Gut microbiome, synbiotic SIM01 trial, Hong Kong vaccinees
560 stool samples from Hong Kong vaccinees (elderly and diabetic) receiving SARS-CoV-2 vaccination, studying SIM01 synbiotic (three Bifidobacterium strains) versus placebo in an intervention design with baseline and postvaccination timepoints. machine-written summary
560 samples · 560 runs · HK · Age unknown · 2025 · 5.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,680 sample values (country, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,680 sample values (collection date, health condition, health condition detail) · PMC12375777 |
| ○ 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 |
intervention — arms not resolved
Synbiotic (probiotic + prebiotic) design randomized_controlled_trial · SIM01 synbiotic (3 Bifidobacterium strains) vs placebo, 3 months post-vaccination
“received 3 months of SIM01” — abstract:40851072 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Genera, mean relative abundance over 549 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 | 560 | 100% | 560 | |||
| health_condition | 560 | 100% | 560 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 560 | 100% | 560 | |||
| health_condition_detail | 560 | 100% | 560 | |||
| latitude | 560 | 100% | 560 | |||
| longitude | 560 | 100% | 560 |
- The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients. 2025 PMID 40851072 PMC12375777 own_data
Archive description
Modulation of Gut Microbiota to Enhance Health and Immunity of Vulnerable Individuals During 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 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44568956 | collection_date | 2021-04/2022-03 | R3 | 0.70 | paper.fulltext.methods | general population of Hong Kong from April 2021 to March 2022 |
| SAMN44568956 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong |
| SAMN44568956 | health_condition | intervention_cohort | R3 | 0.70 | paper.fulltext.abstract | received a gut microbiota-derived synbiotic formula (SIM01) or placebo |
| SAMN44568956 | health_condition_detail | vulnerable individuals (elderly or T2DM) receiving synbiotic vs placebo post COVID-19 vaccination | R3 | 0.70 | paper.fulltext.abstract | received a gut microbiota-derived synbiotic formula (SIM01) or placebo |
| SAMN44568956 | latitude | 22.1500 | R1 | 0.90 | biosample.attribute:lat_lon | 22.15 N 114.1001 E |
| SAMN44568956 | longitude | 114.1001 | R1 | 0.90 | biosample.attribute:lat_lon | 22.15 N 114.1001 E |
Sequencing
560 runs over 560 samples · mean 5.96 Gbp per run (median 5.36 Gbp, total 3,338.80 Gbp; 560 runs with a base count) · layout PAIRED 560 · platform ILLUMINA 560 · models Illumina NovaSeq 6000 (560) · 98% of runs with a Sandpiper profile · first public 2025-08-26
Authors (15)
Zhang L first · Wang S · Wong MCS · Mok CKP · Ching JYL · Mak JWY · Chen C · Huo B · Yan S · Cheung CP · Chiu EOL · Fung EYT · Cheong PK · Chan FKL · Ng SC last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1181778.csv.gz (14.7 KB) · parquet (95.2 KB) — all 560 samples, every field with route and confidence · PRJNA1181778_determinations.csv.gz (21.4 KB) — 3,360 evidence rows