Gut microbiome in metformin therapy for T2D, Latvia
226 gut microbiome samples from adults with type 2 diabetes in Latvia, studied before and after metformin drug therapy in an intervention design to find biomarkers predicting treatment efficacy. machine-written summary
226 samples · 226 runs · LV · Adult · 2023 · 6.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 904 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 452 sample values (health condition, health condition detail) · PMC11178274 |
| ○ 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 not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population type2_diabetes · Metformin monotherapy in newly diagnosed T2D, sampled before/after
“before and after metformin therapy” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
66 of 160 people sampled more than once (132 samples; median 2, up to 2 per person) · follow-up median 2 mo (max 2 mo) · median interval between samples 2 mo (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Baseline (M0, pre-therapy) and M3m (3 months after metformin therapy onset), same subjects sampled twice per EXISTING_TIMEPOINT_LABELS ['1','3'] and n_subjects_with_more_than_1_sample=66”; stated follow-up 3 mo.
Each row is one person (36 shown of 66); 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 | 226 | 100% | ||||
| country | 226 | 100% | 226 | |||
| health_condition | 226 | 100% | 226 | |||
| subject_id | 226 | 100% | 226 | |||
| collection_date | 226 | 100% | 226 | |||
| health_condition_detail | 226 | 100% | 226 | |||
| timepoint_label | 226 | 100% | 226 |
- Gut microbiome encoded purine and amino acid pathways present prospective biomarkers for predicting metformin therapy efficacy in newly diagnosed T2D patients. 2024 PMID 38868903 PMC11178274 own_data
Archive description
Background Metformin is widely used for treating type 2 diabetes mellitus (T2D). However, the efficacy of metformin monotherapy is highly variable within the human population. Understanding the potential indirect or synergistic effects of metformin on gut microbiota composition and encoded functions could potentially offer new insights into predicting treatment efficacy and designing more personalized treatments in the future. We combined targeted metabolomics and metagenomic profiling of gut microbiomes in newly diagnosed T2D patients before and after metformin therapy to identify potential pre-treatment biomarkers and functional signatures for metformin efficacy and induced changes in Good metformin therapy responders.
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 encoded purine”
- body site study.description · “of metformin on gut microbiota composition 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 |
|---|---|---|---|---|---|---|
| SAMEA114090918 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA114090918 | country | LV | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Latvia |
| SAMEA114090918 | health_condition | type2_diabetes | R3 | 0.60 | paper.fulltext.results | newly diagnosed and metformin treatment naive T2D patients |
| SAMEA114090918 | health_condition_detail | newly diagnosed, treatment-naive T2D patients | R3 | 0.60 | paper.fulltext.results | newly diagnosed and metformin treatment naive T2D patients |
| SAMEA114090918 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | S1-1 |
| SAMEA114090918 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | S1-1 |
Sequencing
226 runs over 226 samples · mean 7.02 Gbp per run (median 6.74 Gbp, total 1,587.54 Gbp; 226 runs with a base count) · layout PAIRED 226 · platform DNBSEQ 226 · models DNBSEQ-G400 (226) · 0% of runs with a Sandpiper profile · first public 2023-08-13 – 2023-11-03
Authors (14)
Elbere I first · Orlovskis Z · Ansone L · Silamikelis I · Jagare L · Birzniece L · Megnis K · Leskovskis K · Vaska A · Turks M · Klavins K · Pirags V · Briviba M · Klovins J last
Downloads
PRJEB62817.csv.gz (6.7 KB) · parquet (78.8 KB) — all 226 samples, every field with route and confidence · PRJEB62817_determinations.csv.gz (9.7 KB) — 1,356 evidence rows