Gut microbiome and mental distress in pregnancy, Sweden & USA
Shotgun metagenomics of 926 fecal samples from 530 pregnant women across 2nd and 3rd trimester in Swedish (n=765) and U.S. (n=161) cohorts, examining gut microbiome composition and gut-brain modules in relation to mental distress. machine-written summary
926 samples · 1,004 runs · SE, US · Adult · 2024 · 12.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,770 sample values (age, bmi, collection date, country, health condition, health condition detail, sex, subject id) |
| ✓ Abstract / description | 2,085 sample values (collection date, location region, location site) |
| ○ Full text | read; no usable statement or table · PMC11925571, PMC12690974, PMC6830667 |
| ○ 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 |
longitudinal
396 of 530 people sampled more than once (792 samples; median 2, up to 2 per person) · follow-up median 3 mo (max 11 mo) · median interval between samples 3 mo (time from collection dates).
Each row is one person (36 shown of 396); 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 | 926 | 100% | ||||
| country | 926 | 100% | 926 | |||
| health_condition | 872 | 94% | 872 | |||
| subject_id | 926 | 100% | 926 | |||
| collection_date | 926 | 100% | 693 | 233 | ||
| detailed_location | 926 | 100% | ||||
| location_region | 926 | 100% | 926 | |||
| location_site | 926 | 100% | 926 | |||
| sex | 926 | 100% | 926 | |||
| timepoint_label | 926 | 100% | 926 | |||
| age_at_collection_days | 918 | 99% | 918 | |||
| health_condition_detail | 872 | 94% | 872 | |||
| bmi | 711 | 77% | 711 |
- Cohort profile: the Biology, Affect, Stress, Imaging and Cognition (BASIC) study on perinatal depression in a population-based Swedish cohort. 2019 PMID 31641004 PMC6830667 cites_accession
- Predicting allergy and postpartum depression from an incomplete compositional microbiome. 2025 PMID 41353127 PMC12690974 cites_accession
- Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts. 2025 PMID 40115744 PMC11925571 own_data
Archive description
With the population-based, prospective Biology, Affect, Stress, Imaging and Cognition (BASIC) cohort, we aim to investigate the biopsychosocial aetiological processes involved in perinatal depression (PND) and to pinpoint its predictors in order to improve early detection. From September 2009 to November 2018, the BASIC study at Uppsala University Hospital, Sweden, has enrolled 5492 women, in 6478 pregnancies, of which 46.3% first-time pregnancies and with an average age of 31.5 years. After inclusion around gestational week 16–18, participants are followed-up with data collection points around gestational week 32, at childbirth, as well as three times postpartum: after 6 weeks, 6 months and 1 year. At the last follow-up, 70.8% still remain in the cohort.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by curator_audit with confidence 0.45. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (1004)”
- host runs.environment_material · “Feces (1004)”
- body site runs.scientific_name · “human gut metagenome (1004)”
- body site runs.environment_material · “Feces (1004)”
- life stage study.description · “with an average age of 31.5 years”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114289787 | age_at_collection_days | 11688.0 | R1 | 0.85 | biosample.attribute:host_age | 32 years |
| SAMEA114289801 | age_at_collection_days | 13149.0 | R1 | 0.85 | sample.attr.host_age | 36 |
| SAMEA114289787 | bmi | 21.51 | R1 | 0.85 | biosample.attribute:host_body_mass_index | 21.51 kg/m2 |
| SAMEA114289787 | collection_date | 2017-01-03 | R1 | 0.85 | biosample.attribute:collection_date | 2017-01-03 |
| SAMEA114289849 | collection_date | 2009-09/2018-11 | R4 | 0.50 | paper.abstract | From September 2009 to November 2018 |
| SAMEA114289787 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA114289787 | health_condition | neurological_psychiatric | R1 | 0.85 | biosample.attribute:host_disease_status_at_3rd_trimester | Depressed |
| SAMEA114289814 | health_condition | neurological_psychiatric | R1 | 0.85 | biosample.attribute:host_disease_status_at_2nd_trimester | Depressed |
| SAMEA114289787 | health_condition_detail | depressed at 3rd trimester of pregnancy | R1 | 0.85 | biosample.attribute:host_disease_status_at_3rd_trimester | Depressed |
| SAMEA114289814 | health_condition_detail | depressed at 2nd trimester of pregnancy | R1 | 0.85 | biosample.attribute:host_disease_status_at_2nd_trimester | Depressed |
| SAMEA114289787 | location_region | Uppsala | R4 | 0.50 | paper.abstract | BASIC study at Uppsala University Hospital, Sweden |
| SAMEA114289787 | location_site | Uppsala University Hospital | R4 | 0.50 | paper.abstract | BASIC study at Uppsala University Hospital, Sweden |
| SAMEA114289787 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA114289787 | subject_id | 24423 | R1 | 0.85 | biosample.attribute:host_subject_id | 24423 |
| SAMEA114289787 | timepoint_label | 3rd trimester | R1 | 0.85 | biosample.attribute:description | fecal sample from Subject 24423 taken in the 3rd trimester |
Sequencing
1,004 runs over 926 samples · mean 12.08 Gbp per run (median 11.94 Gbp, total 12,132.56 Gbp; 1,004 runs with a base count) · layout PAIRED 1,004 · platform DNBSEQ 1,004 · models DNBSEQ-G400 (1,004) · 0% of runs with a Sandpiper profile · first public 2024-08-29 – 2024-09-23
Authors (13)
Axfors C first · Bränn E · Henriksson HE · Hellgren C · Kunovac Kallak T · Fransson E · Lager S · Iliadis SI · Sylvén S · Papadopoulos FC · Ekselius L · Sundström-Poromaa I · Skalkidou A last
Downloads
PRJEB62678.csv.gz (32.6 KB) · parquet (114.0 KB) — all 926 samples, every field with route and confidence · PRJEB62678_determinations.csv.gz (77.2 KB) — 9,855 evidence rows