Resistome of healthy Swiss adults' stool, cross-sectional
88 stool samples from healthy adults in Switzerland were analyzed by shotgun metagenomics to assess gut resistome and colonization with extended-spectrum cephalosporin-resistant Enterobacterales, comparing native versus pre-enriched sample processing in a cross-sectional design. machine-written summary
88 samples · 113 runs · CH · Age unknown · 2023 · 3.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 528 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 352 sample values (health condition, health condition detail, location locality, location site) · PMC10501143, PMC11358271 |
| ○ 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
25 of 42 people sampled more than once (71 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 60 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 | 88 | 100% | ||||
| country | 88 | 100% | 88 | |||
| health_condition | 88 | 100% | 88 | |||
| subject_id | 88 | 100% | 88 | |||
| collection_date | 88 | 100% | 88 | |||
| detailed_location | 88 | 100% | ||||
| health_condition_detail | 88 | 100% | 88 | |||
| latitude | 88 | 100% | 88 | |||
| location_locality | 88 | 100% | 88 | |||
| location_region | 88 | 100% | 88 | |||
| location_site | 88 | 100% | 88 | |||
| longitude | 88 | 100% | 88 |
- Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. 2023 PMID 37720151 PMC10501143 own_data
- Nanopore R10.4 metagenomic detection of bla<sub>CTX-M</sub>/bla<sub>DHA</sub> antimicrobial resistance genes and their genetic environments in stool. 2024 PMID 39198442 PMC11358271 own_data
Archive description
Using native and pre-enriched stool, we performed shotgun metagenomic sequencing to characterize the microbiome and resistome of stool samples from healthy individuals.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “stool samples from healthy people”
- body site study.title · “stool samples from healthy people”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33099809 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN33099809 | country | CH | R1 | 0.90 | sample.attr.geo_loc_name | Switzerland |
| SAMN33099809 | health_condition | healthy_control | R3 | 0.60 | paper.fulltext.results | 42 healthy volunteers |
| SAMN33099809 | health_condition_detail | 42 healthy volunteers | R3 | 0.60 | paper.fulltext.results | 42 healthy volunteers |
| SAMN33099809 | latitude | 46.9479 | R1 | 0.90 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN33099809 | location_locality | Bern | R3 | 0.70 | paper.fulltext.methods | IFIK; Bern, Switzerland |
| SAMN33099809 | location_region | Bern | R1 | 0.60 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN33099809 | location_site | Institute for Infectious Diseases (IFIK), Bern | R3 | 0.70 | paper.fulltext.methods | ship their samples to the Institute for Infectious Diseases |
| SAMN33099809 | longitude | 7.4223 | R1 | 0.90 | biosample.attribute:lat_lon | 46.947928 N 7.422277 E |
| SAMN33099809 | subject_id | S1-CAM-01 | R1 | 0.70 | sample.name_rule:alias | S1-CAM-01 |
Sequencing
113 runs over 88 samples · mean 2.48 Gbp per run (median 2.78 Gbp, total 280.78 Gbp; 113 runs with a base count) · layout PAIRED 63, SINGLE 50 · platform ILLUMINA 63, OXFORD_NANOPORE 50 · models Illumina NovaSeq 6000 (63), MinION (50) · 53% of runs with a Sandpiper profile · first public 2023-02-07 – 2024-02-11
Authors (6)
Campos-Madueno EI first · Aldeia C · Perreten V · Sendi P · Moser AI · Endimiani A last
Downloads
PRJNA931814.csv.gz (3.4 KB) · parquet (74.4 KB) — all 88 samples, every field with route and confidence · PRJNA931814_determinations.csv.gz (6.6 KB) — 880 evidence rows