Journal: bioRxiv

Article Title: The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

doi: 10.64898/2026.05.01.720924

Figure Lengend Snippet: Characteristics of the E. faecium iDR479 digital twin model in terms of number of genes, reactions, and metabolites.

Article Snippet: The strain whose genome was used in this reconstruction is E. faecium TX0016, also known as the DO strain (ATCC BAA-472), isolated from the blood of a patient with infective endocarditis.

Techniques:

Journal: bioRxiv

Article Title: The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

doi: 10.64898/2026.05.01.720924

Figure Lengend Snippet: Schematic representation of a section of the fatty acid, phospholipid and lipoteichoic acid (LTA) biosynthesis pathways in E. faecium DO, as visualized by Escher. Enzymes are shown in blue, while key metabolites are highlighted in red. The pathways include the conversion of acyl-ACP to phosphatidic acid, CDP-diacylglycerol, phosphatidylglycerol, cardiolipin, and the synthesis of LTA from diacylglycerol.

Article Snippet: The strain whose genome was used in this reconstruction is E. faecium TX0016, also known as the DO strain (ATCC BAA-472), isolated from the blood of a patient with infective endocarditis.

Techniques:

Journal: bioRxiv

Article Title: The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

doi: 10.64898/2026.05.01.720924

Figure Lengend Snippet: Amino acid auxotrophy experiments of E. faecium DO. (A) Mean final optical density (OD) of E. faecium DO in the absence of single amino acids from the CDM-LAB. Bar chart showing final mean OD values after 24 hours incubation. Each bar represents the mean OD of three biological replicates ± SD for a condition where single amino acid was omitted. Cultures with a final OD < 0.1 are marked in red; those with a final OD > 0.3 are marked in blue; and ambiguous growth (OD between 0.1 and 0.3) is color-coded in green. A repeated one-way ANOVA test was performed to compare growth (final average OD 600 ) across amino acid omissions. Results were significantly different ( p value = 0.0024, ≤ 0.05). This was followed by Tukey’s multiple comparisons post hoc test. (B) Repeated passaging of cultures grown in the absence of lysine, phenylalanine, and tyrosine, respectively, results in adaptation to omissions. (C) Individual comparison of each amino acid between the experimental results of the amino acid leave-out experiments (EXP) and the simulation results of the model iDR479 (GEM). Purple squares indicate growth, and green squares indicate no-growth

Article Snippet: The strain whose genome was used in this reconstruction is E. faecium TX0016, also known as the DO strain (ATCC BAA-472), isolated from the blood of a patient with infective endocarditis.

Techniques: Incubation, Passaging, Comparison