Gut metagenome of hospitalized COVID-19 patients, New York
36 stool samples from hospitalized COVID-19 patients in New York, USA, studied in a case-control design examining gut microbiome, viral RNA, and immune markers. machine-written summary
36 samples · 36 runs · US · Age unknown · 2020 · 1.49 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 216 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 36 sample values (location site) · PMC10411309, PMC11581176, PMC8233421 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 72 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: “Stool collected longitudinally during acute and convalescent phases; median 16 days (range 2-66) between samples”.
Genera, mean relative abundance over 26 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 | 36 | 100% | 36 | |||
| health_condition | 36 | 100% | 36 | |||
| subject_id | 36 | 100% | 36 | |||
| collection_date | 36 | 100% | 36 | |||
| detailed_location | 36 | 100% | ||||
| health_condition_detail | 36 | 100% | 36 | |||
| latitude | 36 | 100% | 36 | |||
| location_region | 36 | 100% | 36 | |||
| location_site | 36 | 100% | 36 | |||
| longitude | 36 | 100% | 36 |
- Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. 2021 PMID 34172783 PMC8233421 own_data
- SARS-CoV-2-specific IgA and limited inflammatory cytokines are present in the stool of select patients with acute COVID-19 2020 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
3 more
- Robust cross-cohort gut microbiome associations with COVID-19 severity. 2023 PMID 37550964 PMC10411309
- Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID. 2024 PMID 39551951 PMC11581176
- Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes 2022
Archive description
16S and metagenomic sequences from individuals with acute COVID19
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host study.title · “human stool Metagenome from acute COVID19+ subjects”
- body site study.title · “human stool Metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16049475 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN16049475 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN16049475 | health_condition | other_infection | R2 | 0.75 | external.gmrepo source | phenotype: COVID-19 |
| SAMN16049475 | health_condition_detail | COVID-19 | R2 | 0.75 | external.gmrepo source | phenotype: COVID-19 |
| SAMN16049475 | latitude | 40.7100 | R1 | 0.90 | biosample.attribute:lat_lon | 40.71 N 74.00 W |
| SAMN16049475 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN16049475 | location_site | Mount Sinai Hospital | R3 | 0.70 | paper.fulltext.methods | admitted to the Mount Sinai Hospital for COVID-19 infection |
| SAMN16049475 | longitude | -74.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 40.71 N 74.00 W |
| SAMN16049475 | subject_id | MH001827_V1 | R1 | 0.85 | sample.attr.subject_id | MH001827_V1 |
Sequencing
36 runs over 36 samples · mean 1.39 Gbp per run (median 1.49 Gbp, total 50.07 Gbp; 36 runs with a base count) · layout PAIRED 36 · platform ILLUMINA 36 · models Illumina HiSeq 4000 (36) · 72% of runs with a Sandpiper profile · first public 2020-10-20
Authors (51)
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 · Yao L first · Devotta H · Li J · Lunjani N · Sadlier C · Lavelle A · Albrich WC · Walter J · O'Toole PW · O'Mahony L last · Britton GJ first · Chen-Liaw A · Cossarini F · Liu Y last · Livanos AE · Spindler MP · Plitt T · Eggers J · Mogno I · Gonzalez-Reiche AS · Siu S · Tankelevich M · Grinspan LT · Dixon RE · Jha D · Martinez-Delgado G · Amanat F · Hoagland DA · tenOever BR · Dubinsky MC · Merad M · Bakel Hv · Krammer F · Bongers G · Mehandru S · Faith JJ last
Downloads
PRJNA660883.csv.gz (1.8 KB) · parquet (71.5 KB) — all 36 samples, every field with route and confidence · PRJNA660883_determinations.csv.gz (3.1 KB) — 324 evidence rows