Gut microbiome in T2D adults, BBR/probiotic RCT, China
1191 gut metagenome samples from adults with type 2 diabetes in Shanghai, China, from a randomized, double-blind, placebo-controlled trial testing berberine and/or probiotics alongside antibiotic pretreatment. machine-written summary
1,192 samples · 1,192 runs · CN · Adult · 2021 · 10.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 10,786 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2 sample values (health condition, health condition detail) · PMC11170963, PMC11438002, PMC7538905, PMC8318886, PMC8726654 |
| ✓ Supplementary tables | 3,022 sample values (age, bmi, intervention, sex, subject id, timepoint) |
| – 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
405 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy Non-antibiotic pharmaceutical given as the study intervention (metformin Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population type2_diabetes · Berberine and/or probiotics vs placebo, with gentamycin run-in pretreatment
“receive BBR, probiotic with BBR, probiotics, or placebo” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
405 of 409 people sampled more than once (1,188 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “stool after 1-week gentamycin run-in, at baseline (treatment start), and post-treatment at week 13 (end of 12-week intervention)”.
Each row is one person (1 shown of 405); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1,192 | 100% | ||||
| country | 1,192 | 100% | 1,192 | |||
| health_condition | 1,192 | 100% | 1,191 | 1 | ||
| subject_id | 1,192 | 100% | 830 | 362 | ||
| health_condition_detail | 1,192 | 100% | 1,191 | 1 | ||
| intervention | 1,192 | 100% | 808 | 384 | ||
| timepoint_label | 1,192 | 100% | 2 | 1,190 | ||
| collection_date | 1,191 | 100% | 1,191 | |||
| detailed_location | 1,191 | 100% | ||||
| latitude | 1,191 | 100% | 1,191 | |||
| location_region | 1,191 | 100% | 1,191 | |||
| longitude | 1,191 | 100% | 1,191 | |||
| antibiotic_exposure | 808 | 68% | 808 | |||
| age_at_collection_days | 362 | 30% | 362 | |||
| bmi | 362 | 30% | 362 | |||
| sex | 362 | 30% | 362 |
- Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study). 2020 PMID 33024120 PMC7538905 own_data
- Combined berberine and probiotic treatment as an effective regimen for improving postprandial hyperlipidemia in type 2 diabetes patients: a double blinded placebo controlled randomized study. 2022 PMID 34923903 PMC8726654 own_data
- Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. 2021 PMID 34226711 PMC8318886 unsure
- Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs. 2024 PMID 38882498 PMC11170963 unsure
- Clinical significance of the genetically variable landscape of the gut microbiome in patients with gestational diabetes mellitus patients. 2024 PMID 39347390 PMC11438002 unsure
Archive description
We conducted a randomized, double-blind, placebo-controlled trial on newly diagnosed type 2 diabetes (T2D) patients from 20 centers in China. Eligible participants (n= 409) were randomly assigned (1:1:1:1) to receive BBR, probiotic with BBR, probiotics, or placebo for 3 months. Compared to the placebo, BBR effectively decreased the glycated hemoglobin (HbA1c) and blood lipids with its substantial impact on the gut microbiome.
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 · “The gut microbiome related effect”
- body site study.description · “impact on the gut microbiome.”
- body site study.description · “hemoglobin (HbA1c) and blood lipids with its”
- 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 |
|---|---|---|---|---|---|---|
| SAMN15421765 | age_at_collection_days | 21549.75 | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!Age (Years)] | 59 |
| SAMN15421765 | antibiotic_exposure | no | R1 | 0.85 | sample.name_rule:isolation_source | R0101_base |
| SAMN15421765 | bmi | 26.54 | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!BMI (kg/m^2)] | 26.54 |
| SAMN15421765 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN15421765 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shanghai |
| SAMN15421765 | health_condition | type2_diabetes | R1 | 0.85 | sample.name_rule:isolation_source | R0101_base |
| SAMN15422692 | health_condition | type2_diabetes | R3 | 0.70 | paper.fulltext.methods | newly diagnosed T2D according to the World Health Organization criteria |
| SAMN15421765 | health_condition_detail | base | R1 | 0.85 | sample.name_rule:isolation_source | R0101_base |
| SAMN15422692 | health_condition_detail | newly diagnosed T2D according to the World Health Organization criteria | R3 | 0.70 | paper.fulltext.methods | newly diagnosed T2D according to the World Health Organization criteria |
| SAMN15421765 | intervention | no_intervention | R1 | 0.85 | sample.name_rule:isolation_source | R0101_base |
| SAMN15421767 | intervention | drug_therapy | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!Intervention] | Berberine |
| SAMN15421765 | latitude | 31.2300 | R1 | 0.90 | biosample.attribute:lat_lon | 31.23 N 121.47 E |
| SAMN15421765 | location_region | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai |
| SAMN15421765 | longitude | 121.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 31.23 N 121.47 E |
| SAMN15421765 | sex | male | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!Sex] | male |
| SAMN15421766 | subject_id | R0101 | R1 | 0.70 | sample.name_rule:alias | R0101V2 |
| SAMN15422692 | subject_id | R1417 | R1 | 0.70 | sample.name_rule:library_name | library_name: R1417V5; isolation_source R1417_treat |
| SAMN15421765 | subject_id | R0101 | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!Patient ID] | R0101 |
| SAMN15421766 | timepoint_label | V2 | R1 | 0.70 | sample.name_rule:alias | R0101V2 |
| SAMN15422692 | timepoint_label | V5 | R1 | 0.70 | sample.name_rule:library_name | library_name: R1417V5 |
| SAMN15421765 | timepoint_label | D0 | R2 | 0.85 | paper.supp.IMT2-3-e179-s001.xlsx[ Table S2!Time] | D0 |
Sequencing
1,192 runs over 1,192 samples · mean 11.22 Gbp per run (median 10.73 Gbp, total 13,369.46 Gbp; 1,192 runs with a base count) · layout PAIRED 1,192 · platform BGISEQ 1,192 · models BGISEQ-500 (1,192) · 0% of runs with a Sandpiper profile · first public 2021-09-01
Authors (61)
Zhang Y first · Gu Y · Ren H · Wang S · Zhong H · Zhao X · Ma J · Gu X · Xue Y · Huang S · Yang J · Chen L · Chen G · Qu S · Liang J · Qin L · Huang Q · Peng Y · Li Q · Wang X · Kong P · Hou G · Gao M · Shi Z · Li X · Qiu Y · Zou Y · Yang H · Wang J · Xu G · Lai S · Li J · Ning G · Wang W last · Montassier E first · Valdés-Mas R · Batard E · Zmora N · Dori-Bachash M · Suez J · Elinav E last · Li C · Li T · Yang F · Yuan F · Li M · Zhu J · Wu K · Kristiansen K · Zhang K first · Hu M · Yang W · Hu Z · Rong Y · Luo B · Wang M · Cheng Y · Zhang R · Lv N · Zhou Q · Zhang X last
Downloads
PRJNA643353.csv.gz (34.7 KB) · parquet (119.0 KB) — all 1,192 samples, every field with route and confidence · PRJNA643353_determinations.csv.gz (118.4 KB) — 13,810 evidence rows