Gut microbiota in T2D diet intervention, China
220 gut metagenome samples from adults in China, from a diet intervention study (WTP diet vs usual care) in type 2 diabetes patients, examining gut microbiota changes and clinical parameters. machine-written summary
220 samples · 220 runs · CN · Adult · 2018 · 15.01 Gbp / sample
One study deposited as 2 BioProjects (392 catalog samples together): PRJEB14155 · PRJEB15179 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,540 sample values (collection date, country, health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10408196, PMC10989819 |
| – 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 resolved
Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · population type2_diabetes · WTP diet vs usual care in T2D patients
“T2D patients were randomly divided into two groups receiving WTP diet or” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
110 of 110 people sampled more than once (220 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 194 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 | 220 | 100% | ||||
| country | 220 | 100% | 220 | |||
| health_condition | 220 | 100% | 220 | |||
| subject_id | 220 | 100% | 220 | |||
| collection_date | 220 | 100% | 220 | |||
| health_condition_detail | 220 | 100% | 220 | |||
| intervention | 220 | 100% | 220 | |||
| timepoint_label | 220 | 100% | 220 |
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196 unsure
- A neural network-based framework to understand the type 2 diabetes-related alteration of the human gut microbiome. 2022 PMID 38868565 PMC10989819 unsure
Archive description
T2D patients were randomly divided into two groups receiving WTP diet or usual care. The gut microbiota changed and the host clinical parameters were improved. Several key bacteria were identified.
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 · “diet to modulate gut microbiota to alleviate”
- body site study.description · “usual care. The gut microbiota changed and”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA4385395 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA4385395 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA4385395 | health_condition | type2_diabetes | R1 | 0.70 | biosample.name_rule:alias | 1U001 |
| SAMEA4385395 | health_condition_detail | T2D patients (project description) | R1 | 0.70 | biosample.name_rule:alias | 1U001 |
| SAMEA4385395 | intervention | no_intervention | R1 | 0.70 | biosample.name_rule:alias | 1U001 |
| SAMEA4385395 | subject_id | U001 | R1 | 0.70 | biosample.name_rule:alias | 1U001 |
| SAMEA4385395 | timepoint_label | 1 | R1 | 0.70 | biosample.name_rule:alias | 1U001 |
Sequencing
220 runs over 220 samples · mean 14.83 Gbp per run (median 15.01 Gbp, total 3,262.75 Gbp; 220 runs with a base count) · layout PAIRED 220 · platform ILLUMINA 220 · models Illumina HiSeq 2500 (220) · 88% of runs with a Sandpiper profile · first public 2018-03-11
Authors (11)
Chen J first · Siliceo SL · Ni Y · Nielsen HB · Xu A · Panagiotou G last · Guo S first · Zhang H · Chu Y · Jiang Q · Ma Y last
Downloads
PRJEB15179.csv.gz (6.0 KB) · parquet (77.6 KB) — all 220 samples, every field with route and confidence · PRJEB15179_determinations.csv.gz (13.6 KB) — 1,540 evidence rows