Gut microbiota and resistome in Swiss expatriates abroad
Nanopore metagenomic sequencing of 144 stool samples from Swiss expatriates in African and European countries, comparing microbiota composition and antimicrobial resistance gene profiles across geographic regions. machine-written summary
144 samples · 144 runs · CH · Age unknown · 2025 · 0.61 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 864 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 144 sample values (health condition detail) |
| ✓ Full text | 144 sample values (health condition) · PMC12920924 |
| ○ 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 — not resolved
72 of 72 people sampled more than once (144 samples; median 2, up to 2 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 144 | 100% | ||||
| country | 144 | 100% | 144 | |||
| health_condition | 144 | 100% | 144 | |||
| subject_id | 144 | 100% | 144 | |||
| collection_date | 144 | 100% | 144 | |||
| detailed_location | 144 | 100% | ||||
| health_condition_detail | 144 | 100% | 144 | |||
| latitude | 144 | 100% | 144 | |||
| location_region | 144 | 100% | 144 | |||
| longitude | 144 | 100% | 144 |
- Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics. 2026 PMID 41634308 PMC12920924 own_data
Archive description
This nanopore-based shotgun metagenomic sequencing study characterised the microbiota composition and resistome of Swiss expatriates living in European and African countries. In particular, we investigated whether exposure to high-endemic regions could influence overall changes in microbiota composition, as well as the acquisition of antimicrobial resistance genes via mobile genetic elements, such as plasmids.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Swiss Expatriates living Abroad”
- body site sample.attr.isolation_source · “Native stool from S1-AUT-01_R_batch5 (n=144/144)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN49777684 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN49777684 | country | CH | R1 | 0.90 | sample.attr.geo_loc_name | Switzerland |
| SAMN49777684 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | collected in Switzerland upon the return of healthy volunteers |
| SAMN49777684 | health_condition_detail | Healthy / control | R4 | 0.50 | paper.abstract | Stool samples from expatriates residing in African and European countries |
| SAMN49777684 | latitude | 46.9479 | R1 | 0.90 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN49777684 | location_region | Bern | R1 | 0.60 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN49777684 | longitude | 7.4223 | R1 | 0.90 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN49777684 | subject_id | AUT-01 | R1 | 0.70 | sample.name_rule:alias | S1-AUT-01_batch4 |
Sequencing
144 runs over 144 samples · mean 0.68 Gbp per run (median 0.61 Gbp, total 98.26 Gbp; 144 runs with a base count) · layout SINGLE 144 · platform OXFORD_NANOPORE 144 · models MinION (144) · 0% of runs with a Sandpiper profile · first public 2025-07-04 – 2025-07-06
Authors (3)
Campos-Madueno EI first · Aldeia C · Endimiani A last
Downloads
PRJNA1285875.csv.gz (4.2 KB) · parquet (75.4 KB) — all 144 samples, every field with route and confidence · PRJNA1285875_determinations.csv.gz (8.2 KB) — 1,152 evidence rows