Gut metagenome, bariatric surgery, France
271 gut metagenome samples from adults with obesity in France, studied in an intervention design comparing adjustable gastric banding and Roux-en-Y gastric bypass, with follow-up post-surgery. machine-written summary
271 samples · 867 runs · FR · Adult · 2019 · 2.21 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 688 sample values (country, subject id, timepoint) |
| ✓ Abstract / description | 542 sample values (health condition, health condition detail) |
| ✓ Full text | 813 sample values (antibiotic exposure, location locality, location site) · PMC7143256, PMC8536095 |
| ○ 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 |
longitudinal — not resolved
50 of 81 people sampled more than once (170 samples; median 3, up to 5 per person). Schedule stated by the source: “stool at 1, 3 and 12 months post-bariatric surgery” (time origin: surgery); stated follow-up 12 mo.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 271 | 100% | ||||
| country | 271 | 100% | 271 | |||
| health_condition | 271 | 100% | 271 | |||
| subject_id | 201 | 74% | 201 | |||
| antibiotic_exposure | 271 | 100% | 271 | |||
| detailed_location | 271 | 100% | ||||
| health_condition_detail | 271 | 100% | 271 | |||
| location_locality | 271 | 100% | 271 | |||
| location_site | 271 | 100% | 271 | |||
| timepoint_label | 216 | 80% | 216 |
- Major microbiota dysbiosis in severe obesity: fate after bariatric surgery. 2019 PMID 29899081 PMC7143256 own_data
- Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. 2021 PMID 34680891 PMC8536095 unsure
Archive description
Dysbiosis, including decreased gut microbial richness (MGR) and composition modifications, associates with adverse metabolism in lean, overweight or moderate obesity, but lacks characterization in severe obesity. Bariatric surgery (BS) improves body composition and metabolism in severe obesity which featuresand is associated with gut microbiota modifications. Here, we characterized the importance of dysbiosis and functional alterations in severe obesity and assessed whether BS procedures would rescue this dysbiosis. Methods61 Sixty-one severely obese subjects, candidate to adjustable gastric banding (AGB, n=20) or Roux-en-Y-gastric bypass (RYGB n=41), were enrolled. 24 of them were followed at 1, 3 and 12 months post-BS. Gut microbiota and serum metabolomeics were analyzed using shotgun metagenomics and LC-MS technology, respectively. ResultsLow gene richness (LGC) concerned was present in 75% of patients and associated with detrimental fat composition (increased trunk-fat mass) and cardiometabolic complications (type-2 diabetes, hypertension and its severity). 78 Seventy-eight metagenomic species (MGS) were signatures of LGC , among which 50 % associated with adverse body composition and metabolic phenotypes. Nine serum metabolites (including Glutarate, 3-Methoxyphenylacetic Acid, and L-Histidine) and functional modules containing protein families involved in their metabolism were strongly modified byassociated with MGR. Gut microbiome showed significant increase of MGR one-year post-BS. Yet, RYGB patients remained with major dysbiosis one year post-BS, despite better improvement of their metabolism compared to AGB. Conclusions: We found signatures of major dysbiosis in severe obesity which include decreased MGR and related-functional alterations linked with metabolic deteriorations. The lack of full rescue post-BS, plead call for added strategies to improve the gut microbiota ecosystem and microbiome-host interactions in severe obesity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “Sixty-one severely obese subjects, candidate to”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5357218 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | No patients had received antibiotic treatment for three months pre-BS |
| SAMEA5357218 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA5357218 | health_condition | obesity | R4 | 0.50 | study.description | Sixty-one severely obese subjects |
| SAMEA5357218 | health_condition_detail | All subjects had severe obesity | R4 | 0.50 | study.description | Sixty-one severely obese subjects |
| SAMEA5357218 | location_locality | Paris | R3 | 0.70 | paper.fulltext.methods | Pitié-Salpêtrière Hospital Obesity Unit, Paris |
| SAMEA5357218 | location_site | Pitié-Salpêtrière Hospital Obesity Unit | R3 | 0.70 | paper.fulltext.methods | Pitié-Salpêtrière Hospital Obesity Unit, Paris |
| SAMEA5357237 | subject_id | 105 | R1 | 0.70 | sample.name_rule:alias | Atox105_0 |
| SAMEA5357237 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | Atox105_0 |
Sequencing
867 runs over 271 samples · mean 0.76 Gbp per run (median 0.63 Gbp, total 661.55 Gbp; 867 runs with a base count) · layout SINGLE 867 · platform ABI_SOLID 867 · models AB 5500xl Genetic Analyzer (867) · 0% of runs with a Sandpiper profile · first public 2019-02-16
Authors (20)
Aron-Wisnewsky J first · Prifti E · Belda E · Ichou F · Kayser BD · Dao MC · Verger EO · Hedjazi L · Bouillot JL · Chevallier JM · Pons N · Le Chatelier E · Levenez F · Ehrlich SD · Dore J · Zucker JD · Clément K last · Alili R first · Le P · Wirth T
Downloads
PRJEB23292.csv.gz (7.7 KB) · parquet (80.2 KB) — all 271 samples, every field with route and confidence · PRJEB23292_determinations.csv.gz (12.5 KB) — 2,043 evidence rows