Gut microbiome in bariatric surgery patients, Auckland NZ
87 gut microbiome samples from adults with obesity in Auckland, New Zealand, studied in an intervention design comparing changes following RYGB or SG bariatric surgery. machine-written summary
87 samples · 87 runs · NZ · Adult · 2020 · 4.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 697 sample values (bmi, collection date, country, diet, diet detail, intervention, location locality, subject id) |
| ✓ Abstract / description | 174 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
Surgical procedure studied before/after (bariatric surgery design randomized_controlled_trial · population obesity · Randomised RYGB vs sleeve gastrectomy bariatric surgery
“randomisation to RYGB or SG bariatric surgery” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
43 of 44 people sampled more than once (86 samples; median 2, up to 2 per person) · follow-up median 8 d (max 10 d) · median interval between samples 8 d (time from collection dates). Schedule stated by the source: “paired stool samples pre-surgery and 1 year post-surgery” (time origin: surgery); stated follow-up 12 mo.
Each row is one person (9 shown of 43); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 77 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 | 87 | 100% | ||||
| country | 87 | 100% | 87 | |||
| health_condition | 87 | 100% | 87 | |||
| subject_id | 87 | 100% | 87 | |||
| bmi | 87 | 100% | 87 | |||
| collection_date | 87 | 100% | 87 | |||
| detailed_location | 87 | 100% | ||||
| health_condition_detail | 87 | 100% | 87 | |||
| intervention | 87 | 100% | 87 | |||
| location_locality | 87 | 100% | 87 | |||
| timepoint_label | 87 | 100% | 87 | |||
| diet | 44 | 51% | 44 | |||
| diet_detail | 44 | 51% | 44 |
- Gut Microbial Predictors of Type 2 Diabetes Remission Following Bariatric Surgery. 2020 PMID 32447634 own_data
Archive description
To determine gut bacterial and predicted functional changes following randomisation to RYGB or SG bariatric surgery
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.title · “Gut microbiome changes after”
- body site study.description · “To determine gut bacterial and predicted”
- 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 |
|---|---|---|---|---|---|---|
| SAMN13258083 | bmi | 40.7 | R1 | 0.90 | sample.attr.host_body_mass_index | 40.7 |
| SAMN13258083 | collection_date | 2016-09-15 | R1 | 0.90 | biosample.attribute:collection_date | 2016-09-15 |
| SAMN13258083 | country | NZ | R1 | 0.90 | sample.attr.geo_loc_name | New Zealand:Auckland |
| SAMN13258083 | diet | therapeutic_or_study_diet | R1 | 0.90 | biosample.attribute:host_diet | VLCD |
| SAMN13258083 | diet_detail | VLCD | R1 | 0.90 | biosample.attribute:host_diet | VLCD |
| SAMN13258083 | health_condition | type2_diabetes | R4 | 0.50 | paper.abstract | 44 participants with T2D randomised to banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) |
| SAMN13258083 | health_condition_detail | participants with T2D | R4 | 0.50 | paper.abstract | 44 participants with T2D randomised to banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) |
| SAMN13258083 | intervention | surgery | R1 | 0.85 | biosample.attribute:misc_param | SG |
| SAMN13258083 | location_locality | Auckland | R1 | 0.85 | biosample.attribute:geo_loc_name | New Zealand:Auckland |
| SAMN13258083 | subject_id | 10 | R1 | 0.70 | sample.name_rule:TITLE | 10T0 |
| SAMN13258083 | timepoint_label | Pre-Surgery | R1 | 0.85 | biosample.attribute:DESCRIPTION | Pre-Surgery |
Sequencing
87 runs over 87 samples · mean 4.32 Gbp per run (median 4.33 Gbp, total 376.22 Gbp; 87 runs with a base count) · layout PAIRED 87 · platform ILLUMINA 87 · models Illumina HiSeq 2000 (87) · 89% of runs with a Sandpiper profile · first public 2020-08-08 – 2020-08-09
Authors (0)
No author record.
Downloads
PRJNA588805.csv.gz (3.5 KB) · parquet (74.8 KB) — all 87 samples, every field with route and confidence · PRJNA588805_determinations.csv.gz (7.9 KB) — 871 evidence rows