Gut microbiome and COVID-19 severity in Boston, MA adults
Case-control study of 241 stool samples from hospitalized adult COVID-19 patients (severe vs moderate disease) in Boston, MA, examining links between gut microbial taxa, pathways, and stool metabolites and disease severity. machine-written summary
241 samples · 241 runs · US · Age unknown · 2023 · 3.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,568 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 241 sample values (location site) · PMC10337137 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 482 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
9 of 42 people sampled more than once (28 samples; median 3, up to 5 per person) · follow-up median 28 d (max 53 d) · median interval between samples 10 d (time from collection dates). Schedule stated by the source: “Stool collected as frequently as once daily during hospitalization, variable per patient; 241 samples from 127 patients.”.
Each row is one person (9 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 222 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 | 241 | 100% | ||||
| country | 241 | 100% | 241 | |||
| health_condition | 241 | 100% | 241 | |||
| subject_id | 61 | 25% | 61 | |||
| collection_date | 241 | 100% | 241 | |||
| detailed_location | 241 | 100% | ||||
| health_condition_detail | 241 | 100% | 241 | |||
| latitude | 241 | 100% | 241 | |||
| location_locality | 241 | 100% | 241 | |||
| location_region | 241 | 100% | 241 | |||
| location_site | 241 | 100% | 241 | |||
| longitude | 241 | 100% | 241 | |||
| timepoint_label | 61 | 25% | 61 |
- Metagenomic assessment of gut microbial communities and risk of severe COVID-19. 2023 PMID 37438797 PMC10337137 own_data
- Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure. 2024 PMID 38830853 PMC11148165 unsure
Archive description
The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, the relationship of the gut microbiome to COVID-19 severity is unknown.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.title · “assessment of gut microbial communities”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35368950 | collection_date | 2020-04-16 | R1 | 0.90 | biosample.attribute:collection_date | 2020-04-16 |
| SAMN35368950 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston, MA |
| SAMN35368950 | health_condition | other_infection | R2 | 0.75 | external.gmrepo source | phenotype: COVID-19 |
| SAMN35368950 | health_condition_detail | COVID-19 | R2 | 0.75 | external.gmrepo source | phenotype: COVID-19 |
| SAMN35368950 | latitude | 42.3601 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN35368950 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston, MA |
| SAMN35368950 | location_region | Massachusetts | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Boston, MA |
| SAMN35368950 | location_site | Massachusetts General Hospital | R3 | 0.70 | paper.fulltext.methods | hospitalized patients aged ≥ 18 years with confirmed COVID-19 at the Massachusetts |
| SAMN35368950 | longitude | -71.0589 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN35368950 | subject_id | 101607 | R1 | 0.70 | sample.name_rule:alias | 101607_1 |
| SAMN35368950 | timepoint_label | 1 | R1 | 0.60 | sample.name_rule:alias | 101607_1 |
Sequencing
241 runs over 241 samples · mean 4.17 Gbp per run (median 3.80 Gbp, total 1,004.68 Gbp; 241 runs with a base count) · layout PAIRED 241 · platform ILLUMINA 241 · models Illumina NovaSeq 6000 (241) · 92% of runs with a Sandpiper profile · first public 2023-08-21
Authors (47)
Nguyen LH first · Okin D · Drew DA · Battista VM · Jesudasen SJ · Kuntz TM · Bhosle A · Thompson KN · Reinicke T · Lo CH · Woo JE · Caraballo A · Berra L · Vieira J · Huang CY · Das Adhikari U · Kim M · Sui HY · Magicheva-Gupta M · McIver L · Goldberg MB · Kwon DS · Huttenhower C · Chan AT · Lai PS last · Kitsios GD first · Sayed K · Fitch A · Yang H · Britton N · Shah F · Bain W · Evankovich JW · Qin S · Wang X · Li K · Patel A · Zhang Y · Radder J · Dela Cruz C · Okin DA · Van Tyne D · Benos PV · Methé B · Lai P · Morris A · McVerry BJ last
Downloads
PRJNA976404.csv.gz (7.7 KB) · parquet (81.2 KB) — all 241 samples, every field with route and confidence · PRJNA976404_determinations.csv.gz (17.2 KB) — 2,291 evidence rows