Gut microbiome in COVID-19 vs controls, Luxembourg
125 gut metagenome samples from asymptomatic-to-moderate COVID-19 patients and healthy controls in Luxembourg, in a case-control study of microbiome virulence factor and antimicrobial resistance gene abundance. machine-written summary
125 samples · 125 runs · LU · Age unknown · 2022 · 2.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 440 sample values (collection date, country, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 185 sample values (collection date, location site) · PMC9995755 |
| ✓ Supplementary tables | 590 sample values (age, bmi, health condition, health condition detail, sex) |
| – 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 |
Genera, mean relative abundance over 114 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 | 125 | 100% | ||||
| country | 125 | 100% | 125 | |||
| health_condition | 118 | 94% | 118 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 125 | 100% | 65 | 60 | ||
| detailed_location | 125 | 100% | ||||
| latitude | 125 | 100% | 125 | |||
| location_site | 125 | 100% | 125 | |||
| longitude | 125 | 100% | 125 | |||
| age_at_collection_days | 118 | 94% | 118 | |||
| bmi | 118 | 94% | 118 | |||
| health_condition_detail | 118 | 94% | 118 | |||
| sex | 118 | 94% | 118 |
- Altered infective competence of the human gut microbiome in COVID-19. 2023 PMID 36894986 PMC9995755 own_data
- Altered infective competence of the human gut microbiome in COVID-19 2022 own_data
Archive description
The effects of SARS-CoV-2 infections comprise of many heterogeneous symptoms including several involving the human gastrointestinal tract. Reports, thus far, have shown pronounced effects of COVID-19 on the gastrointestinal microbiome. However, these studies report differences between severe cases of infection compared to healthy controls, where in particular the loss of commensal taxa are reported. However, it remains unclear whether microbiome alterations including functional shifts are a common effect of COVID-19. Here, we used high-resolution, systematic multi-omic analyses to resolve differences in the gut microbiome following COVID-19. We find an increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19 patients. Importantly, these genes are encoded and expressed by taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19 patients. We also found an enrichment in the expression of rotavirus C genes in COVID-19 patients compared to healthy controls. Collectively, our analyses identify an altered and increased infective proficiency of the gut microbiome in COVID-19 patients, which may cause acute and possibly future burden conferred by other infective agents.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Altered infective proficiency of the gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31264540 | age_at_collection_days | 19358 | R2 | 0.85 | paper.supp.40168_2023_1472_MOESM5_ESM.xlsx[Metadata filtred!age] | 53 |
| SAMN31264540 | bmi | 22.27 | R2 | 0.85 | paper.supp.40168_2023_1472_MOESM5_ESM.xlsx[Metadata filtred!bmi] | 22.265625 |
| SAMN31264540 | collection_date | 2020-05-04 | R1 | 0.90 | biosample.attribute:collection_date | 2020-05-04 |
| SAMN31264605 | collection_date | 2020-05/2020-10 | R3 | 0.70 | paper.fulltext.methods | Between May and October 2020, stool samples were collected |
| SAMN31264540 | country | LU | R1 | 0.90 | sample.attr.geo_loc_name | Luxembourg |
| SAMN31264540 | health_condition | other_infection | R2 | 0.80 | paper.supp.40168_2023_1472_MOESM5_ESM.xlsx[Metadata filtred!cohort] | cohort: SARS-CoV-2 positive |
| SAMN31264540 | health_condition_detail | SARS-CoV-2 positive | R2 | 0.80 | paper.supp.40168_2023_1472_MOESM5_ESM.xlsx[Metadata filtred!cohort] | cohort: SARS-CoV-2 positive |
| SAMN31264540 | latitude | 49.6000 | R1 | 0.90 | biosample.attribute:lat_lon | 49.6 N 6.13 E |
| SAMN31264540 | location_site | Integrated BioBank of Luxembourg (IBBL) | R3 | 0.70 | paper.fulltext.methods | Samples and data were collected at the Integrated BioBank of Luxembourg |
| SAMN31264540 | longitude | 6.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 49.6 N 6.13 E |
| SAMN31264540 | sex | female | R2 | 0.85 | paper.supp.40168_2023_1472_MOESM5_ESM.xlsx[Metadata filtred!sex] | female |
Sequencing
125 runs over 125 samples · mean 3.08 Gbp per run (median 2.71 Gbp, total 385.33 Gbp; 125 runs with a base count) · layout PAIRED 125 · platform ILLUMINA 125 · models NextSeq 500 (125) · 91% of runs with a Sandpiper profile · first public 2022-10-21
Authors (27)
de Nies L first · Galata V · Martin-Gallausiaux C · Despotovic M · Busi SB · Snoeck CJ · Delacour L · Budagavi DP · Laczny CC · Habier J · Lupu PC · Halder R · Fritz JV · Marques T · Sandt E · O'Sullivan MP · Ghosh S · Satagopam V · CON-VINCE Consortium · Krüger R · Fagherazzi G · Ollert M · Hefeng FQ · May P · Wilmes P last · Lupu P · O’Sullivan MP
Downloads
PRJNA890008.csv.gz (5.1 KB) · parquet (77.2 KB) — all 125 samples, every field with route and confidence · PRJNA890008_determinations.csv.gz (9.3 KB) — 1,215 evidence rows