Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

Henrique Machado, Liam L. Weng, Nicholas Dillon, Yara Seif, Michelle Holland, Jonathan E. Pekar, Jonathan M. Monk, Victor Nizet, Bernhard O. Palsson, Adam M. Feist*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Staphylococcus aureus is a Gram-positive pathogenic bacterium that colonizes an estimated one-third of the human population and can cause a wide spectrum of disease, ranging from superficial skin infections to life-threatening sepsis. The adaptive mechanisms that contribute to the success of this pathogen remain obscure partially due to a lack of knowledge of its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes; however, such approaches rely on a chemically defined minimal medium as a basis to investigate the requirements of the cell. In this study, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated and validated to support growth of three S. aureus strains: LAC and TCH1516 (USA300 lineage), as well as D592 (USA100 lineage). The formulated SMM was used in an adaptive laboratory evolution experiment to probe the various mutational trajectories of all three strains leading to optimized growth capabilities. The evolved strains were phenotypically characterized for their growth rate and antimicrobial susceptibility. Strains were also resequenced to examine the genetic basis for observed changes in phenotype and to design follow-up metabolite supplementation assays. Our results reveal evolutionary trajectories that arose from strain-specific metabolic requirements. SMM and the evolved strains can also serve as important tools to study antibiotic resistance phenotypes of S. aureusIMPORTANCE As researchers try to understand and combat the development of antibiotic resistance in pathogens, there is a growing need to thoroughly understand the physiology and metabolism of the microbes. Staphylococcus aureus is a threatening pathogen with increased antibiotic resistance and well-studied virulence mechanisms. However, the adaptive mechanisms used by this pathogen to survive environmental stresses remain unclear, mostly due to the lack of information about its metabolic requirements. Defining the minimal metabolic requirements for S. aureus growth is a first step toward unraveling the mechanisms by which it adapts to metabolic stresses. Here, we present the development of a chemically defined minimal medium supporting growth of three S. aureus strains, and we reveal key genetic mutations contributing to improved growth in minimal medium.
Original languageEnglish
Article numbere01773-19
JournalApplied and Environmental Microbiology
Volume85
Issue number21
Pages (from-to)1-13
Number of pages13
ISSN0099-2240
DOIs
Publication statusPublished - 2019

Keywords

  • Adaptive laboratory evolution
  • Staphylococcus aureus
  • Systems biology

Cite this

Machado, Henrique ; Weng, Liam L. ; Dillon, Nicholas ; Seif, Yara ; Holland, Michelle ; Pekar, Jonathan E. ; Monk, Jonathan M. ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M. / Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. In: Applied and Environmental Microbiology. 2019 ; Vol. 85, No. 21. pp. 1-13.
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title = "Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus",
abstract = "Staphylococcus aureus is a Gram-positive pathogenic bacterium that colonizes an estimated one-third of the human population and can cause a wide spectrum of disease, ranging from superficial skin infections to life-threatening sepsis. The adaptive mechanisms that contribute to the success of this pathogen remain obscure partially due to a lack of knowledge of its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes; however, such approaches rely on a chemically defined minimal medium as a basis to investigate the requirements of the cell. In this study, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated and validated to support growth of three S. aureus strains: LAC and TCH1516 (USA300 lineage), as well as D592 (USA100 lineage). The formulated SMM was used in an adaptive laboratory evolution experiment to probe the various mutational trajectories of all three strains leading to optimized growth capabilities. The evolved strains were phenotypically characterized for their growth rate and antimicrobial susceptibility. Strains were also resequenced to examine the genetic basis for observed changes in phenotype and to design follow-up metabolite supplementation assays. Our results reveal evolutionary trajectories that arose from strain-specific metabolic requirements. SMM and the evolved strains can also serve as important tools to study antibiotic resistance phenotypes of S. aureusIMPORTANCE As researchers try to understand and combat the development of antibiotic resistance in pathogens, there is a growing need to thoroughly understand the physiology and metabolism of the microbes. Staphylococcus aureus is a threatening pathogen with increased antibiotic resistance and well-studied virulence mechanisms. However, the adaptive mechanisms used by this pathogen to survive environmental stresses remain unclear, mostly due to the lack of information about its metabolic requirements. Defining the minimal metabolic requirements for S. aureus growth is a first step toward unraveling the mechanisms by which it adapts to metabolic stresses. Here, we present the development of a chemically defined minimal medium supporting growth of three S. aureus strains, and we reveal key genetic mutations contributing to improved growth in minimal medium.",
keywords = "Adaptive laboratory evolution, Staphylococcus aureus, Systems biology",
author = "Henrique Machado and Weng, {Liam L.} and Nicholas Dillon and Yara Seif and Michelle Holland and Pekar, {Jonathan E.} and Monk, {Jonathan M.} and Victor Nizet and Palsson, {Bernhard O.} and Feist, {Adam M.}",
year = "2019",
doi = "10.1128/aem.01773-19",
language = "English",
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Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. / Machado, Henrique; Weng, Liam L.; Dillon, Nicholas; Seif, Yara; Holland, Michelle; Pekar, Jonathan E.; Monk, Jonathan M.; Nizet, Victor; Palsson, Bernhard O.; Feist, Adam M.

