Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species.
Chronic wounds are often colonized by consortia comprised of different bacterial species growing as biofilms on a complex mixture of wound exudate. Bacteria growing in biofilms exhibit phenotypes distinct from planktonic growth, often rendering the application of antibacterial compounds ineffective. Computational modeling represents a complementary tool to experimentation for generating fundamental knowledge and developing more effective treatment strategies for chronic wound biofilm consortia.



We developed spatiotemporal models to investigate the multispecies metabolism of a biofilm consortium comprised of two common chronic wound isolates: the aerobe Pseudomonas aeruginosa and the facultative anaerobe Staphylococcus aureus. By combining genome-scale metabolic reconstructions with partial differential equations for metabolite diffusion, the models were able to provide both temporal and spatial predictions with genome-scale resolution. The models were used to analyze the metabolic differences between single species and two species biofilms and to demonstrate the tendency of the two bacteria to spatially partition in the multispecies biofilm as observed experimentally. Nutrient gradients imposed by supplying glucose at the bottom and oxygen at the top of the biofilm induced spatial partitioning of the two species, with S. aureus most concentrated in the anaerobic region and P. aeruginosa present only in the aerobic region. The two species system was predicted to support a maximum biofilm thickness much greater than P. aeruginosa alone but slightly less than S. aureus alone, suggesting an antagonistic metabolic effect of P. aeruginosa on S. aureus. When each species was allowed to enhance its growth through consumption of secreted metabolic byproducts assuming identical uptake kinetics, the competitiveness of P. aeruginosa was further reduced due primarily to the more efficient lactate metabolism of S. aureus. Lysis of S. aureus by a small molecule inhibitor secreted from P. aeruginosa and/or P. aeruginosa aerotaxis were predicted to substantially increase P. aeruginosa competitiveness in the aerobic region, consistent with in vitro experimental studies.



Our biofilm modeling approach allows the prediction of individual species metabolism and interspecies interactions in both time and space with genome-scale resolution. This study yielded new insights into the multispecies metabolism of a chronic wound biofilm, in particular metabolic factors that may lead to spatial partitioning of the two bacterial species. We believe that P. aeruginosa lysis of S. aureus combined with nutrient competition is a particularly relevant scenario for which model predictions could be tested experimentally.
Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA.
Poonam
P
Phalak
Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA.
Jin
J
Chen
Department of Chemical and Biological Engineering and Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
Ross P
RP
Carlson
Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. henson@ecs.umass.edu.
Michael A
MA
Henson
D018441:Biofilms; D064688:Metabolic Flux Analysis; D008954:Models, Biological; D011550:Pseudomonas aeruginosa / Q000166:cytology / Q000378:metabolism* / Q000502:physiology; D013211:Staphylococcus aureus / Q000166:cytology / Q000378:metabolism* / Q000502:physiology; D014947:Wounds and Injuries / Q000382:microbiology*
Biofilms; Metabolic modeling; Wound infections