Gut microbiome and COVID-19 vaccine immunity in Hong Kong
248 longitudinal stool samples from healthy adult BNT162b2 and CoronaVac vaccinees in Hong Kong, studying associations between gut microbiota and durability of vaccine-induced antibody responses. machine-written summary
248 samples · 248 runs · HK · Adult · 2023 · 4.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,935 sample values (collection date, country, intervention, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 496 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10518331 |
| ○ 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 |
intervention — arms not resolved
Vaccination as the study intervention design observational_with_procedure · population healthy_control · BNT162b2 or CoronaVac COVID-19 vaccination, followed longitudinally
“121 BNT162b2 and 40 CoronaVac vaccinees” — abstract:37743379 (study level; per-sample arms are in the intervention column below)
longitudinal
49 of 153 people sampled more than once (144 samples; median 3, up to 3 per person) · follow-up median 6 mo (max 6 mo) · median interval between samples 30 d (time from timepoint labels). Schedule stated by the source: “Samples labeled D0 (day 0/baseline), M0, M1, M6 per subject; 153 subjects, 248 samples total, not all subjects have all timepoints.” (time origin: intervention_start); stated follow-up 6 mo.
Each row is one person (36 shown of 49); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 233 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 | 248 | 100% | ||||
| country | 248 | 100% | 248 | |||
| health_condition | 248 | 100% | 248 | |||
| subject_id | 248 | 100% | 248 | |||
| collection_date | 248 | 100% | 248 | |||
| detailed_location | 248 | 100% | ||||
| health_condition_detail | 248 | 100% | 248 | |||
| latitude | 248 | 100% | 248 | |||
| location_region | 248 | 100% | 248 | |||
| longitude | 248 | 100% | 248 | |||
| timepoint_label | 248 | 100% | 248 | |||
| intervention | 199 | 80% | 199 |
- Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines. 2023 PMID 37743379 PMC10518331 unsure
Archive description
Gut microbiota modulates immunogenicity to COVID-19 vaccines. We followed up a longitudinal cohort of BNT162b2 and CoronaVac vaccinees to investigate the associations between baseline gut microbiota and durable immunity to the vaccines, and to determine the persistence and recovery of vaccination-related gut microbiota alterations at 6 months post-vaccination.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult 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 · “vaccines and the gut microbiome”
- body site study.description · “Gut microbiota modulates immunogenicity”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114328379 | collection_date | 2021-06-16 | R1 | 0.90 | biosample.attribute:collection_date | 2021-06-16 |
| SAMEA114328379 | country | HK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Hong Kong |
| SAMEA114328379 | health_condition | healthy_control | R4 | 0.30 | study.description | BNT162b2 and CoronaVac vaccinees |
| SAMEA114328379 | health_condition_detail | COVID-19 vaccine recipients (BNT162b2 or CoronaVac) | R4 | 0.50 | paper.abstract | 121 BNT162b2 and 40 CoronaVac vaccinees |
| SAMEA114328379 | intervention | vaccine | R1 | 0.85 | biosample.attribute:description | SinoVac |
| SAMEA114328379 | latitude | 22.2689 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.2689 114.1292 |
| SAMEA114328379 | location_region | Central and Western | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.2689 114.1292 |
| SAMEA114328379 | longitude | 114.1292 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.2689 114.1292 |
| SAMEA114328379 | subject_id | HKU003 | R1 | 0.70 | sample.name_rule:alias | HKU003-M6 |
| SAMEA114328379 | timepoint_label | M6 | R1 | 0.70 | sample.name_rule:alias | HKU003-M6 |
Sequencing
248 runs over 248 samples · mean 4.11 Gbp per run (median 4.20 Gbp, total 1,018.36 Gbp; 248 runs with a base count) · layout PAIRED 248 · platform ILLUMINA 248 · models Illumina NovaSeq 6000 (248) · 94% of runs with a Sandpiper profile · first public 2023-09-06
Authors (22)
Peng Y first · Zhang L · Mok CKP · Ching JYL · Zhao S · Wong MKL · Zhu J · Chen C · Wang S · Yan S · Qin B · Liu Y · Zhang X · Cheung CP · Cheong PK · Ip KL · Fung ACH · Wong KKY · Hui DSC · Chan FKL · Ng SC · Tun HM last
Downloads
PRJEB60773.csv.gz (7.6 KB) · parquet (80.3 KB) — all 248 samples, every field with route and confidence · PRJEB60773_determinations.csv.gz (17.8 KB) — 2,431 evidence rows