Vaginal shotgun metagenomes, healthy women, cross-sectional
45 vaginal microbiome samples from healthy women, analyzed by shotgun metagenomics in a cross-sectional design focused on Lactobacillus crispatus and vaginal microbiota composition. machine-written summary
45 samples · 45 runs · Age unknown · 2021 · 36.3 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 81 sample values (collection date, subject id) |
| ✓ Abstract / description | 90 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked · PMC8091109 |
| ○ 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
4 of 4 people sampled more than once (36 samples; median 9, up to 9 per person) · follow-up median 8 d (max 8 d) · median interval between samples 1 d (time from collection dates).
Each row is one person (4 shown); 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 45 | 100% | 45 | |||
| subject_id | 36 | 80% | 36 | |||
| collection_date | 45 | 100% | 45 | |||
| health_condition_detail | 45 | 100% | 45 |
- Comparative genome analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment. 2021 PMID 33579685 PMC8091109 own_data
Archive description
Comparative genomics analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment
How this project entered the registry
Classified as human vaginal / urogenital / gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host study.title · “human vaginal environment”
- body site study.title · “human vaginal environment”
- body site sample.attr.isolation_source · “stool (n=36/45)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15339891 | collection_date | 2020-04-23 | R1 | 0.90 | biosample.attribute:collection_date | 2020-04-23 |
| SAMN15339891 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | 94 healthy vaginal microbiome samples |
| SAMN15339891 | health_condition_detail | healthy vaginal microbiota | R4 | 0.50 | paper.abstract | healthy vaginal environment |
| SAMN15339900 | subject_id | S1 | R1 | 0.70 | sample.name_rule:alias | S1 |
Sequencing
45 runs over 45 samples · mean 36.0 Mbp per run (median 36.3 Mbp, total 1.62 Gbp; 45 runs with a base count) · layout PAIRED 45 · platform ILLUMINA 45 · models Illumina MiSeq (45) · 0% of runs with a Sandpiper profile · first public 2021-02-09
Authors (10)
Mancabelli L first · Mancino W · Lugli GA · Milani C · Viappiani A · Anzalone R · Longhi G · van Sinderen D · Ventura M · Turroni F last
Downloads
PRJNA641015.csv.gz (1.9 KB) · parquet (70.8 KB) — all 45 samples, every field with route and confidence · PRJNA641015_determinations.csv.gz (1.9 KB) — 171 evidence rows