Gut metagenomes in COVID-19 patients vs controls, Hong Kong
274 stool samples from adults in Shatin, Hong Kong, comparing gut microbiome composition between COVID-19 patients and healthy controls in a cross-sectional study, including serial samples after SARS-CoV-2 clearance. machine-written summary
274 samples · 274 runs · HK · Adult · 2021 · 5.50 Gbp / sample · cohort Variation in the metagenomic analysis of fecal mic
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,684 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10411309, PMC7804842 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 156 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Serial stool samples from COVID-19 patients during hospitalisation and up to 30 days after SARS-CoV-2 clearance; 41/100 patients provided multiple samples”; stated follow-up 30 d.
Genera, mean relative abundance over 241 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 | 274 | 100% | ||||
| country | 274 | 100% | 274 | |||
| health_condition | 274 | 100% | 196 | 78 | ||
| subject_id | 0 | 0% | ||||
| detailed_location | 274 | 100% | ||||
| health_condition_detail | 274 | 100% | 196 | 78 | ||
| latitude | 274 | 100% | 274 | |||
| location_locality | 274 | 100% | 274 | |||
| longitude | 274 | 100% | 274 | |||
| collection_date | 196 | 72% | 196 |
- Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. 2021 PMID 33431578 PMC7804842 own_data
- Association Between Altered Microbiota Composition and Immune System-Related Genes in COVID-19 Infection. 2025 PMID 38456962 own_data
- Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. 2022 PMID 36068270 PMC9446638 unsure
- Robust cross-cohort gut microbiome associations with COVID-19 severity. 2023 PMID 37550964 PMC10411309 unsure
- Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. 2024 PMID 38930440 PMC11205787 unsure
6 more
- Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach. 2024 PMID 39475247 PMC11619352
- Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID. 2024 PMID 39551951 PMC11581176
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
- <i>Akkermansia muciniphila</i> primes lung-resident antiviral immunity via the gut-lung axis during SARS-CoV-2 infection. 2026 PMID 41836373 PMC12982362
- Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes 2022
- Two dimensions of chemical variation of the human microbiome across body sites and in COVID-19 patients 2023
Archive description
Stool samples were collected from in-hospital COVID-19 patients to characterise gut microbiome community composition associated with this disease.
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 · “Gut metagenomes of patients”
- body site study.description · “Stool samples were collected”
- 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 |
|---|---|---|---|---|---|---|
| SAMN15723009 | collection_date | 2020-03 | R1 | 0.90 | biosample.attribute:collection_date | 2020-03 |
| SAMN15722979 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong: Shatin |
| SAMN15723009 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:description | COVID-19 |
| SAMN15722979 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN15723009 | health_condition_detail | COVID-19 | R1 | 0.85 | biosample.attribute:description | COVID-19 |
| SAMN15722979 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN15722979 | latitude | 22.3800 | R1 | 0.90 | biosample.attribute:lat_lon | 22.38 N 114.2 E |
| SAMN15722979 | location_locality | Shatin | R1 | 0.85 | biosample.attribute:geo_loc_name | Hong Kong: Shatin |
| SAMN15722979 | longitude | 114.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 22.38 N 114.2 E |
Sequencing
274 runs over 274 samples · mean 6.79 Gbp per run (median 5.50 Gbp, total 1,859.20 Gbp; 274 runs with a base count) · layout PAIRED 274 · platform ILLUMINA 274 · models Illumina NovaSeq 6000 (274) · 88% of runs with a Sandpiper profile · first public 2021-01-12 – 2021-01-13
Authors (41)
Ahmadi Badi S first · Kariman A · Bereimipour A · Shojaie S · Aghsadeghi M · Khatami S · Masotti A last · Pusadkar V first · Mazumder A · Azad A · Patil D · Azad RK last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Xu Z first · Yeoh YK · Tun HM · Fei N · Zhang J · Morrison M · Kamm MA · Yu J · Chan FKL · Ng SC last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last · Ke S first · Weiss ST · Liu Y last
Downloads
PRJNA650244.csv.gz (7.4 KB) · parquet (80.0 KB) — all 274 samples, every field with route and confidence · PRJNA650244_determinations.csv.gz (11.2 KB) — 1,840 evidence rows