examining effects of two-week elderberry (Sambucus nigra) extract intake in an intervention design. machine-written summary
48 samples · 48 runs · IT · Age unknown · 2025 · 20.44 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 336 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 96 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – 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 observational_with_procedure · In vitro SHIME gut model exposed to elderberry extract, not human administration
longitudinal — not resolved
2 of 2 people sampled more than once (48 samples; median 24, up to 24 per person).
Genera, mean relative abundance over 47 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 | 48 | 100% | 48 | |||
| health_condition | 48 | 100% | 48 | |||
| subject_id | 48 | 100% | 48 | |||
| collection_date | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 48 | |||
| latitude | 48 | 100% | 48 | |||
| location_region | 48 | 100% | 48 | |||
| longitude | 48 | 100% | 48 | |||
| timepoint_label | 48 | 100% | 48 |
Archive description
This study investigated whether a polyphenol- and fiber-rich elderberry extract could beneficially modulate the human gut microbiome. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME), inoculated with fecal samples from two donors, was used. Intake of the extract for two weeks induced donor-specific shifts in microbial composition and predicted function, supporting its potential for personalized gut health strategies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN50012359 | collection_date | 2023-10 | R1 | 0.90 | biosample.attribute:collection_date | 2023-10 |
| SAMN50012359 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy: South Tyrol |
| SAMN50012359 | health_condition | healthy_control | R4 | 0.35 | study.description | fecal samples from two donors |
| SAMN50012359 | health_condition_detail | Donors for in vitro SHIME ecosystem study; no disease stated | R4 | 0.35 | study.description | fecal samples from two donors |
| SAMN50012359 | latitude | 46.4790 | R1 | 0.90 | biosample.attribute:lat_lon | 46.478951 N 11.330913 E |
| SAMN50012359 | location_region | South Tyrol | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy: South Tyrol |
| SAMN50012359 | longitude | 11.3309 | R1 | 0.90 | biosample.attribute:lat_lon | 46.478951 N 11.330913 E |
| SAMN50012359 | subject_id | D1 | R1 | 0.70 | sample.name_rule:alias | DC_D1_T0A |
| SAMN50012359 | timepoint_label | 0 | R1 | 0.85 | sample.attr.sampling_day | 0 |
Sequencing
48 runs over 48 samples · mean 21.01 Gbp per run (median 20.44 Gbp, total 1,008.49 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina NovaSeq X Plus (48) · 98% of runs with a Sandpiper profile · first public 2025-08-26
Authors (0)
No author record.
Downloads
PRJNA1293117.csv.gz (2.1 KB) · parquet (71.5 KB) — all 48 samples, every field with route and confidence · PRJNA1293117_determinations.csv.gz (3.6 KB) — 432 evidence rows