Enterococcus faecalis YN771

This study elucidates the effects of different oxygen concentrations on Enterococcus faecalis YN771 and its oxygen adaptation mechanisms through integrated transcriptomic and metabolomic analyses. Figure 1 presents scanning electron microscopy images of E. faecalis YN771 under varying oxygen levels, demonstrating the impact of oxygen concentration on cellular growth and morphology. Figure 2 displays mass spectrometry analysis of microaerobic samples, while Table 2's gas chromatography results indicate that oxygen concentration variations lead to significant changes in individual fatty acid components.
Transcriptional changes were identified through comparative analysis of YN771's complete transcriptome under different oxygen conditions. Principal component analysis (PCA) revealed distinct transcriptomic differences (Figure 3A), with Figure 3B providing a visual comparison of differentially expressed gene (DEG) numbers across oxygen conditions. GO enrichment analysis showed that during the transition from anaerobic to microaerobic conditions (Figure 4A), DEGs were primarily involved in fatty acid biosynthesis and metabolism. The shift from microaerobic to aerobic culture (Figure 4B) revealed differential gene expression related to cell structure formation (particularly extracellular components and cell walls), morphology regulation, lipid metabolism, and growth-related compound synthesis.

Compared to anaerobic and aerobic groups, significant gene expression differences (Figure 4C) were associated with aerobic energy metabolism, macromolecule (protein, lipid, nucleic acid) synthesis, sulfur metabolism, and oxidative stress adaptation. The anaerobic-to-aerobic transition (Figure 4D) involved differential gene functions in carbon utilization, energy metabolism, macromolecule synthesis, sulfur metabolism, and oxidative stress adaptation.
KEGG analysis demonstrated oxygen-dependent metabolic regulation, showing:
- Aerobic vs. microaerobic conditions (Figure 5A): energy metabolism remodeling, carbon utilization optimization, coenzyme synthesis
- Microaerobic vs. anaerobic (Figure 5B): membrane structure optimization, energy adjustment, cofactor synthesis
- Aerobic vs. anaerobic (Figure 5C): enhanced aerobic respiration, efficient carbon use
- Aerobic vs. microaerobic (Figure 5D): redox balance strengthening, metabolic enhancement
Multivariate analysis confirmed significant aerobic/anaerobic differences (PCA in Figure 6A, OPLS-DA in Figure 6B). Anaerobic condition metabolites showed distinct regulation patterns (Figure 7, Tables 3-4). KEGG pathway analysis (Figure 8A-B) identified 13 significantly altered secondary pathways, primarily in metabolism categories.
Integration of transcriptomic and metabolomic data revealed 12 core metabolic pathways (Table 5). RT-qPCR validation (Figure 9) confirmed consistent expression patterns of virulence factors and metabolic enzymes across oxygen conditions, supporting transcriptome reliability.