Menstrual cycle & contraceptive effects on vaginal, fecal
2824 samples from 160 healthy Danish women across oral, vaginal, rectal, and fecal sites, sampled during menstrual, follicular, and luteal phases under different contraceptive regimens. Cross-sectional assessment of sequencing methodologies for vaginal microbiome characterization. machine-written summary
2,825 samples · 2,825 runs · DK, SE · Adult · 2020 · 0.23 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 | 29,983 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, latitude) |
| ✓ Abstract / description | 1,264 sample values (location locality) |
| ✓ Full text | 8,347 sample values (health condition, health condition detail, location site, sex) · PMC11249552, PMC11331738, PMC13216312, PMC7677004, PMC8018275, PMC9247429 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,561 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design non_randomized_controlled · population healthy_control · Hormonal contraceptives: combined oral contraceptive or levonorgestrel IUS vs non-hormonal methods
“combined oral contraceptive (COC, n = 52) or levonorgestrel intrauterine system” — abstract:35553675 (study level; per-sample arms are in the intervention column below)
longitudinal
160 of 160 people sampled more than once (627 samples; median 4, up to 4 per person) · follow-up median 18 d (max 18 d) · median interval between samples 9 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “menses CD1-3, follicular CD8-12, luteal CD18-22 for fecal/vaginal; vaginal also amplicon over 6 weeks and shotgun over 4 weeks in subsets”; stated follow-up 42 d.
Each row is one person (36 shown of 160); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 568 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 | 2,825 | 100% | ||||
| country | 2,825 | 100% | 2,825 | |||
| health_condition | 2,825 | 100% | 948 | 1,877 | ||
| subject_id | 2,825 | 100% | 2,825 | |||
| antibiotic_exposure | 2,825 | 100% | 1,264 | 1,561 | ||
| collection_date | 2,825 | 100% | 2,825 | |||
| detailed_location | 2,825 | 100% | ||||
| health_condition_detail | 2,825 | 100% | 762 | 2,063 | ||
| location_locality | 2,825 | 100% | 1,561 | 1,264 | ||
| location_site | 2,825 | 100% | 2,825 | |||
| sex | 2,825 | 100% | 1,243 | 1,582 | ||
| latitude | 2,824 | 100% | 2,824 | |||
| longitude | 2,824 | 100% | 2,824 | |||
| timepoint_label | 2,507 | 89% | 2,507 | |||
| bmi | 2,302 | 81% | 2,302 | |||
| age_at_collection_days | 1,582 | 56% | 1,582 | |||
| location_region | 1,264 | 45% | 1,264 | |||
| smoking_status | 1,262 | 45% | 1,262 | |||
| medication | 1,102 | 39% | 1,102 | |||
| medication_detail | 63 | 2% | 63 |
- Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome. 2020 PMID 33208514 PMC7677004 own_data
- Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar. 2021 PMID 33816334 PMC8018275 own_data
- The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle. 2022 PMID 35553675 PMC9247429 own_data
- Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women. 2024 PMID 39015337 PMC11249552 own_data
- Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes. 2024 PMID 39160615 PMC11331738 own_data
1 more
- Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy. 2026 PMID 42203854 PMC13216312
Archive description
Oral, vaginal, rectal and fecal samples from 160 healthy young women under different contraceptive regimens over the course of a full menstrual cycle. * Rectal swabs: one per woman, in the menstrual phase * Saliva samples: 3 per woman (menstrual, follicular, luteal) * Fecal samples: 3 per woman (menstrual, follicular, luteal) * Vaginal samples: 3 per woman (menstrual, follicular, luteal) * Vaginal samples: 39 amplicon samples over a 6 week period, 15 women * Vaginal samples: 28 shotgun samples over a 4 week period, 49 women
How this project entered the registry
Classified as human gut / stool / oral cavity / vaginal / urogenital mixed assays of adult by sonnet_x2 with confidence 0.78. Assay mixed.
