Gut microbiome in type 1 diabetes pregnancy, Australia
134 gut metagenome samples from pregnant women in Australia (SA, QLD, WA, NSW, VIC), comparing those with type 1 diabetes (68) to healthy controls (66) in a cross-sectional study. machine-written summary
134 samples · 134 runs · AU · Adult · 2020 · 7.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,138 sample values (age, bmi, collection date, country, health condition, health condition detail, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 38 sample values (sex) · PMC8349100 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 132 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
33 of 66 people sampled more than once (101 samples; median 3, up to 6 per person) · follow-up median 5 mo (max 3.1 y) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Up to three study visits during pregnancy, ideally one per trimester (T1, T2, T3)”.
Each row is one person (33 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 121 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 | 134 | 100% | ||||
| country | 134 | 100% | 134 | |||
| health_condition | 134 | 100% | 68 | 66 | ||
| subject_id | 134 | 100% | 134 | |||
| age_at_collection_days | 134 | 100% | 134 | |||
| bmi | 134 | 100% | 134 | |||
| collection_date | 134 | 100% | 134 | |||
| health_condition_detail | 134 | 100% | 68 | 66 | ||
| sex | 134 | 100% | 96 | 38 | ||
| timepoint_label | 124 | 93% | 124 | |||
| detailed_location | 112 | 84% | ||||
| location_region | 112 | 84% | 112 |
- Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome. 2021 PMID 34362459 PMC8349100 own_data
Archive description
Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome
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_maternal_only”
- body site study.title · “function of the gut microbiome”
- body site study.description · “function of the gut microbiome”
- life stage external_curation.infant_catalog · “infant triage reason_code age_maternal_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14001054 | age_at_collection_days | 9421.0 | R1 | 0.85 | sample.attr.host_age | 25.8 |
| SAMN14001054 | bmi | 19.1 | R1 | 0.90 | sample.attr.host_body_mass_index | 19.1 |
| SAMN14001054 | collection_date | 2016-03-31 | R1 | 0.90 | biosample.attribute:collection_date | 2016-03-31 |
| SAMN14001054 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: WA |
| SAMN14001057 | health_condition | type1_diabetes | R1 | 0.90 | biosample_attr | T1D |
| SAMN14001054 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN14001057 | health_condition_detail | T1D | R1 | 0.90 | sample.attr.host_disease | T1D |
| SAMN14001054 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN14001057 | location_region | South Australia | R1 | 0.75 | biosample.attribute:geo_loc_name | Australia: SA |
| SAMN14001054 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN18022843 | sex | female | R3 | 0.70 | paper.fulltext.methods | 70 pregnancies in women participating in the ENDIA |
| SAMN14001054 | subject_id | 378 | R1 | 0.85 | sample.attr.host_subject_id | 378 |
| SAMN14001054 | timepoint_label | T1 | R1 | 0.85 | biosample.attribute:pregnancy_trimester | T1 |
| SAMN18022843 | timepoint_label | T3 | R1 | 0.70 | sample.name_rule:alias | 0369_2_T3_M |
Sequencing
134 runs over 134 samples · mean 7.14 Gbp per run (median 7.06 Gbp, total 957.07 Gbp; 134 runs with a base count) · layout PAIRED 134 · platform ILLUMINA 134 · models Illumina NovaSeq 6000 (134) · 90% of runs with a Sandpiper profile · first public 2020-02-18 – 2021-05-23
Authors (26)
Roth-Schulze AJ first · Penno MAS · Ngui KM · Oakey H · Bandala-Sanchez E · Smith AD · Allnutt TR · Thomson RL · Vuillermin PJ · Craig ME · Rawlinson WD · Davis EA · Harris M · Soldatos G · Colman PG · Wentworth JM · Haynes A · Barry SC · Sinnott RO · Morahan G · Bediaga NG · Smyth GK · Papenfuss AT · Couper JJ · Harrison LC · ENDIA Study Group last
Downloads
PRJNA604850.csv.gz (6.2 KB) · parquet (78.4 KB) — all 134 samples, every field with route and confidence · PRJNA604850_determinations.csv.gz (12.0 KB) — 1,308 evidence rows