Spatially-resolved metabolic cooperativity within dense bacterial colonies

Abstract

BackgroundThe 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.ResultsHere we show that a cell’s position within an in silicoEscherichia 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0155-1) contains supplementary material, which is available to authorized users.

Modelling nutritional mutualisms: challenges and opportunities for data integration

“…Although this method has yet to be applied to plant‐microbe mutualisms, it has led to the illumination of a cross‐feeding relationship between bacteria growing in colonies (Cole et al . ). Cole et al .…”

“…The existence of these groups was confirmed by imaging bacteria that express the green fluorescent protein when they consume acetate (Cole et al . ).…”

Synthetic Ecology of Microbes: Mathematical Models and Applications

“…COMETS enabled the study of how pairs of cross-feeding colonies may be affected by the interposition of a third colony in between them, highlighting the complex dependency of inter-species interactions on spatial organization. A modeling strategy similar to COMETS was used to model the emergence of acetate cross-feeding sub-populations in colonies of E. coli growing on an agar plate 216 .…”

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“…For example, the gut is full of pockets of distinct microbial communities that constrain the ability of a given microbe to interact with other microbes, and factors such as diet influence patterns of spatial clustering [81]. Even in simple communities with little complex spatial structure, simulations reveal that where a particular microbe resides within a community matters [82]. Harcombe et al [83] have used constraint-based models to make the surprising prediction that when two collaborative, cross-feeding colonies of the gut microbes E. coli and S. enterica are separated by a competitor colony of S. enterica , growth of the original S. enterica colony increases, and they have confirmed these results experimentally.…”