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: A comparison between carbon utilization in iDR479 model and experimental data indicates 85% concordance (68 out of 80) between the model predictions and the Biolog phenotypic array results. (B) A comparison between AA essentiality results in iDR479 model and experimental data. The model achieved 100% concordance compared with the leave-out experimental results. TP : True positive, the model and the experimental data predict a positive result. TN: True negative, the model and amino acid leave out experiments predict a positive result. FN: False negative, the model predicts a negative result while experimental data predicts a positive result. FP: False positive, the model predicts a positive result while experimental data predicts a negative result.

Article Snippet: Model curation integrated existing knowledge of E. faecium annotations and metabolic pathways with insights from our experimental analyses Reconstruction was guided and refined through experimental validation, using Biolog phenotypic microarrays for carbon source utilization and amino acid leave-out growth assays for amino acid auxotrophies.

Techniques: Comparison

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: Model curation integrated existing knowledge of E. faecium annotations and metabolic pathways with insights from our experimental analyses Reconstruction was guided and refined through experimental validation, using Biolog phenotypic microarrays for carbon source utilization and amino acid leave-out growth assays for amino acid auxotrophies.

Techniques: Incubation, Passaging, Comparison