T1D multiplex families, gut microbiome, Luxembourg
184 faecal samples from a Luxembourg family study of type 1 diabetes, including healthy controls and type 1 and type 2 diabetes cases; cross-sectional, multi-omics design examining microbiota, lifestyle and genetic background. machine-written summary
184 samples · 184 runs · LU · Age unknown · 2016 · 3.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,116 sample values (age, bmi, collection date, country, family id, family role, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10939349, PMC12440900, PMC6780314, PMC8715853, PMC9795701 |
| ✓ Supplementary tables | 179 sample values (age, bmi, health condition, health condition detail, sex) |
| ✓ External resources | 59 sample values (antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: sequence archive and supplementary table disagree for 1 sample (e.g. 3287.0 vs 12418) — withheld; bmi: sequence archive and supplementary table disagree for 1 sample (e.g. 24.0 vs 38.0) — withheld; health condition: sequence archive and supplementary table disagree for 14 samples (e.g. healthy_control vs liver_disease) — withheld; sex: sequence archive and supplementary table disagree for 1 sample (e.g. male vs female) — withheld.
The sources disagree on 15 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 (17)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN09837400 | age | 3287.0 (sequence archive) | 12418 (supplementary table) | withheld: neither value published |
| SAMN09837400 | bmi | 24.0 (sequence archive) | 38.0 (supplementary table) | withheld: neither value published |
| SAMN04571734 | health condition | healthy_control (supplementary table) | liver_disease (curatedMetagenomicData) | withheld: neither value published |
| SAMN04571735 | health condition | healthy_control (supplementary table) | liver_disease (curatedMetagenomicData) | withheld: neither value published |
| SAMN04571736 | health condition | healthy_control (supplementary table) | liver_disease (curatedMetagenomicData) | withheld: neither value published |
| SAMN09837361 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837362 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837363 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837364 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837365 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837438 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837439 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837440 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837441 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837442 | health condition | type2_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09842366 | health condition | type1_diabetes (sequence archive) | healthy_control (supplementary table) | withheld: neither value published |
| SAMN09837400 | sex | male (sequence archive) | female (supplementary table) | withheld: neither value published |
longitudinalfamiliesmother–infantparent–childsiblings
44 of 44 people sampled more than once (184 samples; median 4, up to 6 per person) · follow-up median 2 mo (max 4 mo) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “Three visits (V1, V2, V3) at intervals of 4-8 weeks” (time origin: enrolment).
Each row is one person (32 shown of 44); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
T1D multiplex families: 7 families committed (M01-M08), parents, children, siblings; family M11 withheld · 7 families with 32 sampled people (7 with a parent and a child).
motherfatherchildsibling · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 7 linked groups from explicit relations. 44 people in the project overall.
Families (7)
Genera, mean relative abundance over 158 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 184 | 100% | ||||
| country | 184 | 100% | 184 | |||
| health_condition | 168 | 91% | 81 | 87 | ||
| subject_id | 184 | 100% | 184 | |||
| collection_date | 184 | 100% | 184 | |||
| latitude | 184 | 100% | 184 | |||
| longitude | 184 | 100% | 184 | |||
| age_at_collection_days | 183 | 99% | 181 | 2 | ||
| sex | 183 | 99% | 181 | 2 | ||
| health_condition_detail | 182 | 99% | 92 | 90 | ||
| timepoint_label | 182 | 99% | 182 | |||
| bmi | 179 | 97% | 175 | 4 | ||
| family_id | 152 | 83% | 152 | |||
| family_role | 152 | 83% | 152 | |||
| antibiotic_exposure | 53 | 29% | 53 |
- Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. 2016 PMID 27723761 own_data
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract. 2016 PMID 27445992 PMC4914512 own_data
- Extensive transmission of microbes along the gastrointestinal tract. 2019 PMID 30747106 PMC6424576 own_data
- Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. 2019 PMID 31546776 PMC6780314 own_data
11 more
- Macrel: antimicrobial peptide screening in genomes and metagenomes. 2020 PMID 33384902 PMC7751412
- Quantitative Analysis and Visualization of the Interaction Between Intestinal Microbiota and Type 1 Diabetes in Children Based on Multi-Databases. 2021 PMID 34976889 PMC8715853
- Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses. 2022 PMID 36578059 PMC9795701
- Functional prediction of proteins from the human gut archaeome. 2024 PMID 38486809 PMC10939349
