Metformin and gut microbiome in T2D, Latvia, longitudinal
203 stool samples from Latvian adults in a longitudinal drug-therapy study, comparing healthy individuals and newly-diagnosed type 2 diabetes patients to assess how metformin affects gut microbiome composition and relates to treatment efficacy. machine-written summary
203 samples · 203 runs · LV · Adult · 2021 · 0.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,015 sample values (health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 203 sample values (country) · PMC7598494 |
| ○ 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 |
intervention · arms resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population type2_diabetes · Metformin 2x850mg/day; healthy and newly-diagnosed T2D patients sampled over time
“35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points” — abstract:33125401 (study level; per-sample arms are in the intervention column below)
longitudinal
85 of 85 people sampled more than once (203 samples; median 2, up to 3 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 2.0 y (time from timepoint labels). Schedule stated by the source: “Healthy cohort sampled at M0, M24h, M7d; T2D cohort sampled at M0 and M7d relative to metformin start.” (time origin: intervention_start); stated follow-up 7 d.
Each row is one person (1 shown of 85); 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 | 203 | 100% | ||||
| country | 203 | 100% | 203 | |||
| health_condition | 203 | 100% | 203 | |||
| subject_id | 203 | 100% | 203 | |||
| health_condition_detail | 203 | 100% | 203 | |||
| intervention | 203 | 100% | 203 | |||
| timepoint_label | 203 | 100% | 203 |
- Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients. 2020 PMID 33125401 PMC7598494 own_data
- Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. 2024 PMID 38767350 PMC11237675 unsure
Archive description
BackgroundThe study was conducted to investigate the effects of metformin treatment on the human gut microbiome’s taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with the therapeutic efficacy and tolerance.MethodsIn this longitudinal observational study, stool samples for shotgun metagenomic sequencing based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose – determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by ≥12.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%).ResultsMetformin reduced the alpha diversity of microbiota in healthy controls (p=0.02) but not in T2D patients. Reduction in the abundance of Clostridium bartlettii overlapped between both study groups, and a large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR=0.01) in Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts.ConclusionsMetformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.
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 · “Baseline gut microbiome composition predicts”
- body site study.description · “on the human gut microbiome’s taxonomic 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 |
|---|---|---|---|---|---|---|
| SAMEA10018470 | country | LV | R3 | 0.70 | paper.fulltext.abstract | Latvian population |
| SAMEA10018470 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | S1_M0-H |
| SAMEA10018470 | health_condition_detail | H | R1 | 0.70 | sample.name_rule:alias | S1_M0-H |
| SAMEA10018470 | intervention | drug_therapy | R1 | 0.70 | sample.name_rule:alias | S1_M0-H |
| SAMEA10018470 | subject_id | S1 | R1 | 0.70 | sample.name_rule:alias | S1_M0-H |
| SAMEA10018470 | timepoint_label | M0 | R1 | 0.70 | sample.name_rule:alias | S1_M0-H |
Sequencing
203 runs over 203 samples · mean 1.12 Gbp per run (median 0.95 Gbp, total 227.69 Gbp; 203 runs with a base count) · layout SINGLE 203 · platform ION_TORRENT 203 · models Ion Torrent Proton (203) · 0% of runs with a Sandpiper profile · first public 2021-10-22
Authors (21)
Elbere I first · Silamikelis I · Dindune II · Kalnina I · Briviba M · Zaharenko L · Silamikele L · Rovite V · Gudra D · Konrade I · Sokolovska J · Pirags V · Klovins J last · Van Syoc E first · Nixon MP · Silverman JD · Luo Y · Gonzalez FJ · Patterson AD · Rogers CJ · Ganda E last
Downloads
PRJEB39500.csv.gz (5.7 KB) · parquet (76.7 KB) — all 203 samples, every field with route and confidence · PRJEB39500_determinations.csv.gz (11.3 KB) — 1,218 evidence rows