Gut microbiome changes, COVID-19 vs travel, Hong Kong
Longitudinal study of 96 gut microbiome samples from Hong Kong, comparing changes during the first COVID-19 pandemic wave with pre-pandemic international travel-related changes in microbiome and resistome. machine-written summary
96 samples · 96 runs · HK · Age unknown · 2021 · 6.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 672 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
32 of 32 people sampled more than once (96 samples; median 3, up to 3 per person) · follow-up median 13 mo (max 17 mo) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Fecal sample before travel, after travel, and during the first wave of COVID-19 in Hong Kong” (time origin: other).
Each row is one person (32 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 96 | 100% | 96 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 96 | 100% | 96 | |||
| collection_date | 96 | 100% | 96 | |||
| detailed_location | 96 | 100% | ||||
| latitude | 96 | 100% | 96 | |||
| location_region | 96 | 100% | 96 | |||
| longitude | 96 | 100% | 96 | |||
| timepoint_label | 96 | 100% | 96 |
- Gut microbiome and resistome changes during the first wave of the COVID-19 pandemic in comparison with pre-pandemic travel-related changes. 2021 PMID 33949663 PMC8135950 own_data
Archive description
Using metagenomic sequencing, we comparatively examined the changes in gut microbiome and resistome following pre-pandemic international travels and during the first wave of COVID-19 pandemic.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.title · “human gut microbiome during the first wave”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8023226 | collection_date | 2018-12-21 | R1 | 0.90 | biosample.attribute:collection_date | 2018-12-21 |
| SAMEA8023226 | country | HK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Hong Kong |
| SAMEA8023226 | latitude | 22.3193 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.3193� N 114.1694� E |
| SAMEA8023226 | location_region | Kowloon City | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.3193� N 114.1694� E |
| SAMEA8023226 | longitude | 114.1694 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.3193� N 114.1694� E |
| SAMEA8023226 | subject_id | 13 | R1 | 0.70 | sample.name_rule:alias | TH13-BT |
| SAMEA8023226 | timepoint_label | Fecal sample collected before travel | R1 | 0.85 | biosample.attribute:description | Fecal sample collected before travel |
Sequencing
96 runs over 96 samples · mean 6.39 Gbp per run (median 6.42 Gbp, total 613.46 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform DNBSEQ 96 · models DNBSEQ-G400 (96) · 0% of runs with a Sandpiper profile · first public 2021-08-30
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB43044.csv.gz (3.7 KB) · parquet (74.5 KB) — all 96 samples, every field with route and confidence · PRJEB43044_determinations.csv.gz (6.1 KB) — 672 evidence rows