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e faecium tx0016  (ATCC)


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    ATCC e faecium tx0016
    Characteristics of the E. faecium iDR479 digital twin model in terms of number of genes, reactions, and metabolites.
    E Faecium Tx0016, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/e+faecium+tx0016/bio_rxiv__64898__2026__05__01__720924-32-10-19?v=ATCC
    Average 94 stars, based on 24 article reviews
    e faecium tx0016 - by Bioz Stars, 2026-07
    94/100 stars

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    1) Product Images from "The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data"

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

    Journal: bioRxiv

    doi: 10.64898/2026.05.01.720924


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

    Techniques Used:

    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.
    Figure Legend 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.

    Techniques Used:

    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
    Figure Legend 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

    Techniques Used: Incubation, Passaging, Comparison



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    Image Search Results


    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:

    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.

    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:

    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

    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

    LESA mass spectra of bacterial colonies. Comparison of extraction solvent systems, acetonitrile/water/formic acid 50:45:5 and 60:35:5 for (a) E. faecalis V583 and (b) E. faecium E745. (c) LESA MS analysis of K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11 with the 60:35:5 extraction solvent system.

    Journal: Journal of the American Society for Mass Spectrometry

    Article Title: Liquid Extraction Surface Analysis Mass Spectrometry of ESKAPE Pathogens

    doi: 10.1021/jasms.0c00466

    Figure Lengend Snippet: LESA mass spectra of bacterial colonies. Comparison of extraction solvent systems, acetonitrile/water/formic acid 50:45:5 and 60:35:5 for (a) E. faecalis V583 and (b) E. faecium E745. (c) LESA MS analysis of K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11 with the 60:35:5 extraction solvent system.

    Article Snippet: The whole organism proteome databases were downloaded in XML format from the UniProt Web site ( uniprot.org ) for E. faecium ATCC BAA-472/TX0016/DO (UP000005269, 3059 entries, 15 638 proteoforms), E. faecalis ATCC 700802/V583 (UP000001415, 3240 entries, 17,469 proteoforms), S. aureus NCTC8325 (UP000008816, 2889 entries, 14 793 proteoforms), K. pneumoniae ATCC 700721 (UP000000265, 5126 entries, 26 531 proteoforms), A. baumannii AYE (UP000002446, 3652 entries, 18 616 proteoforms), P. aeruginosa ATCC 15692/PA01 (UP000002438, 5563 entries, 29 775 proteoforms), and E. cloacae S611 (UP000017834, 3989 entries, 20 832 proteoforms).

    Techniques: Comparison, Extraction, Solvent