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PRJNA910923 SRP412385

Metformin and gut microbiota in T2D, Zhengzhou, China

Gut microbiota accelerate metformin-induced vitamin B12 deficiency

26 gut metagenome samples from adult type 2 diabetes patients in Zhengzhou, China, in a prospective intervention study examining metformin drug therapy and vitamin B12 deficiency. machine-written summary

26 samples · 26 runs · CN · Adult · 2023 · 10.72 Gbp / sample

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Sources
✓Sequence archive 273○Abstract / description✓Full text 26○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive273 sample values (age, collection date, country, health condition, health condition detail, intervention, latitude, location locality)
○ Abstract / descriptionread; no usable statement
✓ Full text26 sample values (location site) · PMC10366088
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

drugdrug26 samples
single arm: samples on the intervention (no pre-intervention samples labelled)

Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population type2_diabetes · Metformin treatment 3-6 months in T2D patients

“3 to 6 months metformin treatments” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
2 sampling locations · 1 country
Age
adult26
Condition
type2_diabetes26
Sex
male16
female10
Country
CN26
Body site
primary26
Collected 2019–2020
2019: 18 samples2020: 8 samples20192020
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 3 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 23 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 10.72 Gbp per sample0130Gbp
Community composition
Megamonas 12.4%Bacteroides 11.2%Bifidobacterium 9.1%Phocaeicola 7.6%Roseburia 6.2%Blautia_A 5.5%Faecalibacterium 4.2%Mediterraneibacter 2.1%Fusicatenibacter 2.1%Prevotella 2.0%Collinsella 1.4%Lachnospira 1.4%not assigned to a genus 2.3%other genera 32.6%

Genera, mean relative abundance over 24 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category26 100%
country26 100%26
health_condition26 100%26
subject_id0 0%
age_at_collection_days26 100%26
collection_date26 100%26
detailed_location26 100%
health_condition_detail26 100%26
intervention26 100%26
latitude26 100%26
location_locality26 100%26
location_site26 100%26
longitude26 100%26
sex26 100%26
location_region13 50%13
Papers (1)
  • Bacteroides ovatus accelerates metformin-induced vitamin B12 deficiency in type 2 diabetes patients by accumulating cobalamin. 2023 PMID 37488134 PMC10366088 own_data
Details
Archive description

In this study, we designed a prospective clinical trial to study vitamin B12 deficiency patients pertinent to gut microbiota in 3 to 6 months metformin treatments.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “gut metagenome”
  • life stage sample.attr.host_age · “47 (n=24/26)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN32151044age_at_collection_days22280.2R10.70sample.attr.host_age61
SAMN32151044collection_date2019-11R10.90biosample.attribute:collection_date2019-11
SAMN32151044countryCNR10.90sample.attr.geo_loc_nameChina: Zhengzhou
SAMN32151044health_conditiontype2_diabetesR10.90biosample_attrType 2 Diabetes Mellitus
SAMN32151044health_condition_detailType 2 Diabetes MellitusR10.90sample.attr.host_diseaseType 2 Diabetes Mellitus
SAMN32151044interventiondrug_therapyR10.85biosample.attribute:chem_administrationmetformin
SAMN32151044latitude34.7600R10.90biosample.attribute:lat_lon34.76 N 113.62 E
SAMN32151044location_localityZhengzhouR10.85biosample.attribute:geo_loc_nameChina: Zhengzhou
SAMN32151044location_regionHenan ShengR10.60biosample.attribute:lat_lon34.76 N 113.62 E
SAMN32151044location_siteZhengzhou Central Hospital Affiliated to Zhengzhou UniversityR30.70paper.fulltext.methodsZhengzhou Central Hospital Affiliated to Zhengzhou University
SAMN32151044longitude113.6200R10.90biosample.attribute:lat_lon34.76 N 113.62 E
SAMN32151044sexmaleR10.90sample.attr.host_sexmale
Sequencing

26 runs over 26 samples · mean 10.57 Gbp per run (median 10.72 Gbp, total 274.82 Gbp; 26 runs with a base count) · layout PAIRED 26 · platform ILLUMINA 26 · models Illumina NovaSeq 6000 (26) · 92% of runs with a Sandpiper profile · first public 2023-07-25

Authors (8)

Chen M first · Shu Y · Li Q · Kang Z · Liu T · Zhou H · Huang W · Zhang W last

Downloads

PRJNA910923.csv.gz (2.0 KB) · parquet (72.6 KB) — all 26 samples, every field with route and confidence · PRJNA910923_determinations.csv.gz (3.2 KB) — 299 evidence rows

Samples (26 · every field this project has values for · hover a cell for its source)
Loading the sample table…