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Spatially-resolved metabolic cooperativity within dense bacterial colonies.

Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z - BMC Syst Biol (2015)

Bottom Line: Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli.The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions.The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois, 1110 W. Green St., Urbana, 61801, IL, USA. zan@illinois.edu.

ABSTRACT

Background: The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of these subpopulations-their potential for competition as well as cooperation-requires both a metabolic model capable of accounting for a wide range of environmental conditions, and a detailed dynamic description of the cells' shared extracellular space.

Results: Here we show that a cell's position within an in silico Escherichia coli colony grown on glucose minimal agar can drastically affect its metabolism: "pioneer" cells at the outer edge engage in rapid growth that expands the colony, while dormant cells in the interior separate two spatially distinct subpopulations linked by a cooperative form of acetate crossfeeding that has so far gone unnoticed. Our hybrid simulation technique integrates 3D reaction-diffusion modeling with genome-scale flux balance analysis (FBA) to describe the position-dependent metabolism and growth of cells within a colony. Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli. The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions. Furthermore, the height-to-width ratios of both the experimental and simulated colonies are in good agreement over a growth period of 48 hours.

Conclusions: Our modeling paradigm can accurately reproduce a number of known features of E. coli colony growth, as well as predict a novel one that had until now gone unrecognized. The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

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Growth rates and substrate profiles over time.(A) The colony is colored by growth rate and shown in cross-section. The fastest-growing cells (red) inhabit the colony periphery, while much of the interior shows little or no growth (blue) due to nutrient depletion. The grey diagonal line shows the linear radial growth of the colony. (B) Oxygen concentration within the same colony in cross-section at 12, 13, and 14 hours. Between 13 and 14 hours, a well-defined anoxic region forms in the center of the colony. The penetration of oxygen into this colony is between 50 and 60 μm. (C) Glucose concentration in cross-section at 14, 15, and 16 hours. Beyond 14 hours, the glucose concentration in the colony interior rapidly falls, and beyond 15 hours, much of the colony interior, in addition to being anoxic, is also glucose-starved.
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Fig6: Growth rates and substrate profiles over time.(A) The colony is colored by growth rate and shown in cross-section. The fastest-growing cells (red) inhabit the colony periphery, while much of the interior shows little or no growth (blue) due to nutrient depletion. The grey diagonal line shows the linear radial growth of the colony. (B) Oxygen concentration within the same colony in cross-section at 12, 13, and 14 hours. Between 13 and 14 hours, a well-defined anoxic region forms in the center of the colony. The penetration of oxygen into this colony is between 50 and 60 μm. (C) Glucose concentration in cross-section at 14, 15, and 16 hours. Beyond 14 hours, the glucose concentration in the colony interior rapidly falls, and beyond 15 hours, much of the colony interior, in addition to being anoxic, is also glucose-starved.

Mentions: The physical growth of the simulated colonies was found to proceed through two phases. During the initial 15 hours, the dimensions of the colonies grew approximately exponentially. Beyond this time, however, the colonies’ radial expansions slowed to a constant rate of about 0.011 μm s −1 (see Figure 6A). These findings agree extremely well with an experimental study of E. coli growth under nearly identical conditions (solid agar medium with M9 salts, glucose, and trace elements) that reported an exponential-to-linear transition occurring around 12 hours after inoculation onto agar plates and a radial expansion rate of around 0.008 μm s −1 [28]. Our own experimental colonies (on the same solid medium) grew slightly slower with a radial expansion rate of approximately 0.007 μm s −1 (see Additional file 1: Figure S5).Figure 6


Spatially-resolved metabolic cooperativity within dense bacterial colonies.

Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z - BMC Syst Biol (2015)

Growth rates and substrate profiles over time.(A) The colony is colored by growth rate and shown in cross-section. The fastest-growing cells (red) inhabit the colony periphery, while much of the interior shows little or no growth (blue) due to nutrient depletion. The grey diagonal line shows the linear radial growth of the colony. (B) Oxygen concentration within the same colony in cross-section at 12, 13, and 14 hours. Between 13 and 14 hours, a well-defined anoxic region forms in the center of the colony. The penetration of oxygen into this colony is between 50 and 60 μm. (C) Glucose concentration in cross-section at 14, 15, and 16 hours. Beyond 14 hours, the glucose concentration in the colony interior rapidly falls, and beyond 15 hours, much of the colony interior, in addition to being anoxic, is also glucose-starved.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4376365&req=5

Fig6: Growth rates and substrate profiles over time.(A) The colony is colored by growth rate and shown in cross-section. The fastest-growing cells (red) inhabit the colony periphery, while much of the interior shows little or no growth (blue) due to nutrient depletion. The grey diagonal line shows the linear radial growth of the colony. (B) Oxygen concentration within the same colony in cross-section at 12, 13, and 14 hours. Between 13 and 14 hours, a well-defined anoxic region forms in the center of the colony. The penetration of oxygen into this colony is between 50 and 60 μm. (C) Glucose concentration in cross-section at 14, 15, and 16 hours. Beyond 14 hours, the glucose concentration in the colony interior rapidly falls, and beyond 15 hours, much of the colony interior, in addition to being anoxic, is also glucose-starved.
Mentions: The physical growth of the simulated colonies was found to proceed through two phases. During the initial 15 hours, the dimensions of the colonies grew approximately exponentially. Beyond this time, however, the colonies’ radial expansions slowed to a constant rate of about 0.011 μm s −1 (see Figure 6A). These findings agree extremely well with an experimental study of E. coli growth under nearly identical conditions (solid agar medium with M9 salts, glucose, and trace elements) that reported an exponential-to-linear transition occurring around 12 hours after inoculation onto agar plates and a radial expansion rate of around 0.008 μm s −1 [28]. Our own experimental colonies (on the same solid medium) grew slightly slower with a radial expansion rate of approximately 0.007 μm s −1 (see Additional file 1: Figure S5).Figure 6

Bottom Line: Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli.The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions.The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois, 1110 W. Green St., Urbana, 61801, IL, USA. zan@illinois.edu.

ABSTRACT

Background: The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of these subpopulations-their potential for competition as well as cooperation-requires both a metabolic model capable of accounting for a wide range of environmental conditions, and a detailed dynamic description of the cells' shared extracellular space.

Results: Here we show that a cell's position within an in silico Escherichia coli colony grown on glucose minimal agar can drastically affect its metabolism: "pioneer" cells at the outer edge engage in rapid growth that expands the colony, while dormant cells in the interior separate two spatially distinct subpopulations linked by a cooperative form of acetate crossfeeding that has so far gone unnoticed. Our hybrid simulation technique integrates 3D reaction-diffusion modeling with genome-scale flux balance analysis (FBA) to describe the position-dependent metabolism and growth of cells within a colony. Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli. The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions. Furthermore, the height-to-width ratios of both the experimental and simulated colonies are in good agreement over a growth period of 48 hours.

Conclusions: Our modeling paradigm can accurately reproduce a number of known features of E. coli colony growth, as well as predict a novel one that had until now gone unrecognized. The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

Show MeSH
Related in: MedlinePlus