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 and elderly 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 Dynamics and”
• body site study.description · “The gut microbiome has been”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• life stage sample.attr.host_age · “70 (n=254/946)”

946 runs over 946 samples · mean 96.1 Mbp per run (median 93.1 Mbp, total 90.88 Gbp; 946 runs with a base count) · layout PAIRED 946 · platform ILLUMINA 946 · models Illumina MiSeq (946) · 0% of runs with a Sandpiper profile · first public 2023-09-29

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 · Udekwu KI · Rudnicki W · Frolova A

PRJEB64515.csv.gz (28.8 KB) · parquet (115.6 KB) — all 946 samples, every field with route and confidence · PRJEB64515_determinations.csv.gz (84.4 KB) — 11,025 evidence rows