Longitudinal diet and gut microbiota study in Germany
149 longitudinal gut metagenome samples from Germany, studying long-term effects of diet on gut microbiota composition, including amino acid auxotrophy distribution. machine-written summary
149 samples · 149 runs · DE · Age unknown · 2021 · 4.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,043 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10689445 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
65 of 84 people sampled more than once (130 samples; median 2, up to 2 per person) · follow-up median 3.0 y (max 3.0 y) · median interval between samples 3.0 y (time from visit codes mapped to the stated schedule).
Each row is one person (36 shown of 65); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 139 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 | 149 | 100% | 149 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 149 | 100% | 149 | |||
| collection_date | 149 | 100% | 149 | |||
| detailed_location | 149 | 100% | ||||
| latitude | 149 | 100% | 149 | |||
| location_region | 149 | 100% | 149 | |||
| longitude | 149 | 100% | 149 | |||
| timepoint_label | 149 | 100% | 149 |
- Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. 2023 PMID 37891427 PMC10689445 unsure
Archive description
Longitudinal effects of diet on human gut microbiota composition employing shotgun metagenomics data analysis
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “human gut microbiota composition”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA10813519 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMEA10813519 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA10813519 | latitude | 54.3213 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.32133 10.13489 |
| SAMEA10813519 | location_region | Schleswig-Holstein | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.32133 10.13489 |
| SAMEA10813519 | longitude | 10.1349 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.32133 10.13489 |
| SAMEA10813519 | subject_id | BSP_0018 | R1 | 0.70 | sample.name_rule:alias | BSP_0018.F1 |
| SAMEA10813519 | timepoint_label | TimePoint 1 | R1 | 0.85 | biosample.attribute:description | TimePoint 1 |
Sequencing
149 runs over 149 samples · mean 4.90 Gbp per run (median 4.95 Gbp, total 730.32 Gbp; 149 runs with a base count) · layout PAIRED 149 · platform ILLUMINA 149 · models Illumina MiSeq (149) · 93% of runs with a Sandpiper profile · first public 2021-11-29
Authors (13)
Starke S first · Harris DMM · Zimmermann J · Schuchardt S · Oumari M · Frank D · Bang C · Rosenstiel P · Schreiber S · Frey N · Franke A · Aden K · Waschina S last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB48605.csv.gz (4.9 KB) · parquet (76.0 KB) — all 149 samples, every field with route and confidence · PRJEB48605_determinations.csv.gz (7.5 KB) — 1,043 evidence rows