Gut and oral microbiome in COVID-19, Cork, Ireland
Cross-sectional study of 101 faecal and saliva samples from adults and elderly individuals in Cork, Ireland, characterising virome and bacteriome across acute and recovery stages of SARS-CoV-2 infection. machine-written summary
101 samples · 101 runs · IE · Adult · 2025 · 3.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 897 sample values (age, antibiotic exposure, collection date, country, latitude, location region, longitude, sex) |
| ✓ Abstract / description | 202 sample values (health condition, health condition detail) |
| – 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 |
longitudinal
28 of 43 people sampled more than once (82 samples; median 3, up to 4 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 38 d (time from collection dates). Schedule stated by the source: “archive time labels: T1, T2, T3” (time origin: infection_onset).
Each row is one person (27 shown of 28); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 95 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 | 101 | 100% | ||||
| country | 101 | 100% | 101 | |||
| health_condition | 101 | 100% | 101 | |||
| subject_id | 97 | 96% | 97 | |||
| age_at_collection_days | 101 | 100% | 101 | |||
| collection_date | 101 | 100% | 101 | |||
| detailed_location | 101 | 100% | ||||
| health_condition_detail | 101 | 100% | 101 | |||
| latitude | 101 | 100% | 101 | |||
| location_region | 101 | 100% | 101 | |||
| longitude | 101 | 100% | 101 | |||
| sex | 101 | 100% | 101 | |||
| timepoint_label | 82 | 81% | 82 | |||
| antibiotic_exposure | 11 | 11% | 11 |
Archive description
Analysis of both the virome and bacteriome from faecal and saliva samples, in various acute and recovery stages of COVID-19
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.82. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- life stage sample.attr.host_age · “51 (n=76/101)”
- life stage sample.attr.host_age · “75 (n=20/101)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43457766 | age_at_collection_days | 22280.2 | R1 | 0.70 | sample.attr.host_age | 61 |
| SAMN43457820 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | Co-amoxiclav x2/7, Clarithro x1/7 |
| SAMN43457766 | collection_date | 2020-08-26 | R1 | 0.90 | biosample.attribute:collection_date | 2020-08-26 |
| SAMN43457766 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN43457766 | health_condition | other_infection | R4 | 0.50 | study.title | during SARS-COV-2 infection |
| SAMN43457766 | health_condition_detail | COVID-19 patients in acute and recovery stages | R4 | 0.50 | study.title | during SARS-COV-2 infection |
| SAMN43457766 | latitude | 51.8800 | R1 | 0.90 | biosample.attribute:lat_lon | 51.88 N 8.51 W |
| SAMN43457766 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN43457766 | longitude | -8.5100 | R1 | 0.90 | biosample.attribute:lat_lon | 51.88 N 8.51 W |
| SAMN43457766 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN43457766 | subject_id | CUH001 | R1 | 0.70 | sample.name_rule:alias | CUH001_T1 |
| SAMN43457766 | timepoint_label | T1 | R1 | 0.70 | sample.name_rule:alias | CUH001_T1 |
Sequencing
101 runs over 101 samples · mean 4.89 Gbp per run (median 3.59 Gbp, total 494.22 Gbp; 101 runs with a base count) · layout PAIRED 101 · platform ILLUMINA 101 · models Illumina NovaSeq 6000 (101) · 96% of runs with a Sandpiper profile · first public 2025-09-03 – 2025-09-21
Authors (0)
No author record.
Downloads
PRJNA1155319.csv.gz (4.4 KB) · parquet (76.1 KB) — all 101 samples, every field with route and confidence · PRJNA1155319_determinations.csv.gz (8.9 KB) — 1,099 evidence rows