In: Applied and Environmental Microbiology, Vol. 85, No. 21, e01773-19, 2019, p. 1-13.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

AU - Machado, Henrique

AU - Weng, Liam L.

AU - Dillon, Nicholas

AU - Seif, Yara

AU - Holland, Michelle

AU - Pekar, Jonathan E.

AU - Monk, Jonathan M.

AU - Nizet, Victor

AU - Palsson, Bernhard O.

AU - Feist, Adam M.

PY - 2019

Y1 - 2019

N2 - Staphylococcus aureus is a Gram-positive pathogenic bacterium that colonizes an estimated one-third of the human population and can cause a wide spectrum of disease, ranging from superficial skin infections to life-threatening sepsis. The adaptive mechanisms that contribute to the success of this pathogen remain obscure partially due to a lack of knowledge of its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes; however, such approaches rely on a chemically defined minimal medium as a basis to investigate the requirements of the cell. In this study, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated and validated to support growth of three S. aureus strains: LAC and TCH1516 (USA300 lineage), as well as D592 (USA100 lineage). The formulated SMM was used in an adaptive laboratory evolution experiment to probe the various mutational trajectories of all three strains leading to optimized growth capabilities. The evolved strains were phenotypically characterized for their growth rate and antimicrobial susceptibility. Strains were also resequenced to examine the genetic basis for observed changes in phenotype and to design follow-up metabolite supplementation assays. Our results reveal evolutionary trajectories that arose from strain-specific metabolic requirements. SMM and the evolved strains can also serve as important tools to study antibiotic resistance phenotypes of S. aureusIMPORTANCE As researchers try to understand and combat the development of antibiotic resistance in pathogens, there is a growing need to thoroughly understand the physiology and metabolism of the microbes. Staphylococcus aureus is a threatening pathogen with increased antibiotic resistance and well-studied virulence mechanisms. However, the adaptive mechanisms used by this pathogen to survive environmental stresses remain unclear, mostly due to the lack of information about its metabolic requirements. Defining the minimal metabolic requirements for S. aureus growth is a first step toward unraveling the mechanisms by which it adapts to metabolic stresses. Here, we present the development of a chemically defined minimal medium supporting growth of three S. aureus strains, and we reveal key genetic mutations contributing to improved growth in minimal medium.

AB - Staphylococcus aureus is a Gram-positive pathogenic bacterium that colonizes an estimated one-third of the human population and can cause a wide spectrum of disease, ranging from superficial skin infections to life-threatening sepsis. The adaptive mechanisms that contribute to the success of this pathogen remain obscure partially due to a lack of knowledge of its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes; however, such approaches rely on a chemically defined minimal medium as a basis to investigate the requirements of the cell. In this study, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated and validated to support growth of three S. aureus strains: LAC and TCH1516 (USA300 lineage), as well as D592 (USA100 lineage). The formulated SMM was used in an adaptive laboratory evolution experiment to probe the various mutational trajectories of all three strains leading to optimized growth capabilities. The evolved strains were phenotypically characterized for their growth rate and antimicrobial susceptibility. Strains were also resequenced to examine the genetic basis for observed changes in phenotype and to design follow-up metabolite supplementation assays. Our results reveal evolutionary trajectories that arose from strain-specific metabolic requirements. SMM and the evolved strains can also serve as important tools to study antibiotic resistance phenotypes of S. aureusIMPORTANCE As researchers try to understand and combat the development of antibiotic resistance in pathogens, there is a growing need to thoroughly understand the physiology and metabolism of the microbes. Staphylococcus aureus is a threatening pathogen with increased antibiotic resistance and well-studied virulence mechanisms. However, the adaptive mechanisms used by this pathogen to survive environmental stresses remain unclear, mostly due to the lack of information about its metabolic requirements. Defining the minimal metabolic requirements for S. aureus growth is a first step toward unraveling the mechanisms by which it adapts to metabolic stresses. Here, we present the development of a chemically defined minimal medium supporting growth of three S. aureus strains, and we reveal key genetic mutations contributing to improved growth in minimal medium.

KW - Adaptive laboratory evolution

KW - Staphylococcus aureus

KW - Systems biology

U2 - 10.1128/aem.01773-19

DO - 10.1128/aem.01773-19

M3 - Journal article

VL - 85

SP - 1

EP - 13

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

IS - 21

M1 - e01773-19

ER -