Gut metagenome of Hong Kong travellers before/after travel
180 stool samples from healthy adult Hong Kong residents, collected before and after international travel, in a longitudinal study of gut microbiome and antibiotic resistance gene changes associated with travel. machine-written summary
180 samples · 180 runs · HK · Adult · 2023 · 6.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,768 sample values (age, antibiotic exposure, bmi, country, latitude, longitude, sex, smoking status) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 362 sample values (antibiotic exposure, health condition, health condition detail) · PMC10628765 |
| ○ 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
90 of 90 people sampled more than once (180 samples; median 2, up to 2 per person). Schedule stated by the source: “Each subject sampled twice: pre-trip and post-trip (before and after international travel)” (time origin: other).
Genera, mean relative abundance over 164 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 | 180 | 100% | ||||
| country | 180 | 100% | 180 | |||
| health_condition | 180 | 100% | 180 | |||
| subject_id | 180 | 100% | 180 | |||
| antibiotic_exposure | 180 | 100% | 178 | 2 | ||
| health_condition_detail | 180 | 100% | 180 | |||
| latitude | 180 | 100% | 180 | |||
| longitude | 180 | 100% | 180 | |||
| timepoint_label | 180 | 100% | 180 | |||
| smoking_status | 176 | 98% | 176 | |||
| age_at_collection_days | 174 | 97% | 174 | |||
| sex | 172 | 96% | 172 | |||
| bmi | 168 | 93% | 168 |
- Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis. 2023 PMID 36864573 PMC10628765 own_data
Archive description
To characterise the changes in the gut metagenomes of Chinese international travellers before and after travel
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut metagenomes of healthy”
- body site study.description · “changes in the gut metagenomes of Chinese”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.age · “19 (n=22/180)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28078811 | age_at_collection_days | 8034.0 | R1 | 0.85 | sample.attr.age | 22 |
| SAMN28078811 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN28078852 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | used antibiotics within last three months before travel |
| SAMN28078811 | bmi | 20.45 | R1 | 0.90 | sample.attr.bmi | 20.446742023841672 |
| SAMN28078811 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong |
| SAMN28078811 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.abstract | 90 healthy Chinese adult residents of Hong Kong |
| SAMN28078811 | health_condition_detail | healthy Chinese adult residents | R3 | 0.70 | paper.fulltext.abstract | 90 healthy Chinese adult residents of Hong Kong |
| SAMN28078811 | latitude | 22.1800 | R1 | 0.90 | biosample.attribute:lat_lon | 22.18 N 114.10 E |
| SAMN28078811 | longitude | 114.1000 | R1 | 0.90 | biosample.attribute:lat_lon | 22.18 N 114.10 E |
| SAMN28078811 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN28078811 | smoking_status | never | R1 | 0.80 | biosample.attribute:smoking | No |
| SAMN28078811 | subject_id | TRM-C001 | R1 | 0.85 | sample.attr.subject_number | TRM-C001 |
| SAMN28078811 | timepoint_label | Pre-trip | R1 | 0.85 | sample.attr.time_point | Pre-trip |
Sequencing
180 runs over 180 samples · mean 6.40 Gbp per run (median 6.42 Gbp, total 1,152.71 Gbp; 180 runs with a base count) · layout PAIRED 180 · platform ILLUMINA 180 · models Illumina NovaSeq 6000 (180) · 91% of runs with a Sandpiper profile · first public 2023-03-07
Authors (14)
Cheung MK first · Ng RWY · Lai CKC · Zhu C · Au ETK · Yau JWK · Li C · Wong HC · Wong BCK · Kwok KO · Chen Z · Chan PKS · Lui GCY · Ip M last
Downloads
PRJNA834885.csv.gz (6.2 KB) · parquet (78.5 KB) — all 180 samples, every field with route and confidence · PRJNA834885_determinations.csv.gz (15.9 KB) — 2,130 evidence rows