Gut/oral/skin microbiome, isolated Yanomami village
Cross-sectional study of 22 fecal, oral, and skin microbiota samples from an isolated, previously uncontacted Yanomami Amerindian village in Venezuela, characterizing microbiome diversity and functional antibiotic resistance genes. machine-written summary
22 samples · 22 runs · VE · Age unknown · 2015 · 38.9 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 132 sample values (age, antibiotic exposure, collection date, country, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4517851 |
| ○ 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 |
community — not resolved
15 individuals from one isolated, previously uncontacted Yanomami village in Venezuela; no family/dyad structure stated..
Genera, mean relative abundance over 1 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 22 | 100% | 22 | |||
| age_at_collection_days | 22 | 100% | 22 | |||
| antibiotic_exposure | 22 | 100% | 22 | |||
| collection_date | 22 | 100% | 22 | |||
| sex | 22 | 100% | 22 |
- The microbiome of uncontacted Amerindians. 2015 PMID 26229982 PMC4517851 own_data
- High conservation of the dental plaque microbiome community across populations with differing subsistence strategies and levels of market integration 2022 unsure
Archive description
Antibiotic resistance genes isolated from fecal and oral microbiota and E. coli isolates of previously uncontacted Yanomami Amerindians and Puerto Rican individuals
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and child and adolescent by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal and oral microbiota”
- life stage sample.attr.age · “20 years (n=11/22)”
- life stage sample.attr.age · “11 years (n=6/22)”
- life stage sample.attr.age · “19 (n=5/22)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02736856 | age_at_collection_days | 4018.0 | R1 | 0.90 | sample.attr.host_age | 11 years |
| SAMN02736856 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:geo loc name | Venezuela |
| SAMN02736856 | collection_date | 2009-04-25 | R1 | 0.90 | biosample.attribute:collection_date | 2009-04-25 |
| SAMN02736856 | country | VE | R1 | 0.90 | sample.attr.geo_loc_name | Venezuela |
| SAMN02736856 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN02736856 | subject_id | 3 | R1 | 0.85 | sample.attr.individual | 3 |
Sequencing
22 runs over 22 samples · mean 71.2 Mbp per run (median 38.9 Mbp, total 1.57 Gbp; 22 runs with a base count) · layout SINGLE 22 · platform ILLUMINA 22 · models NextSeq 500 (22) · 18% of runs with a Sandpiper profile · first public 2015-04-22
Authors (29)
Clemente JC first · Pehrsson EC · Blaser MJ · Sandhu K · Gao Z · Wang B · Magris M · Hidalgo G · Contreras M · Noya-Alarcón · Noya-Alarcón Ó · Lander O · McDonald J · Cox M · Walter J · Oh PL · Ruiz JF · Rodriguez S · Shen N · Song SJ · Metcalf J · Knight R · Dantas G · Dominguez-Bello MG last · Velsko IM first · Gallois S · Stahl R · Henry AG · Warinner C last
Downloads
PRJNA245336.csv.gz (1.6 KB) · parquet (70.2 KB) — all 22 samples, every field with route and confidence · PRJNA245336_determinations.csv.gz (1.5 KB) — 132 evidence rows