Gut DNA virome in healthy Wayampi adults, French Guiana
Cross-sectional study of 31 faecal samples from healthy adult Wayampi Amerindians in Trois-Sauts, French Guiana, analyzing DNA viral communities; eight donors were prior ESBL-producing Enterobacteria carriers. machine-written summary
31 samples · 31 runs · GF · Adult · 2018 · 0.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 124 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 155 sample values (health condition, lifestyle, lifestyle detail, location locality, subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
community — not resolvedtribe — not resolved
31 adults sampled from one isolated Wayampi Amerindian community in Trois-Sauts, French Guiana.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 31 | 100% | ||||
| country | 31 | 100% | 31 | |||
| health_condition | 31 | 100% | 31 | |||
| subject_id | 31 | 100% | 31 | |||
| collection_date | 31 | 100% | 31 | |||
| detailed_location | 31 | 100% | ||||
| latitude | 31 | 100% | 31 | |||
| lifestyle | 31 | 100% | 31 | |||
| lifestyle_detail | 31 | 100% | 31 | |||
| location_locality | 31 | 100% | 31 | |||
| longitude | 31 | 100% | 31 |
- Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenisation of their faecal virome, but its distribution is not entirely random. 2018 PMID 29272453 own_data
Archive description
Samples were collected from 31 healthy adult Wayampi Amerindians from Trois-Sauts (French Guiana) in the 2010 campaign (October). Originaly, samples were collected and used to test for Enterobacteria producing extended spectrum beta-lactamases (E-ESBL) intestinal carriage.Samples consisted of faeces (n=31) from 31 different volunteers (18 females and 13 males).Eight individuals had been previously chatracterised as ESBL carrieres and the rest as noncarriers).Demographic, lifestyle, environment, and medical history data had been also collected.For all samples, the metagenomic analysis of the DNA viral communities was carried out, using the Illumina MiSeq with 300 bp x2 chemistry.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “DNA virome of faeces from healthy adult”
- body site study.description · “spectrum beta-lactamases (E-ESBL) intestinal carriage.Samples consisted of”
- life stage study.title · “faeces from healthy adult Wayampi Amerindians.”
- life stage study.description · “from 31 healthy adult Wayampi Amerindians from”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104161572 | collection_date | 2010 | R1 | 0.90 | biosample.attribute:collection_date | 2010 |
| SAMEA104161572 | country | GF | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | French Guiana |
| SAMEA104161572 | health_condition | healthy_control | R4 | 0.50 | study.title | healthy adult Wayampi Amerindians |
| SAMEA104161572 | latitude | 2.2450 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 2.245 -52.8772 |
| SAMEA104161572 | lifestyle | indigenous_community | R4 | 0.50 | paper.abstract | isolated community of the Wayampi Amerindians |
| SAMEA104161572 | lifestyle_detail | Wayampi Amerindians, described as an isolated community | R4 | 0.50 | paper.abstract | isolated community of the Wayampi Amerindians |
| SAMEA104161572 | location_locality | Trois-Sauts | R4 | 0.45 | ena.study_description | from Trois-Sauts (French Guiana) |
| SAMEA104161572 | longitude | -52.8772 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 2.245 -52.8772 |
| SAMEA104161572 | subject_id | SAMEA104161572 | R4 | 0.65 | design.one_sample_per_subject:description | Samples consisted of faeces (n=31) from 31 different volunteers (18 females and 13 males) |
Sequencing
31 runs over 31 samples · mean 0.19 Gbp per run (median 0.19 Gbp, total 5.98 Gbp; 31 runs with a base count) · layout PAIRED 31 · platform ILLUMINA 31 · models Illumina MiSeq (31) · 0% of runs with a Sandpiper profile · first public 2018-01-11
Authors (0)
No author record.
Downloads
PRJEB21741.csv.gz (1.8 KB) · parquet (71.6 KB) — all 31 samples, every field with route and confidence · PRJEB21741_determinations.csv.gz (2.4 KB) — 279 evidence rows