Gut microbiota in obese weight-loss diet, Germany
92 longitudinal stool samples from German adults with obesity across six time points of a one-year inulin-enriched low-calorie diet program plus follow-up, studying gut microbiota changes linked to weight-loss success. machine-written summary
92 samples · 92 runs · DE · Adult · 2015 · 2.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 368 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10408196, PMC11009399, PMC11081829, PMC11934572, PMC12764784, PMC13269251, PMC4769288, PMC6440052, PMC9051138, PMC9370776 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 276 sample values (antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – 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 Prebiotic / dietary fibre supplement design single_arm_before_after · population obesity · Very low calorie inulin-enriched diet, weight-loss program over 24 months
“very low calorie inulin-enriched formula diet” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
16 of 16 people sampled more than once (92 samples; median 6, up to 6 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 6 mo (time from timepoint labels). Schedule stated by the source: “stool at baseline, month 3, 6, 12, 18 and 24” (time origin: intervention_start); stated follow-up 2.0 y.
Each row is one person (16 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 80 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 | 92 | 100% | ||||
| country | 92 | 100% | 92 | |||
| health_condition | 92 | 100% | 92 | |||
| subject_id | 92 | 100% | 92 | |||
| antibiotic_exposure | 92 | 100% | 92 | |||
| collection_date | 92 | 100% | 92 | |||
| health_condition_detail | 92 | 100% | 92 | |||
| timepoint_label | 92 | 100% | 92 |
- Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing. 2016 PMID 26919743 PMC4769288 own_data
- Diet-Related Metabolic Perturbations of Gut Microbial Shikimate Pathway-Tryptamine-tRNA Aminoacylation-Protein Synthesis in Human Health and Disease. 2019 PMID 30944520 PMC6440052 own_data
- Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy. 2022 PMID 35956358 PMC9370776 own_data
- A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. 2022 PMID 35484115 PMC9051138 unsure
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196 unsure
6 more
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. 2024 PMID 38565143 PMC11081829
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- A review of neural networks for metagenomic binning. 2025 PMID 40131312 PMC11934572
- The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels. 2025 PMID 41331251 PMC12764784
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
To gain more insight into the interconnection between microbiota, obesity and diet, we analyzed the metagenome of 16 patients following a weight-loss program based on a very low calorie inulin-enriched formula diet. In this longitudinal study we used shotgun sequencing of stool DNA to look at taxonomic and functional changes at different phases of the program. In 2 years we sequenced fecal samples at six time points, the baseline (before intervention, = T0), after diet intervention, (3 months later: T3), after reintroduction phase (T6), and three time points at the maintenance phase i.e. month 12 (T12), month 18 (T18) and month 24 (T24). In parallel, clinical parameters were monitored in order to establish potential relationships between microbiota and obesity-associated-disease particularly hypertension, insulin resistance, fatty liver and the metabolic syndrome. Moreover we analyzed the marker potential of microbial parameters for weight loss maintenance success.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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.title · “of the distal gut microbiota in obese”
- body site study.description · “shotgun sequencing of stool DNA to look”
- body site study.description · “insulin resistance, fatty liver and the metabolic”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03922449 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN03922449 | collection_date | 2009-11 | R1 | 0.90 | biosample.attribute:collection_date | 2009-11 |
| SAMN03922449 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany |
| SAMN03922449 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN03922449 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN03922449 | subject_id | AS44 | R1 | 0.85 | sample.attr.patient_name | AS44 |
| SAMN03922449 | timepoint_label | Month_0 | R1 | 0.85 | sample.attr.time_point | Month_0 |
Sequencing
92 runs over 92 samples · mean 2.21 Gbp per run (median 2.03 Gbp, total 203.62 Gbp; 92 runs with a base count) · layout PAIRED 92 · platform ILLUMINA 92 · models Illumina HiSeq 2500 (92) · 87% of runs with a Sandpiper profile · first public 2015-08-12 – 2015-08-13
Authors (34)
Pan S first · Zhu C · Zhao XM · Coelho LP last · Bischoff SC first · Nguyen NK · Seethaler B · Beisner J · Kügler P · Stefan T last · Zorea A first · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R · Mizrahi I last · Heidrich V first · Fackelmann G · Ricci L · Spadazzi R · Baldanzi G · Punčochář M · Catassi G · Marchi P · Modesto M · Piccinno G · Porcari S · Rondinella D · Asnicar F · Valles-Colomer M · Mattarelli P · Ianiro G · Segata N last
Downloads
PRJNA290729.csv.gz (3.3 KB) · parquet (73.4 KB) — all 92 samples, every field with route and confidence · PRJNA290729_determinations.csv.gz (5.6 KB) — 644 evidence rows