Gut microbiome in COVID-19 severity, China, case-control
38 faecal samples from adults and elderly individuals in China, comparing severe/critical versus mild/moderate COVID-19 cases in a case-control design to study gut microbiota and host immune response links. machine-written summary
38 samples · 38 runs · CN · Adult · 2022 · 12.44 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 266 sample values (age, collection date, country, health condition, health condition detail, sex, 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 38 | 100% | ||||
| country | 38 | 100% | 38 | |||
| health_condition | 38 | 100% | 38 | |||
| subject_id | 38 | 100% | 38 | |||
| age_at_collection_days | 38 | 100% | 38 | |||
| collection_date | 38 | 100% | 38 | |||
| health_condition_detail | 38 | 100% | 38 | |||
| sex | 38 | 100% | 38 |
- 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
- Guild-level microbiome signature associated with COVID-19 severity and prognosis 2022 unsure
Archive description
To study the interplay between the gut microbiota and host immune response in COVID-19 patients, we profiled the gut microbiome in 14 severe/critical and 24 mild/moderate COVID-19 cases and analyzed gut microbes' diversity, composition, and features between the two groups. Moreover, we investigated the correlation between the gut microbes and the clinical features (including serology, immune cell composition, and markers related to organ damage) and uncovered potential links between the gut microbe diversity and host immune response post-SARS-CoV-2 infection.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “profiled the gut microbiome in 14 severe/critical”
- life stage sample.attr.host_age · “26 (n=31/38)”
- life stage sample.attr.host_age · “72 (n=6/38)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN24451555 | age_at_collection_days | 11688.0 | R1 | 0.70 | sample.attr.host_age | 32 |
| SAMN24451555 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN24451555 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN24451555 | health_condition | other_infection | R1 | 0.85 | biosample_attr | COVID-19 |
| SAMN24451555 | health_condition_detail | COVID-19 | R1 | 0.90 | sample.attr.host_disease | COVID-19 |
| SAMN24451555 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN24451555 | subject_id | M1 | R1 | 0.70 | sample.name_rule:isolate | isolate M1; TITLE Mild COVID-19 patient 1 |
Sequencing
38 runs over 38 samples · mean 12.21 Gbp per run (median 12.44 Gbp, total 463.90 Gbp; 38 runs with a base count) · layout PAIRED 38 · platform ILLUMINA 38 · models Illumina NovaSeq 6000 (38) · 95% of runs with a Sandpiper profile · first public 2022-03-18
Authors (25)
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 · Guo M first · Wu G · Tan Y · Li Y · Jin X · Qi W · Guo X · Zhang C · Zhu Z · Zhao L last
Downloads
PRJNA792726.csv.gz (2.1 KB) · parquet (71.1 KB) — all 38 samples, every field with route and confidence · PRJNA792726_determinations.csv.gz (2.8 KB) — 266 evidence rows