Gut microbiome in COVID-19 and long COVID, Latvia
Longitudinal shotgun metagenomics study of 419 samples from adults in Latvia, comparing hospitalized COVID-19 patients and healthy controls to examine gut microbiome changes during acute infection and recovery, including post-acute COVID-19 syndrome. machine-written summary
419 samples · 419 runs · LV · Adult · 2024 · 7.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,797 sample values (country, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10779053 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 — not resolved
76 of 308 people sampled more than once (187 samples; median 2, up to 4 per person). Schedule stated by the source: “Hospitalized COVID-19 patients sampled at acute phase, then ~1 month and ~3 months later (33±5 days and 90±4 days after acute phase).” (time origin: diagnosis); stated follow-up 3 mo.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 419 | 100% | ||||
| country | 419 | 100% | 419 | |||
| health_condition | 419 | 100% | 419 | |||
| subject_id | 419 | 100% | 419 | |||
| health_condition_detail | 419 | 100% | 419 | |||
| timepoint_label | 121 | 29% | 121 |
- Gut Microbiome Composition and Dynamics in Hospitalized COVID-19 Patients and Patients with Post-Acute COVID-19 Syndrome. 2024 PMID 38203738 PMC10779053 own_data
Archive description
The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of COVID-19. We aimed to investigate the dynamics and compositional changes in the gut microbiota of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of long COVID-related complications. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for both longitudinal and cross-sectional analyses. Follow-up assessments were conducted at one and three months post-recruitment. We observed a decline in taxonomic diversity among acute, hospitalized COVID-19 patients compared to healthy controls, followed by an increase during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process, suggesting potential population-specificity in the gut microbiota markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, supporting the development of microbiome-based treatment strategies in managing COVID-19 outcomes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut microbiome composition and”
- body site study.description · “The gut microbiome plays a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114718421 | country | LV | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Latvia |
| SAMEA114718421 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:DESCRIPTION | COVID_gut metagenome |
| SAMEA114718421 | health_condition_detail | COVID_gut metagenome | R1 | 0.85 | biosample.attribute:DESCRIPTION | COVID_gut metagenome |
| SAMEA114718421 | subject_id | 0001 | R1 | 0.70 | sample.name_rule:alias | S0001 |
| SAMEA114718439 | timepoint_label | 3 | R1 | 0.70 | sample.name_rule:alias | S0018_3 |
Sequencing
419 runs over 419 samples · mean 8.44 Gbp per run (median 7.42 Gbp, total 3,535.19 Gbp; 419 runs with a base count) · layout PAIRED 419 · platform DNBSEQ 419 · models DNBSEQ-G400 (419) · 0% of runs with a Sandpiper profile · first public 2024-01-01 – 2024-08-08
Authors (12)
Brīvība M first · Silamiķele L · Birzniece L · Ansone L · Megnis K · Silamiķelis I · Pelcmane L · Borisova D · Rozenberga M · Jagare L · Elbere I · Kloviņš J last
Downloads
PRJEB70508.csv.gz (11.2 KB) · parquet (85.3 KB) — all 419 samples, every field with route and confidence · PRJEB70508_determinations.csv.gz (13.3 KB) — 1,797 evidence rows