Gut microbiota changes after gastric bypass in Denmark
33 fecal samples from morbidly obese patients in Denmark, collected before and after Roux-en-Y gastric bypass surgery, in an intervention study of gut microbiota changes following the procedure. machine-written summary
33 samples · 66 runs · DK · Age unknown · 2016 · 7.17 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 207 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 64 sample values (health condition, health condition detail) |
| ✓ Full text | 33 sample values (location site) · PMC11009399, PMC11402979, PMC11958714, PMC4908688, PMC8224199 |
| ✓ Supplementary tables | 24 sample values (subject id, timepoint) |
| ✓ External resources | 2 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design single_arm_before_after · population obesity · Roux-en-Y gastric bypass surgery, sampled before and after
“Roux-en-Y gastric bypass (RYGB) is an effective means” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
13 of 13 people sampled more than once (33 samples; median 3, up to 3 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “Stool samples collected before RYGB, and 3 months and 1 year after surgery” (time origin: surgery); stated follow-up 12 mo.
Each row is one person (13 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 32 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 | 33 | 100% | 33 | |||
| health_condition | 33 | 100% | 1 | 32 | ||
| subject_id | 33 | 100% | 21 | 12 | ||
| collection_date | 33 | 100% | 33 | |||
| detailed_location | 33 | 100% | ||||
| health_condition_detail | 33 | 100% | 1 | 32 | ||
| latitude | 33 | 100% | 33 | |||
| location_region | 33 | 100% | 33 | |||
| location_site | 33 | 100% | 33 | |||
| longitude | 33 | 100% | 33 | |||
| timepoint_label | 33 | 100% | 21 | 12 |
- Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota. 2016 PMID 27306058 PMC4908688 own_data
- A microbial signature following bariatric surgery is robustly consistent across multiple cohorts. 2021 PMID 34159880 PMC8224199 unsure
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399 unsure
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979 unsure
- MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations. 2025 PMID 40171165 PMC11958714 unsure
1 more
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity and glucose homeostasis. Dysbiosis of gut microbiota has been associated with obesity and some of its co-morbidities like type 2 diabetes, and major changes of gut bacterial communities have been hypothesized to mediate part of the beneficial metabolic effects observed after RYGB. This study we describe changes in gut microbial taxonomic composition and functional potential following RYGB.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.title · “morbidly obese patients”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “changes of the individual gut microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3888893 | collection_date | 2010 | R1 | 0.90 | biosample.attribute:collection_date | 2010 |
| SAMEA3888893 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
| SAMEA3888898 | health_condition | obesity | R2 | 0.75 | external.gmrepo source | phenotype: Obesity, Morbid |
| SAMEA3888893 | health_condition | obesity | R4 | 0.50 | paper.abstract | morbidly obese patients who underwent RYGB |
| SAMEA3888898 | health_condition_detail | Obesity, Morbid | R2 | 0.75 | external.gmrepo source | phenotype: Obesity, Morbid |
| SAMEA3888893 | health_condition_detail | morbidly obese patients undergoing RYGB | R4 | 0.50 | paper.abstract | morbidly obese patients who underwent RYGB |
| SAMEA3888893 | latitude | 55.6500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.65 12.47 |
| SAMEA3888893 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.65 12.47 |
| SAMEA3888893 | location_site | Hvidovre Hospital | R3 | 0.70 | paper.fulltext.methods | recruited at Hvidovre Hospital, Denmark |
| SAMEA3888893 | longitude | 12.4700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.65 12.47 |
| SAMEA3888894 | subject_id | F05 | R1 | 0.70 | sample.name_rule:TITLE | F05_Baseline |
| SAMEA3888893 | subject_id | F06 | R2 | 0.85 | paper.supp.13073_2016_312_MOESM2_ESM.xlsx[TableS1_ReadsQC!Subject ID] | F06 |
| SAMEA3888894 | timepoint_label | Baseline | R1 | 0.70 | sample.name_rule:TITLE | F05_Baseline |
| SAMEA3888893 | timepoint_label | 3 MO | R2 | 0.85 | paper.supp.13073_2016_312_MOESM2_ESM.xlsx[TableS1_ReadsQC!Time] | 3 MO |
Sequencing
66 runs over 33 samples · mean 3.63 Gbp per run (median 2.38 Gbp, total 239.79 Gbp; 66 runs with a base count) · layout PAIRED 33, SINGLE 33 · platform ILLUMINA 66 · models Illumina HiSeq 2000 (66) · 48% of runs with a Sandpiper profile · first public 2016-08-21
Authors (30)
Fouladi F first · Carroll IM · Sharpton TJ · Bulik-Sullivan E · Heinberg L · Steffen KJ · Fodor AA last · Zorea A first · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R · Mizrahi I last · Dong W first · Fan X · Guo Y · Wang S · Jia S · Lv N · Yuan T · Pan Y · Xue Y · Chen X · Xiong Q · Yang R · Zhao W · Zhu B last · Shi H first · Li J last
Downloads
PRJEB12947.csv.gz (2.0 KB) · parquet (71.8 KB) — all 33 samples, every field with route and confidence · PRJEB12947_determinations.csv.gz (3.5 KB) — 330 evidence rows