Gut microbiome in COVID-19 patients, Japan, cross-sectional
Cross-sectional study of 208 gut metagenome samples from Japan, comparing COVID-19/other-infection samples (103) with healthy controls (105) to characterize gut microbiome features. machine-written summary
208 samples · 208 runs · JP · Age unknown · 2023 · 6.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 624 sample values (country, health condition, health condition detail) |
| ○ 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 |
Genera, mean relative abundance over 189 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 | 208 | 100% | 208 | |||
| health_condition | 208 | 100% | 208 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 208 | 100% | 208 |
- Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. 2024 PMID 38930440 PMC11205787 unsure
Archive description
We aim to investigate the characteristics of gut microbiome in COVID-19 patients in Japan by performing the metagenomic analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.82. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “gut microbiome in COVID-19 patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00447339 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00447339 | health_condition | other_infection | R1 | 0.70 | sample.name_rule:title | gut microbiome of covid-19-1001 |
| SAMD00447339 | health_condition_detail | COVID-19 patient (title literal 'gut microbiome of covid-19-XXXX'; project title/description: 'gut microbiome in COVID-19 patients') | R1 | 0.70 | sample.name_rule:title | gut microbiome of covid-19-1001 |
Sequencing
208 runs over 208 samples · mean 7.03 Gbp per run (median 6.41 Gbp, total 1,462.42 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 2023-03-04
Authors (5)
Pusadkar V first · Mazumder A · Azad A · Patil D · Azad RK last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJDB13214.csv.gz (5.9 KB) · parquet (76.7 KB) — all 208 samples, every field with route and confidence · PRJDB13214_determinations.csv.gz (5.8 KB) — 624 evidence rows