PRJEB1786 ERP002469
Gut metagenome in European women with glucose control status
Gut metagenome in European women with normal, impaired and diabetic glucose control
Case-control study of 145 gut metagenome samples from European women with type 2 diabetes (102), or as healthy controls (43), all classified as elderly. machine-written summary
145 samples · 145 runs · SE, DE, SK · Adult · 2013 · 2.81 Gbp / sample
Sources
○Sequence archive✓Abstract / description 145○Full text○Supplementary tables✓External resources 966–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 145 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC11351283, PMC4389708, PMC4610706, PMC7218625, PMC8201803, PMC8908641, PMC9592851 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 966 sample values (age, antibiotic exposure, bmi, country, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
10 countries
Age
elderly145
Condition
type2_diabetes53
healthy_control43
Sex
female145
Country
SE130
DE4
SK3
DK2
EE1
FI1
+2 more
Body site
primary145
Sequencing depth per sample · this project all projects
! Self-contradictory metadata
health condition: curatedMetagenomicData and GMrepo disagree for 49 samples (e.g. type2_diabetes vs healthy_control) — withheld.
The sources disagree on 49 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 49)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA1906415 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906416 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906419 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906423 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906425 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906429 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906430 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906434 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906440 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906447 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906452 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906457 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906466 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906468 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906477 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906480 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906485 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906494 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906496 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906498 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906501 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906507 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906510 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906516 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906518 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906526 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906527 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906532 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906534 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906535 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906536 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906537 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906541 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906542 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906544 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906547 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906552 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906555 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906559 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
| SAMEA1906561 | health condition | type2_diabetes (curatedMetagenomicData) | healthy_control (GMrepo) | withheld: neither value published |
Community composition
Roseburia 6.6%Blautia_A 6.4%Faecalibacterium 5.2%Ruminococcoides 4.1%Bacteroides 4.0%Gemmiger 3.2%Phocaeicola 2.2%Bifidobacterium 2.0%Alistipes 2.0%Anaerostipes 1.8%Vescimonas 1.7%Coprococcus 1.6%not assigned to a genus 9.3%other genera 50.0%
Genera, mean relative abundance over 135 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 145 | 100% | ||||
| country | 145 | 100% | 145 | |||
| health_condition | 96 | 66% | 96 | |||
| subject_id | 145 | 100% | 145 | |||
| age_at_collection_days | 145 | 100% | 145 | |||
| antibiotic_exposure | 145 | 100% | 145 | |||
| bmi | 145 | 100% | 145 | |||
| health_condition_detail | 145 | 100% | 145 | |||
| sex | 145 | 100% | 145 |
Papers (45)
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. 2015 PMID 25853934 PMC4389708 own_data
- Type 2 Diabetes Biomarkers of Human Gut Microbiota Selected via Iterative Sure Independent Screening Method. 2015 PMID 26479726 PMC4610706 own_data
- TAMA: improved metagenomic sequence classification through meta-analysis. 2020 PMID 32397982 PMC7218625 own_data
- MetaDecoder: a novel method for clustering metagenomic contigs. 2022 PMID 35272700 PMC8908641 own_data
40 more
- Potential of gut microbiota for lipopolysaccharide biosynthesis in European women with type 2 diabetes based on metagenome. 2022 PMID 36303603 PMC9592851
- The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine. 2024 PMID 39206042 PMC11351283
- The Amordad database engine for metagenomics. 2014 PMID 24974201 PMC4184256
- Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. 2015 PMID 26633628 PMC4681099
- Subspecies in the global human gut microbiome. 2017 PMID 29242367 PMC5740502
- Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures. 2018 PMID 29774017 PMC5943621
- MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations. 2019 PMID 31387630 PMC6683435
- Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy. 2019 PMID 31474368 PMC6736778
- Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. 2020 PMID 31910889 PMC6947943
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. 2020 PMID 31940321 PMC6961876
- MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota. 2020 PMID 31964767 PMC6977071
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. 2020 PMID 32093762 PMC7038607
- Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. 2020 PMID 32534441 PMC7298543
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. 2020 PMID 33372654 PMC7861615
- Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
- Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. 2022 PMID 35087227 PMC8813618
- Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. 2022 PMID 35273169 PMC8913745
- Human disease prediction from microbiome data by multiple feature fusion and deep learning. 2022 PMID 35372808 PMC8971930
- MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples. 2022 PMID 35629336 PMC9143510
- Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders. 2022 PMID 35754734 PMC9213702
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population. 2022 PMID 36564713 PMC9789565
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. 2023 PMID 37188815 PMC10234815
- Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
- Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. 2023 PMID 37932270 PMC10628233
- High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation. 2024 PMID 38233648 PMC11287798
- Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift. 2024 PMID 38265338 PMC10810176
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. 2024 PMID 38767350 PMC11237675
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. 2024 PMID 38884260 PMC11317153
- Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. 2024 PMID 38918632 PMC11620793
- Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria. 2025 PMID 40624564 PMC12235815
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464
- Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations. 2026 PMID 41927536 PMC13057204
- Network topology of the gut microbiome associates with metabolic health in obesity. 2026 PMID 42129189 PMC13172010
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Details
Archive description
Gut metagenome in European women with normal, impaired and diabetic glucose control
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 metagenome in European”
- body site study.description · “Gut metagenome in European”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “metagenome in European women with normal, impaired”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA1906415 | age_at_collection_days | 25202.25 | R2 | 0.75 | external.cmd source | age: 69; age_unit: Year; age_group: Elderly |
| SAMEA1906415 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA1906415 | bmi | 24.0 | R2 | 0.75 | external.cmd source | bmi: 24 |
| SAMEA1906415 | country | SE | R2 | 0.75 | external.cmd source | country: Sweden |
| SAMEA1906417 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA1906415 | health_condition_detail | Glucose Intolerance | R2 | 0.75 | external.cmd source | disease: Glucose Intolerance |
| SAMEA1906415 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA1906415 | subject_id | SAMEA1906415 | R4 | 0.60 | design.one_sample_per_subject:abstract | characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control |
Sequencing
145 runs over 145 samples · mean 3.13 Gbp per run (median 2.81 Gbp, total 453.47 Gbp; 145 runs with a base count) · layout PAIRED 145 · platform ILLUMINA 145 · models Illumina HiSeq 2000 (145) · 93% of runs with a Sandpiper profile · first public 2013-05-16 – 2013-05-21
Authors (63)
Tisza MJ first · Buck CB last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last · Zhu J first · Jiang MZ · Chen X · Li M · Wang YL · Liu C · Liu SJ · Chen WH last · Jiang Y first · Che L · Li SC last · Dong Y first · Wang M · Zhou X · Wang P · Yan K · Wang S · Zhong JC · Li H · Zhao L · Li B · Li J last · Lacruz-Pleguezuelos B first · Pérez-Cuervo A · Coleto-Checa D · Bazán GX · Romero-Tapiador S · Freixer G · Fernández-Cabezas J · Aguilar-Aguilar E · Martín-Segura A · Cárdenas-Roig N · Carrasco-Guijarro L · Fernández LP · Espinosa-Salinas I · Ramírez de Molina A · Morales A · Tolosana R · Ortega-Garcia J · Pancaldi V · Marcos-Zambrano LJ · Carrillo de Santa Pau E last
Downloads
PRJEB1786.csv.gz (5.3 KB) · parquet (77.1 KB) — all 145 samples, every field with route and confidence · PRJEB1786_determinations.csv.gz (14.1 KB) — 1,111 evidence rows
Samples (145 · every field this project has values for · hover a cell for its source)
Loading the sample table…