Placenta, saliva, vaginal, rectal samples at term delivery
223 samples from adult women in Sweden, including placenta biopsies, saliva, and vaginal/rectal swabs collected at delivery; cross-sectional design. Note: the attached paper abstract describes a differently-sized pregnant vs. non-pregnant saliva study and does not clearly match this archive record. machine-written summary
223 samples · 223 runs · SE · Adult · 2020 · 0.17 Gbp / sample · cohort Shotgun metagenomic mapping of saliva reveals insi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,151 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, location locality) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10024458 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure · Cohort defined by planned C-section vs vaginal delivery; samples collected at delivery
Genera, mean relative abundance over 57 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 | 223 | 100% | ||||
| country | 223 | 100% | 223 | |||
| health_condition | 85 | 38% | 85 | |||
| subject_id | 223 | 100% | 223 | |||
| age_at_collection_days | 223 | 100% | 223 | |||
| collection_date | 223 | 100% | 223 | |||
| detailed_location | 223 | 100% | ||||
| location_locality | 223 | 100% | 223 | |||
| sex | 223 | 100% | 223 | |||
| bmi | 211 | 95% | 211 | |||
| medication | 211 | 95% | 211 | |||
| antibiotic_exposure | 149 | 67% | 149 | |||
| health_condition_detail | 88 | 39% | 88 | |||
| medication_detail | 69 | 31% | 69 |
- Evaluation of Modulatory Activities of Lactobacillus crispatus Strains in the Context of the Vaginal Microbiota. 2022 PMID 35266820 PMC9045136 unsure
- Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets. 2023 PMID 36934229 PMC10024458 unsure
- Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy. 2026 PMID 42203854 PMC13216312 unsure
Archive description
Placenta biopsies (16S), and saliva samples, vaginal and rectal swabs (shotgun) collected at delivery for 76 women delivering at term, 50 by planned C-section and 26 vaginally. Also includes 16S for bacterial colonies cultured from placenta biopsies.
How this project entered the registry
Classified as human oral cavity / vaginal / urogenital / gut / stool / other human site / multiple sites shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.title · “babies at term”
- body site study.title · “Placenta biopsies, saliva samples, vaginal and rectal swabs”
- body site run.scientific_name · “oral metagenome”
- body site run.scientific_name · “vaginal metagenome”
- life stage study.description · “76 women delivering at term”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6869294 | age_at_collection_days | 12783.8 | R1 | 0.85 | sample.attr.host_age | 35 |
| SAMEA6869294 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | antibiotic for tonsilitis |
| SAMEA6869312 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:drug usage | none |
| SAMEA6869294 | bmi | 23.05 | R1 | 0.90 | sample.attr.host_body_mass_index | 23.05 |
| SAMEA6869294 | collection_date | 2017-03-13 | R1 | 0.90 | biosample.attribute:collection_date | 2017-03-13 |
| SAMEA6869294 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA6869326 | health_condition | autoimmune_inflammatory | R1 | 0.90 | biosample_attr | hyperthyroidism |
| SAMEA6869326 | health_condition_detail | hyperthyroidism | R1 | 0.90 | sample.attr.host_disease_status | hyperthyroidism |
| SAMEA6869294 | location_locality | Stockholm | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | S�dersjukhuset, Stockholm |
| SAMEA6869312 | medication | none_reported | R1 | 0.90 | biosample.attribute:drug_usage | none |
| SAMEA6869326 | medication | other_medication | R1 | 0.85 | biosample.attribute:drug usage | tiotil |
| SAMEA6869340 | medication_detail | lergigan | R1 | 0.75 | biosample.attribute:drug_usage | lergigan |
| SAMEA6869294 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA6869294 | subject_id | Subject 1 | R1 | 0.85 | sample.attr.host_subject_id | Subject 1 |
Sequencing
223 runs over 223 samples · mean 0.17 Gbp per run (median 0.17 Gbp, total 38.89 Gbp; 223 runs with a base count) · layout SINGLE 223 · platform ILLUMINA 223 · models NextSeq 550 (223) · 74% of runs with a Sandpiper profile · first public 2020-06-14
Authors (39)
Argentini C first · Fontana F · Alessandri G · Lugli GA · Mancabelli L · Ossiprandi MC · van Sinderen D · Ventura M · Milani C · Turroni F last · Panzer JJ first · Romero R · Greenberg JM · Winters AD · Galaz J · Gomez-Lopez N · Theis KR last · De Biase R · Bocchio F · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Bostanci N first · Antony AT · Silbereisen A · Esmaili T · Krog MC · Sterpu I · Bashir Z · Engstrand L · Wiberg-Itzel E · Nielsen HS · Hugerth LW · Schuppe-Koistinen I last
Downloads
PRJEB38528.csv.gz (8.6 KB) · parquet (82.2 KB) — all 223 samples, every field with route and confidence · PRJEB38528_determinations.csv.gz (17.4 KB) — 2,151 evidence rows