Early-Life Gut Microbiome Before/During COVID-19, Hong Kong
Longitudinal cohort of 624 samples from mother-baby dyads in Hong Kong, comparing early gut microbiome maturation before and during the COVID-19 pandemic. machine-written summary
624 samples · 636 runs · HK · Infant / toddler · 2024 · 5.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,144 sample values (collection date, country) |
| ✓ Abstract / description | 624 sample values (location region) |
| ✓ Full text | 624 sample values (location site) · PMC12931694 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolvedmother–infant — not resolved
Schedule stated by the source: “Infant stool at birth, 1 month, 2-3 months, 6 months, and until 12 months postpartum; maternal stool once in 2nd-3rd trimester” (time origin: birth); stated follow-up 12 mo.
Mother-infant dyads: maternal stool (2nd-3rd trimester) and matched infant stool sequenced in same cohorts.
Genera, mean relative abundance over 497 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 | 0 | 0% | ||||
| country | 624 | 100% | 624 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| detailed_location | 624 | 100% | ||||
| location_region | 624 | 100% | 624 | |||
| location_site | 624 | 100% | 624 | |||
| collection_date | 520 | 83% | 520 |
- Impacts of COVID-19 pandemic on early life gut microbiome. PMID 41411654 PMC12931694 curated
Archive description
The two large pre- and during-COVID-19 mother-baby dyad cohorts in the Greater Bay Area of China provided the unique opportunity to assess the effect of increased hygiene standards on early gut microbiome maturation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “on Early Life Gut Microbiome”
- body site study.description · “standards on early gut microbiome maturation.”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “COVID-19 Pandemic on Early Life Gut Microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38318110 | collection_date | 2021 | R1 | 0.85 | biosample.attribute:collection_date | 2021 |
| SAMN38318109 | country | HK | R1 | 0.90 | biosample_attr | Hong Kong |
| SAMN38318109 | location_region | Greater Bay Area | R4 | 0.45 | ena.study_description | Greater Bay Area of China |
| SAMN38318109 | location_site | Prince of Wales Hospital | R3 | 0.70 | paper.fulltext.methods | delivered at the Prince of Wales Hospital |
Sequencing
636 runs over 624 samples · mean 5.78 Gbp per run (median 5.80 Gbp, total 3,676.70 Gbp; 636 runs with a base count) · layout PAIRED 636 · platform ILLUMINA 636 · models Illumina NovaSeq 6000 (636) · 79% of runs with a Sandpiper profile · first public 2024-01-05 – 2024-03-24
Authors (25)
Zhang L first · Xu W · Meng HYH · Ching JYL · Liu Y · Wang S · Yan S · Lin L · Cheong PK · Ip KL · Peng Y · Zhu J · Cheung CP · Leung TF · Leung ASY · Tam WH · Leung TY · Chan PKS · Chang EB · Rubin DT · Claud EC · Wu WKK · Tun HM · Chan FKL · Ng SC last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1031773.csv.gz (17.2 KB) · parquet (96.3 KB) — all 624 samples, every field with route and confidence · PRJNA1031773_determinations.csv.gz (11.1 KB) — 2,392 evidence rows