Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium

Area of Science:

• Microbiology
• Genomics
• Bacteriology

Background:

• Enterococcus faecalis is a common gut bacterium with both probiotic and pathogenic strains.
• Distinguishing between these strains is challenging with traditional methods.

Purpose of the Study:

• To perform whole-genome sequencing of the probiotic strain EF-2001.
• To compare the genome of EF-2001 with pathogenic strains to identify distinguishing features.
• To develop a genomic approach for predicting the probiotic or pathogenic potential of E. faecalis.

Main Methods:

• In-house hybrid assembly for genome sequencing of EF-2001.
• Comparative genomic analysis with pathogenic E. faecalis strains.
• Core- and pan-genome analyses.

Main Results:

• EF-2001 lacks cytolysins, key virulence factors found in pathogenic strains.
• EF-2001 is phylogenetically distinct from pathogenic E. faecalis V583.
• EF-2001 does not possess additional drug-resistance genes beyond those common to all analyzed strains.
• 49 genes specific to EF-2001 were identified, potentially linked to its probiotic functions.

Conclusions:

• Comparative genomics can effectively differentiate probiotic E. faecalis strains from pathogenic ones.
• The genomic features of EF-2001 support its probiotic classification.
• Further study of EF-2001-specific genes may elucidate its beneficial biological activities.