Gut microbiome in post-acute COVID-19 syndrome, Hong Kong
Cross-sectional study of 1676 gut metagenome samples from adults in Hong Kong, examining associations between the gut microbiome and phenotypic manifestations of post-acute COVID-19 syndrome (PACS). machine-written summary
1,676 samples · 1,676 runs · HK · Adult · 2024 · 3.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,347 sample values (collection date, country, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 resolved
Genera, mean relative abundance over 1,513 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 | 1,676 | 100% | ||||
| country | 1,676 | 100% | 1,676 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 643 | 38% | 643 | |||
| collection_date | 1,676 | 100% | 1,676 | |||
| latitude | 1,676 | 100% | 1,676 | |||
| longitude | 1,676 | 100% | 1,676 |
- The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome. 2024 PMID 38657605 own_data
Archive description
Our current understanding of post-acute COVID-19 syndrome (PACS) is limited. In this study, we delineate the role of the gut microbiome in the heterogeneity of PACS and develop a multi-label model for predicting PACS symptoms using both clinical and metagenomic data from 1207 post-COVID-19 subjects. Our processed data covered 585 bacterial species and 500 microbial pathways, altogether explaining 12.7% of the inter-individual variation of PACS. Analysis showed that gut microbiome mediates the associations between host risk factors and PACS. Three gut microbiome-based enterotypes were identified in subjects with PACS and exhibited correlations with different phenotypic manifestations. Symptom-specific gut microbiome signatures were identified for individual symptoms of PACS at both composition and function levels. The trained model showed an accuracy of 0.89 in labelling individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting possible symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrated that gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS and warrants further exploration.
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 microbiome associates with”
- body site study.description · “role of the gut microbiome in the”
- 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 |
|---|---|---|---|---|---|---|
| SAMN40586681 | collection_date | 2024-03 | R1 | 0.90 | biosample.attribute:collection_date | 2024-03 |
| SAMN40586681 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong |
| SAMN40586681 | latitude | 22.3000 | R1 | 0.90 | biosample.attribute:lat_lon | 22.30 N 114.17 E |
| SAMN40586681 | longitude | 114.1700 | R1 | 0.90 | biosample.attribute:lat_lon | 22.30 N 114.17 E |
| SAMN40589952 | subject_id | ID0403 | R1 | 0.85 | biosample.attribute:host | ID0403 |
Sequencing
1,676 runs over 1,676 samples · mean 4.38 Gbp per run (median 3.97 Gbp, total 7,339.00 Gbp; 1,676 runs with a base count) · layout PAIRED 1,676 · platform ILLUMINA 1,676 · models Illumina NovaSeq 6000 (1,676) · 90% of runs with a Sandpiper profile · first public 2024-03-25 – 2024-03-31
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1004982.csv.gz (38.0 KB) · parquet (131.3 KB) — all 1,676 samples, every field with route and confidence · PRJNA1004982_determinations.csv.gz (39.0 KB) — 7,347 evidence rows