- Characterization of the oral virome in patients with diabetes mellitus. 2025 PMID 40969555 PMC12440900
- Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. 2020 PMID 32534441 PMC7298543
- Dispersal strategies shape persistence and evolution of human gut bacteria. 2021 PMID 34111423 PMC8288446
- Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype. 2023 PMID 36706753 PMC9975273
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome. 2025 PMID 40790024 PMC12340149
Archive description
Recent evidence from high-resolution molecular studies suggests links between microbial dysbiosis in the gastrointestinal tract and a number of complex chronic diseases including diabetes mellitus. The present study forms a pilot study for the larger Luxembourg-based Diabetes Multiplex Family Study (MUST). Within the pilot study, we investigate the interplay of the gastrointestinal microbiota, lifestyle and genetic background in an observational study of families with two or more individuals affected by type 1 diabetes mellitus. Faecal samples which have undergone comprehensive biomolecular extractions are currently analysed using a multi-omics approach. Anthropometric data, including demographics, medical history, health status, medication, and dietary habits of all study participants were collected and are integrated with molecular data.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and adolescent and child by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- life stage sample.attr.host_age · “58 years (n=98/184)”
- life stage sample.attr.host_age · “14 years (n=37/184)”
- life stage sample.attr.host_age · “5 years (n=23/184)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04571684 | age_at_collection_days | 22646.0 | R1 | 0.90 | sample.attr.host_age | 62 years |
| SAMN09842354 | age_at_collection_days | 18262 | R2 | 0.85 | paper.supp.elife-42693-supp1.xlsx[Sheet1!age] | 50 |
| SAMN04571684 | antibiotic_exposure | yes | R2 | 0.70 | external.meta2db source | antibiotics: TRUE |
| SAMN04571687 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN04571684 | bmi | 25.0 | R1 | 0.90 | sample.attr.host_body_mass_index | 25 |
| SAMN04571697 | bmi | 18.31 | R2 | 0.85 | paper.supp.elife-42693-supp1.xlsx[Sheet1!bmi] | 18.31 |
| SAMN04571684 | collection_date | 2012-06-01 | R1 | 0.90 | biosample.attribute:collection_date | 2012-06-01 |
| SAMN04571684 | country | LU | R1 | 0.90 | sample.attr.geo_loc_name | Luxembourg |
| SAMN04571684 | family_id | M01 | R1 | 0.70 | biosample.attribute:host_subject_id | host_subject_id M01.1; father of M01.4; brother of M01.3 |
| SAMN04571684 | family_role | father | R1 | 0.85 | biosample.attribute:host_family_relationship | father of M01.4; brother of M01.3 |
| SAMN04571684 | health_condition | type1_diabetes | R1 | 0.90 | biosample_attr | type 1 diabetes mellitus |
| SAMN04571687 | health_condition | healthy_control | R2 | 0.80 | paper.supp.elife-42693-supp1.xlsx[Sheet1!group] | control |
| SAMN04571722 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN04571732 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04571684 | health_condition_detail | type 1 diabetes mellitus | R1 | 0.90 | sample.attr.host_disease | type 1 diabetes mellitus |
| SAMN04571687 | health_condition_detail | control | R2 | 0.85 | paper.supp.elife-42693-supp1.xlsx[Sheet1!group] | control |
| SAMN04571722 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN04571732 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04571684 | latitude | 49.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 49.5 N 6.2 E |
| SAMN04571684 | longitude | 6.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 49.5 N 6.2 E |
| SAMN04571684 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN09842354 | sex | female | R2 | 0.85 | paper.supp.elife-42693-supp1.xlsx[Sheet1!sex] | F |
| SAMN04571684 | subject_id | M01.1 | R1 | 0.85 | sample.attr.host_subject_id | M01.1 |
| SAMN04571684 | timepoint_label | V1 | R1 | 0.70 | sample.name_rule:sample_alias | M01.1-V1-stool |
Sequencing
184 runs over 184 samples · mean 3.61 Gbp per run (median 3.73 Gbp, total 664.59 Gbp; 184 runs with a base count) · layout PAIRED 184 · platform ILLUMINA 184 · models Illumina HiSeq 4000 (119), Illumina HiSeq 2000 (53), NextSeq 500 (12) · 86% of runs with a Sandpiper profile · first public 2016-08-13 – 2020-08-02
Authors (75)
Heintz-Buschart A first · May P · Laczny CC · Lebrun LA · Bellora C · Krishna A · Wampach L · Schneider JG · Hogan A · de Beaufort C · Wilmes P last · Schmidt TS first · Hayward MR · Coelho LP · Li SS · Costea PI · Voigt AY · Wirbel J · Maistrenko OM · Alves RJ · Bergsten E · Sobhani I · Sunagawa S · Zeller G · Bork P last · Tisza MJ first · Buck CB last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Kiguchi Y first · Hamamoto N · Kashima Y · Runtuwene LR · Ishizaka A · Kuze Y · Enokida T · Tanaka N · Tahara M · Kageyama SI · Fujisawa T · Yamashita R · Kanai A · Tuda JSB · Mizutani T · Suzuki Y last · Zhang Y first · Xing G · Mei T · Wang M · Huang C · Yi H · Zhan Y · Yang S · Yan Q · Li S · Chen C last
Downloads
PRJNA289586.csv.gz (7.4 KB) · parquet (80.2 KB) — all 184 samples, every field with route and confidence · PRJNA289586_determinations.csv.gz (22.3 KB) — 2,354 evidence rows