Gut microbiome in hospitalized COVID-19 patients, Poland

The gut microbiome has been recognized as a key player in various disease conditions, including COVID-19. In this study, we conducted an extensive gut microbiome analysis in 204 COVID-19 patients hospitalized in two large hospitals in Poland. By employing both shallow and deep shotgun sequencing methods, we aimed to track the changes in microbiota composition induced by hospitalization and COVID-19 treatment. We investigated the associations between microbiome alterations and clinical procedures, such as antibiotics administration, and outcomes, including ICU referral and survival. Notably, our study included a larger cohort than previously published works, allowing for robust conclusions. Leveraging machine learning techniques, we explored the microbiome's predictive potential for COVID-19 prognosis and assessed its performance compared to traditional baseline classifiers (sex, age, BMI). Additionally, we evaluated the feasibility of shallow shotgun sequencing as a cost-effective alternative for diagnostic use in clinical settings. Our findings provide valuable insights into the gut microbiome's role in COVID-19 patients and its potential as a predictive tool for patient outcomes.

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.description · “The gut microbiome has been”
• body site external_curation.infant_catalog · “body_site_call gut”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

383 runs over 383 samples · mean 9.99 Gbp per run (median 10.05 Gbp, total 3,825.36 Gbp; 383 runs with a base count) · layout PAIRED 383 · platform ILLUMINA 383 · models Illumina NovaSeq 6000 (383) · 8% of runs with a Sandpiper profile · first public 2025-07-11

Kopera K first · Gromowski T · Wydmański W · Skonieczna-Żydecka K · Muszyńska A · Zielińska K · Wierzbicka-Woś A · Kaczmarczyk M · Kadaj-Lipka R · Cembrowska-Lech D · Januszkiewicz K · Kotfis K · Witkiewicz W · Nalewajska M · Feret W · Marlicz W · Łoniewski I · Łabaj PP · Rydzewska G · Kosciolek T last

PRJEB91718.csv.gz (11.6 KB) · parquet (88.1 KB) — all 383 samples, every field with route and confidence · PRJEB91718_determinations.csv.gz (30.2 KB) — 4,242 evidence rows