Fig. 1

Overview of the dataset and microbial composition in different sample types of COVID-19 patients. A Summary of sample and patient information used in this study (left) and distribution of sequencing depth for each sample (right). Uppercase N indicates the number of patients and lower-case n represents the number of samples. Besides disease diagnosis, gender, and sample types, samples were also divided into young (<15 years old), working age (15–60 years old), and old (≥60 years old) groups based on patient age. Samples with nonhuman reads less than 100,000 were labeled in gray and excluded from further analysis. B Comparison of alpha diversity between healthy controls and COVID-19 patients. Wilcox rank-sum test was used. C PCoA and PERMANOVA analysis of the microbial composition using Bray-Curtis distance in healthy controls and COVID-19 patients. Detailed microbial community was also profiled at genus level for pharyngeal (D), sputum (E), and faeces (F) samples. Only the first sample of each subject was used for comparison in B–F