Short-term fiber-rich vs fiber-poor diet switch, Germany
30 fecal samples from healthy adult volunteers in Germany, collected after 5-day fiber-rich and fiber-poor diet phases; shotgun metagenomics intervention study of short-term dietary switching. machine-written summary
12 samples · 30 runs · DE · Adult · 2023 · 4.90 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 84 sample values (collection date, country, health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 24 sample values (location site, sex) · PMC10457203 |
| ○ 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design crossover · population healthy_control · Fiber-rich vs fiber-poor diet 5 days each, stool FMT into germ-free mice
“fiber-rich diet (FRD) and one defined fiber-poor diet” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
6 of 6 people sampled more than once (12 samples; median 2, up to 2 per person). Schedule stated by the source: “Stool collected at end of fiber-rich diet phase (day 5) and end of fiber-poor diet phase (day 10)” (time origin: intervention start); stated follow-up 10 d.
Genera, mean relative abundance over 30 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| health_condition_detail | 12 | 100% | 12 | |||
| intervention | 12 | 100% | 12 | |||
| location_site | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 |
- Short-term dietary changes can result in mucosal and systemic immune depression. 2023 PMID 37580603 PMC10457203 own_data
Archive description
Healthy volunteers were offered one defined fiber-rich diet (FRD) and one defined fiber-poor diet (FPD), both consumed for 5 consecutive days. Stool samples were collected at the end of each dietary switch (i.e. end of fiber-rich, FRD and fiber-poor diet, FPD phases). Shotgun metagenomics and fecal microbiota transfer (FMT) into germ-free (GF) mice were performed.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “5 consecutive days. Stool samples were collected”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “Healthy volunteers were offered one”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113567624 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMEA113567624 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA113567624 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:description | description: Human source: Volunteer 1 - FRD - FS020_HS001_2 |
| SAMEA113567624 | health_condition_detail | Healthy volunteer participating in dietary intervention study | R1 | 0.70 | sample.name_rule:description | description: Human source: Volunteer 1 - FRD - FS020_HS001_2 |
| SAMEA113567624 | intervention | diet_intervention | R1 | 0.70 | sample.name_rule:description | description: Human source: Volunteer 1 - FRD - FS020_HS001_2 |
| SAMEA113567624 | location_site | I. Department of Medicine, University Medical Center Hamburg-Eppendorf | R3 | 0.70 | paper.fulltext.methods | conducted at the I. Department of Medicine, UKE |
| SAMEA113567624 | sex | female | R3 | 0.70 | paper.fulltext.methods | n = 6, all female, 28–50 years of age |
| SAMEA113567624 | subject_id | 1 | R1 | 0.70 | sample.name_rule:description | description: Human source: Volunteer 1 - FRD - FS020_HS001_2 |
| SAMEA113567624 | timepoint_label | FRD | R1 | 0.70 | sample.name_rule:description | description: Human source: Volunteer 1 - FRD - FS020_HS001_2 |
Sequencing
30 runs over 12 samples · mean 5.40 Gbp per run (median 4.90 Gbp, total 162.12 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina NovaSeq 6000 (30) · 100% of runs with a Sandpiper profile · first public 2023-06-02
Authors (33)
Siracusa F first · Schaltenberg N · Kumar Y · Lesker TR · Steglich B · Liwinski T · Cortesi F · Frommann L · Diercks BP · Bönisch F · Fischer AW · Scognamiglio P · Pauly MJ · Casar C · Cohen Y · Pelczar P · Agalioti T · Delfs F · Worthmann A · Wahib R · Jagemann B · Mittrücker HW · Kretz O · Guse AH · Izbicki JR · Lassen KG · Strowig T · Schweizer M · Villablanca EJ · Elinav E · Huber S · Heeren J · Gagliani N last
Downloads
PRJEB62783.csv.gz (1.3 KB) · parquet (71.0 KB) — all 12 samples, every field with route and confidence · PRJEB62783_determinations.csv.gz (2.3 KB) — 108 evidence rows