Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data

Sainan Zhang; Xingwang Liu; Yue Zhao; Ping Wang; Rui Yu; Peigang Xu; Yue Jiang; Liang Cheng

doi:10.1016/j.compbiomed.2023.107400

Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data

Comput Biol Med. 2023 Oct:165:107400. doi: 10.1016/j.compbiomed.2023.107400. Epub 2023 Aug 26.

Authors

Sainan Zhang¹, Xingwang Liu², Yue Zhao³, Ping Wang⁴, Rui Yu⁵, Peigang Xu⁶, Yue Jiang⁷, Liang Cheng⁸

Affiliations

¹ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. Electronic address: zhangsainan@hrbmu.edu.cn.
² College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. Electronic address: xingwangliu@hrbmu.edu.cn.
³ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. Electronic address: 2021020551@hrbmu.edu.cn.
⁴ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. Electronic address: ping.wang@hrbmu.edu.cn.
⁵ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. Electronic address: yurui@hrbmu.edu.cn.
⁶ Chongqing Research Institute of Harbin Institute of Technology, China. Electronic address: peigang.xu@hit.edu.cn.
⁷ Cipher Gene, Ltd., Beijing, 100080, China. Electronic address: yue.jiang.hit@gmail.com.
⁸ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China; NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China. Electronic address: liangcheng@hrbmu.edu.cn.

PMID: 37651767
DOI: 10.1016/j.compbiomed.2023.107400

Abstract

After infection with SARS-CoV-2, the microbiome inside the human body changes dramatically. By re-annotating microbial sequences in bulk RNA-seq and scRNA-seq data of COVID-19 patients, we described the cellular microbial landscape of COVID-19 patients and identified characteristic microorganisms in various tissues. We found that Acinetobacter lwoffii was highly correlated with COVID-19 symptoms and might disrupt some pathways of patients by interacting with the host and other microbes, such as Klebsiella pneumoniae. We further identified characteristic microorganisms specific to cell type, indicating the enrichment preference of some microbes. We also revealed the co-infection of SARS-CoV-2 with hMPV, which may cause the development of COVID-19. Overall, we demonstrated that the presence of intracellular microorganisms in COVID-19 patients and the synergies between microorganisms were strongly correlated with disease progression, providing a theoretical basis for COVID-19 treatment in a certain extent.

Keywords: COVID-19; Cell type-specific microbe; Microbial re-annotation; hMPV co-infection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 Drug Treatment
COVID-19*
Humans
Microbiota* / genetics
RNA-Seq
SARS-CoV-2
Single-Cell Gene Expression Analysis