Endocervical, vaginal, rectal microbiomes, Fijian women, Ct
Case-control metagenomic shotgun sequencing of 30 endocervical, vaginal, and rectal samples from Fijian women, comparing microbiomes between those with and without Chlamydia trachomatis infection. machine-written summary
30 samples · 30 runs · FJ · Adult · 2022 · 1.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 207 sample values (collection date, country, health condition, health condition detail, latitude, longitude, sex, subject id) |
| ✓ Abstract / description | 15 sample values (health condition detail) |
| ✓ Full text | 62 sample values (age, location region, location site) · PMC9241848 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 61 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from BugSigDB, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
10 of 10 people sampled more than once (20 samples; median 2, up to 2 per person) · follow-up median 0 d (max 0 d) · median interval between samples 0 d (time from age at collection).
Each row is one person (2 shown of 10); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 14 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 | 30 | 100% | ||||
| country | 30 | 100% | 30 | |||
| health_condition | 23 | 77% | 14 | 9 | ||
| subject_id | 30 | 100% | 30 | |||
| antibiotic_exposure | 30 | 100% | 30 | |||
| collection_date | 30 | 100% | 30 | |||
| detailed_location | 30 | 100% | ||||
| health_condition_detail | 30 | 100% | 14 | 1 | 15 | |
| latitude | 30 | 100% | 30 | |||
| location_region | 30 | 100% | 30 | |||
| location_site | 30 | 100% | 30 | |||
| longitude | 30 | 100% | 30 | |||
| sex | 30 | 100% | 29 | 1 | ||
| age_at_collection_days | 22 | 73% | 20 | 2 |
- Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study. 2022 PMID 35579443 PMC9241848 own_data
Archive description
Chlamydia trachomatis (Ct) is the primary cause of bacterial sexually transmitted infections worldwide with a disturbing increase in annual rates. While there is a plethora of data on healthy and pathogenic vaginal microbiomes-defining microbial profiles and associations with STIs-far fewer studies have similarly examined the endocervix or rectum. Further, vulnerable populations such as Pacific Islanders remain under-represented in research. We investigated the microbial composition, structure and function of these anatomic microbiomes using metagenomic shotgun sequencing among a Fijian cohort. We found, primarily among Ct-infected women, unique microbial profiles in endocervical, vaginal and rectal microbiomes with an increased diversity and more complex microbial pathways in endocervical compared to vaginal microbiomes. Similarities in microbiome composition across sites for some women suggested intra-genitorectal transmission. These novel insights into genitorectal microbiomes and their purported function require prospective studies to better define Pacific Islander microbiomes and microbial/microbiome interactions that promote Ct infection.
How this project entered the registry
Classified as human vaginal / urogenital / gut / stool / other human site shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human vaginal metagenome”
- body site study.title · “endocervical, vaginal and rectal samples”
- life stage study.description · “among a Fijian cohort”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27572016 | age_at_collection_days | 11688.0 | R2 | 0.70 | external.meta2db source | host_age: 32 |
| SAMN27585142 | age_at_collection_days | 7670 | R3 | 0.85 | paper.body.TABLE 1[Age in yrse] | 21 |
| SAMN27572016 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 1 month |
| SAMN27572016 | collection_date | 2018-03 | R1 | 0.90 | biosample.attribute:collection_date | 2018-03 |
| SAMN27572016 | country | FJ | R1 | 0.90 | sample.attr.geo_loc_name | Fiji |
| SAMN27572016 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:title | Human metagenome isolated from vagina of Ct positive women |
| SAMN27585011 | health_condition | other_infection | R2 | 0.70 | external.meta2db source | chlamydia |
| SAMN27572016 | health_condition_detail | Human metagenome isolated from vagina of Ct positive women | R1 | 0.85 | biosample.attribute:title | Human metagenome isolated from vagina of Ct positive women |
| SAMN27585011 | health_condition_detail | chlamydia | R2 | 0.70 | external.meta2db source | chlamydia |
| SAMN27585064 | health_condition_detail | mixed_case_control: 10 women: 5 with C. trachomatis infection, 5 uninfected controls | R4 | 0.50 | paper.abstract | women with and without C. trachomatis |
| SAMN27572016 | latitude | -17.7656 | R1 | 0.90 | biosample.attribute:lat_lon | 17.76556355 S 177.97467437 E |
| SAMN27572016 | location_region | Central Division, Viti Levu | R3 | 0.70 | paper.fulltext.methods | health centers and outreach clinics in the Central Division, Viti Levu |
| SAMN27572016 | location_site | Fijian Ministry of Health and Medical Services health centers and outreach clinics | R3 | 0.70 | paper.fulltext.methods | Fijian Ministry of Health and Medical Services (MoHMS) health centers |
| SAMN27572016 | longitude | 177.9747 | R1 | 0.90 | biosample.attribute:lat_lon | 17.76556355 S 177.97467437 E |
| SAMN27572016 | sex | female | R1 | 0.85 | biosample.attribute:title | Human metagenome isolated from vagina of Ct positive women |
| SAMN27585011 | sex | female | R2 | 0.70 | external.meta2db source | host_sex: female |
| SAMN27572016 | subject_id | 72 | R1 | 0.70 | sample.name_rule:alias | 72V |
Sequencing
30 runs over 30 samples · mean 3.35 Gbp per run (median 1.14 Gbp, total 100.50 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina HiSeq 2500 (30) · 50% of runs with a Sandpiper profile · first public 2022-04-17
Authors (7)
Bommana S first · Richards G · Kama M · Kodimerla R · Jijakli K · Read TD · Dean D last
Downloads
PRJNA826539.csv.gz (2.2 KB) · parquet (73.4 KB) — all 30 samples, every field with route and confidence · PRJNA826539_determinations.csv.gz (4.8 KB) — 345 evidence rows