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Additional file 1: Figure S1. The COVID-19 related inflammatory biomarkers in patients at different disease stages. Figure S2. Timeline of disease progression and sample collection for COVID-19 patients with multiple samples. Figure S3. The ��-diversity of the gut microbiome among all the participants. Figure S4. The relative abundance of Bacteroides nordii throughout the hospitalization of COVID-19 patients. Figure S5. The relative abundance of Blautia sp. CAF 257 throughout the hospitalization of COVID-19 patients. Figure S6. The relative abundance of Burkholderia contaminans throughout the hospitalization of COVID-19 patients. Figure S7. The relative abundance of Bifidobacterium longum throughout the hospitalization of COVID-19 patients. Figure S8. The associations between COVID-19 related microbial features and RNA modules indicating T cell response. Figure S9. The influence of oral antibiotics uses on the gut microbiome of severe COVID-19 patients. Figure S10. The detail of samples for multi-omics measurement. Figure S11. The profiles of the gut microbiome annotated by the metaproteomics approach. Figure S12. The significantly differential abundant human proteins in fecal samples from COVID-19 patients and controls. Figure S13. The circulating levels of LPS-binding protein in COVID-19 patients. Figure S14. The microbial taxa identified in plasma samples from COVID-19 patients and controls through the proteomic approach.