- host study.description · “human microbiome”
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “vaginal metagenome”
- body site run.scientific_name · “feces metagenome”
- body site run.scientific_name · “oral metagenome”
- life stage study.description · “160 healthy young women”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112857780 | age_at_collection_days | 8391.0 | R1 | 0.85 | sample.attr.host_age | 23 |
| SAMEA112857780 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | no |
| SAMEA122894970 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 2 weeks |
| SAMEA112857780 | bmi | 22.1 | R1 | 0.90 | sample.attr.host_body_mass_index | 22.1 |
| SAMEA6662467 | bmi | 17.86 | R1 | 0.85 | biosample.attribute:host_body_mass_index | 17.86 |
| SAMEA112857780 | collection_date | 2017-11-13 | R1 | 0.90 | biosample.attribute:collection_date | 2017-11-13 |
| SAMEA112857780 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
| SAMEA112857780 | health_condition | allergy_or_atopy | R1 | 0.90 | biosample_attr | allergies |
| SAMEA6662467 | health_condition | cardiometabolic_other | R1 | 0.60 | biosample.attribute:host_disease_status | metabolic disease, allergies |
| SAMEA112857861 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | enrolled 160 healthy women aged 18 to 40 |
| SAMEA112857780 | health_condition_detail | allergies | R1 | 0.90 | sample.attr.host_disease_status | allergies |
| SAMEA6662467 | health_condition_detail | metabolic disease, allergies | R1 | 0.85 | biosample.attribute:host_disease_status | metabolic disease, allergies |
| SAMEA112857834 | health_condition_detail | 160 healthy women | R3 | 0.70 | paper.fulltext.methods | enrolled 160 healthy women aged 18 to 40 |
| SAMEA112857780 | latitude | 55.6700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.67 12.57 |
| SAMEA122894970 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Copenhagen |
| SAMEA112857780 | location_locality | Copenhagen | R4 | 0.50 | paper.abstract | Copenhagen University Hospital, Rigshospitalet, Denmark |
| SAMEA112857780 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.67 12.57 |
| SAMEA112857780 | location_site | Copenhagen University Hospital, Rigshospitalet | R3 | 0.70 | paper.fulltext.methods | Copenhagen University Hospital, Rigshospitalet, Denmark |
| SAMEA112857780 | longitude | 12.5700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.67 12.57 |
| SAMEA112857780 | medication | hormonal_contraceptive_or_hrt | R1 | 0.85 | biosample.attribute:birth_control | birth_control: combined oral contraceptive |
| SAMEA6661929 | medication | ppi | R1 | 0.90 | biosample.attribute:drug_usage | protein-pump inhibitor |
| SAMEA6661929 | medication_detail | protein-pump inhibitor | R1 | 0.90 | biosample.attribute:drug_usage | protein-pump inhibitor |
| SAMEA6661910 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA112857780 | sex | female | R3 | 0.70 | paper.fulltext.methods | 160 healthy women aged 18 to 40 years |
| SAMEA112857780 | smoking_status | never | R1 | 0.90 | biosample.attribute:smoking_status | never |
| SAMEA112857780 | subject_id | 26 | R1 | 0.85 | sample.attr.host_subject_id | 26 |
| SAMEA6662467 | subject_id | 87 | R1 | 0.85 | biosample.attribute:host_subject_id | 87 |
| SAMEA112857780 | timepoint_label | day 4 | R1 | 0.70 | sample.name_rule:alias | subject26_day4 |
| SAMEA6662467 | timepoint_label | menstrual phase | R1 | 0.85 | biosample.attribute:experimental_factor | menstrual phase |
Sequencing
2,825 runs over 2,825 samples · mean 0.53 Gbp per run (median 0.23 Gbp, total 1,503.98 Gbp; 2,825 runs with a base count) · layout SINGLE 1,561, PAIRED 1,264 · platform ILLUMINA 1,561, DNBSEQ 1,264 · models NextSeq 550 (1,561), DNBSEQ-G400 (1,264) · 39% of runs with a Sandpiper profile · first public 2020-09-30 – 2026-06-16
Authors (36)
Hugerth LW first · Pereira M · Zha Y · Seifert M · Kaldhusdal V · Boulund F · Krog MC · Bashir Z · Hamsten M · Fransson E · Svarre-Nielsen H · Schuppe-Koistinen I · Engstrand L last · Bostanci N first · Belibasakis GN · Wannerberger K · Nielsen HS · Nyboe Andersen A · Edfeldt G · Prast-Nielsen S · Schacht SR · Tetens I · Vomstein K · Du J · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Antony AT · Silbereisen A · Esmaili T · Sterpu I · Wiberg-Itzel E
Downloads
PRJEB37731.csv.gz (76.3 KB) · parquet (172.3 KB) — all 2,825 samples, every field with route and confidence · PRJEB37731_determinations.csv.gz (275.3 KB) — 41,155 evidence rows