A multi-omics study of COVID-19 patients and associations of the upper respiratory microbiome to clinical outcomes. human nasopharyngeal metagenome

In this study, we explore how the microbial community might influence the disease's clinical outcomes. To accomplish this, we employed multi-omics techniques on naso-oropharyngeal swab samples of 566 patients (COVID-19/Controls) for the characterization of viruses, bacteria, fungi, and host mRNA transcripts. We performed: 1) Diversity and composition profiling of bacterial and fungal communities through 16S/ITS amplicon sequencing to identify ASVs (Amplicon Sequence Variants) for estimating their abundances; 2) Total RNA sequencing for virus identification and functional analyses, encompassing both human and microbial transcripts; 3) Total DNA metagenomics sequencing for in-depth genomic analyses and recovering of Metagenome-Assembled Genomes (MAGs), which allowed strain-specific identification of bacterial and fungal species, as well as the characterization of the presence of antibiotic resistance genes, virulence factors, and endotoxins.