Gut microbiome in COVID-19 vs healthy controls, Hong Kong
208 fecal samples from Hong Kong, comparing COVID-19 patients (serial samples during hospitalization and after recovery) with non-COVID-19 healthy controls, in a case-control study of gut microbiome function. machine-written summary
208 samples · 208 runs · Age unknown · 2022 · 5.79 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,041 sample values (collection date, health condition, health condition detail, location locality, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10355065, PMC11581176, PMC8529231 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 208 sample values (antibiotic exposure) · from BugSigDB, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: sequence archive and GMrepo disagree for 208 samples (e.g. HK vs CN) — withheld.
The sources disagree on 208 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 208)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN22565315 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565316 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565317 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565318 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565319 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565320 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565321 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565322 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565323 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565324 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565325 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565326 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565327 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565328 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565329 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565330 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565331 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565332 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565333 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565334 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565335 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565336 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565337 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565338 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565339 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565340 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565341 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565342 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565343 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565344 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565345 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565346 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565347 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565348 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565349 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565350 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565351 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565352 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565353 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN22565354 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
longitudinal
44 of 44 people sampled more than once (107 samples; median 2, up to 7 per person) · follow-up median 37 d (max 3 mo) · median interval between samples 20 d (time from collection dates).
Each row is one person (36 shown of 44); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 190 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 | 0 | 0% | ||||
| health_condition | 208 | 100% | 208 | |||
| subject_id | 107 | 51% | 107 | |||
| antibiotic_exposure | 208 | 100% | 208 | |||
| detailed_location | 208 | 100% | ||||
| health_condition_detail | 208 | 100% | 208 | |||
| location_locality | 208 | 100% | 208 | |||
| collection_date | 207 | 100% | 207 | |||
| timepoint_label | 103 | 50% | 103 |
- Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19. 2022 PMID 34687739 PMC8529231 own_data
- Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. 2022 PMID 36068270 PMC9446638 unsure
- Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection. 2022 PMID 36086955 PMC9538590 unsure
- Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis. 2023 PMID 36744910 PMC9973266 unsure
- Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites. 2023 PMID 37468867 PMC10355065 unsure
2 more
- Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID. 2024 PMID 39551951 PMC11581176
- Guild-level microbiome signature associated with COVID-19 severity and prognosis 2022
Archive description
Comparison of gut microbiome between patient with COVID-19 and healthy individual and characterize the gut microbiome alterations in COVID-19 recovery patient.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Gut microbiome sequencing”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN22565315 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN22565490 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMN22565315 | collection_date | 2020-06-12 | R1 | 0.90 | biosample.attribute:collection_date | 2020-06-12 |
| SAMN22565315 | health_condition | other_infection | R1 | 0.70 | sample.name_rule:library_names | COV_1-1 |
| SAMN22565315 | health_condition_detail | COV | R1 | 0.70 | sample.name_rule:library_names | COV_1-1 |
| SAMN22565315 | location_locality | Hong Kong | R1 | 0.75 | biosample.attribute:geo_loc_name | China: HongKong |
| SAMN22565315 | subject_id | COV_1 | R1 | 0.70 | sample.name_rule:library_names | COV_1-1 |
| SAMN22565315 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:library_names | COV_1-1 |
Sequencing
208 runs over 208 samples · mean 6.79 Gbp per run (median 5.79 Gbp, total 1,411.84 Gbp; 208 runs with a base count) · layout PAIRED 208 · platform ILLUMINA 208 · models Illumina NovaSeq 6000 (208) · 91% of runs with a Sandpiper profile · first public 2022-01-01
Authors (64)
Zhang F first · Wan Y · Zuo T · Yeoh YK · Liu Q · Zhang L · Zhan H · Lu W · Xu W · Lui GCY · Li AYL · Cheung CP · Wong CK · Chan PKS · Chan FKL · Ng SC last · Ke S first · Weiss ST · Liu YY last · Mancabelli L first · Milani C · Fontana F · Lugli GA · Tarracchini C · Viappiani A · Ciociola T · Ticinesi A · Nouvenne A · Meschi T · Turroni F · Ventura M last · Zhang D first · Weng S · Xia C · Ren Y · Liu Z · Xu Y · Yang X · Wu R · Peng L · Sun L · Zhu J · Liang X · Jia Y · Wang H · Chen Q · Liu D · Chen Y · Guo H · Han X · Jin Z · Chen C · Li Z · Huang H last · Yao L first · Devotta H · Li J · Lunjani N · Sadlier C · Lavelle A · Albrich WC · Walter J · O'Toole PW · O'Mahony L last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, country. Share metadata
Downloads
PRJNA689961.csv.gz (6.8 KB) · parquet (78.7 KB) — all 208 samples, every field with route and confidence · PRJNA689961_determinations.csv.gz (13.0 KB) — 1,249 evidence rows