Gut metagenomes from rural Kenya, sanitation and AMR study
12 fecal metagenome samples from adults and elderly individuals in a rural Kenyan village, part of a cross-sectional, multi-country study on sanitation access and antibiotic resistance carriage in the human gut. machine-written summary
12 samples · 12 runs · KE · Adult · 2022 · 11.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 90 sample values (age, collection date, country, latitude, location region, longitude, sex, subject id) |
| ✓ Abstract / description | 36 sample values (health condition detail, lifestyle, lifestyle detail) |
| ○ Full text | read; no usable statement or table · PMC10393780 |
| ○ 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 |
Genera, mean relative abundance over 9 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 12 | 100% | 12 | |||
| age_at_collection_days | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 12 | |||
| latitude | 12 | 100% | 12 | |||
| lifestyle | 12 | 100% | 12 | |||
| lifestyle_detail | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 | |||
| detailed_location | 6 | 50% | ||||
| location_region | 6 | 50% | 6 |
- Evaluating the relationship between community water and sanitation access and the global burden of antibiotic resistance: an ecological study. 2023 PMID 37399829 PMC10393780 own_data
Archive description
Metagenomic (llumina) sequencing of human fecal samples from rural Kenya. These samples were combined with others from around the world to assess the association between access to sanitation and antibiotic resistance carriage in human guts.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human fecal samples from rural Kenya”
- life stage sample.attr.host_age · “23 (n=8/12)”
- life stage sample.attr.host_age · “107 (n=4/12)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN22065137 | age_at_collection_days | 8391.0 | R1 | 0.85 | sample.attr.host_age | 23 |
| SAMN22065137 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN22065137 | country | KE | R1 | 0.90 | sample.attr.geo_loc_name | Kenya: rural village |
| SAMN22065137 | health_condition_detail | mixed_case_control: samples assessed for antibiotic resistance carriage | R4 | 0.40 | study.description | assess the association between access to sanitation and antibiotic resistance |
| SAMN22065137 | latitude | 0.2990 | R1 | 0.90 | biosample.attribute:lat_lon | 0.299 N 34.515 E |
| SAMN22065137 | lifestyle | rural_non_industrialized | R4 | 0.40 | ena.study_description | fecal samples from rural Kenya |
| SAMN22065137 | lifestyle_detail | rural Kenya | R4 | 0.40 | ena.study_description | fecal samples from rural Kenya |
| SAMN22065137 | location_region | Kakamega | R1 | 0.60 | biosample.attribute:lat_lon | 0.299 N 34.515 E |
| SAMN22065137 | longitude | 34.5150 | R1 | 0.90 | biosample.attribute:lat_lon | 0.299 N 34.515 E |
| SAMN22065137 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN22065137 | subject_id | SAMN22065137 | R1 | 0.55 | design.one_sample_per_subject:archive | host age: 23; host sex: female; lat lon: 0.299 N 34.515 E |
Sequencing
12 runs over 12 samples · mean 11.78 Gbp per run (median 11.56 Gbp, total 141.41 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina NovaSeq 6000 (12) · 75% of runs with a Sandpiper profile · first public 2022-02-02
Authors (0)
No author record.
Downloads
PRJNA768833.csv.gz (1.4 KB) · parquet (71.4 KB) — all 12 samples, every field with route and confidence · PRJNA768833_determinations.csv.gz (1.9 KB) — 126 evidence rows