Open Access Research article

A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression

De Chang1, Yuanfang Zhu2, Li An1, Jinwen Liu2, Longxiang Su1, Yinghua Guo1, Zhenhong Chen1, Yajuan Wang1, Li Wang1, Junfeng Wang1, Tianzhi Li1, Xiangqun Fang1, Chengxiang Fang2, Ruifu Yang23* and Changting Liu1*

Author Affiliations

1 Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, Beijing 100853, China

2 BGI-Shenzhen, Shenzhen, People’s Republic of China

3 State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

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BMC Microbiology 2013, 13:304  doi:10.1186/1471-2180-13-304

Published: 28 December 2013



For a long time, Enterococcus faecium was considered a harmless commensal of the mammalian gastrointestinal (GI) tract and was used as a probiotic in fermented foods. In recent decades, E. faecium has been recognised as an opportunistic pathogen that causes diseases such as neonatal meningitis, urinary tract infections, bacteremia, bacterial endocarditis and diverticulitis. E. faecium could be taken into space with astronauts and exposed to the space environment. Thus, it is necessary to observe the phenotypic and molecular changes of E. faecium after spaceflight.


An E. faecium mutant with biochemical features that are different from those of the wild-type strain was obtained from subculture after flight on the SHENZHOU-8 spacecraft. To understand the underlying mechanism causing these changes, the whole genomes of both the mutant and the WT strains were sequenced using Illumina technology. The genomic comparison revealed that dprA, a recombination-mediator gene, and arpU, a gene associated with cell wall growth, were mutated. Comparative transcriptomic and proteomic analyses showed that differentially expressed genes or proteins were involved with replication, recombination, repair, cell wall biogenesis, glycometabolism, lipid metabolism, amino acid metabolism, predicted general function and energy production/conversion.


This study analysed the comprehensive genomic, transcriptomic and proteomic changes of an E. faecium mutant from subcultures that were loaded on the SHENZHOU-8 spacecraft. The implications of these gene mutations and expression changes and their underlying mechanisms should be investigated in the future. We hope that the current exploration of multiple “-omics” analyses of this E. faecium mutant will provide clues for future studies on this opportunistic pathogen.

E. faecium; Genome; Transcriptome; Proteome; Multi-omics