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Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species

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ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12918-016-0334-8) contains supplementary material, which is available to authorized users.

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Predictions for a two species biofilm of thickness W = 80 μm (Base case scenario). a Time resolved predictions over the first 50 h at the bottom, middle and top of the biofilm. b Spatially resolved biomass and metabolite concentration predictions after 1000 h. c Spatially resolved effective growth and uptake rate predictions after 10 h
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Fig3: Predictions for a two species biofilm of thickness W = 80 μm (Base case scenario). a Time resolved predictions over the first 50 h at the bottom, middle and top of the biofilm. b Spatially resolved biomass and metabolite concentration predictions after 1000 h. c Spatially resolved effective growth and uptake rate predictions after 10 h

Mentions: When the two species biofilm thickness was set equal to Wmax = 80 μm, pseudo steady-state solutions were obtained after only 50 h of simulation (Fig. 3a). Oxygen was quickly depleted throughout most of the biofilm, except near the biofilm-air interface where an aerobic region was established as observed experimentally [81]. Similarly, glucose was rapidly depleted in all regions except near the tissue-biofilm interface where a glucose rich region was maintained. S. aureus was predicted to quickly establish dominance throughout the biofilm due to its higher local growth rates, especially in the anaerobic region. Initially acetate and succinate levels increased but thereafter they were predicted to decrease due to metabolite removal at the tissue-biofilm boundary. Lactate levels were predicted to remain high throughout the biofilm due to S. aureus synthesis in the anaerobic region and diffusion into the aerobic region. As in the single species biofilms, multispecies biofilm spatial profiles obtained after 1000 h of simulation (Fig. 3b) were characterized by the presence of a glucose rich, anaerobic region near the tissue-biofilm interface and a glucose depleted, aerobic region near the biofilm-air interface. S. aureus was predicted to be dominant throughout the biofilm, especially in the anaerobic region, while P. aeruginosa was predicted to be present only in the aerobic region. Byproduct profiles were similar to those obtained for the S. aureus single species biofilm (see Fig. 2b) with high lactate levels, low acetate levels and no succinate production. We attributed this behavior to partitioning of P. aeruginosa to the aerobic region where the synthesis of byproducts was substantially reduced.Fig. 3


Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species
Predictions for a two species biofilm of thickness W = 80 μm (Base case scenario). a Time resolved predictions over the first 50 h at the bottom, middle and top of the biofilm. b Spatially resolved biomass and metabolite concentration predictions after 1000 h. c Spatially resolved effective growth and uptake rate predictions after 10 h
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Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC5015247&req=5

Fig3: Predictions for a two species biofilm of thickness W = 80 μm (Base case scenario). a Time resolved predictions over the first 50 h at the bottom, middle and top of the biofilm. b Spatially resolved biomass and metabolite concentration predictions after 1000 h. c Spatially resolved effective growth and uptake rate predictions after 10 h
Mentions: When the two species biofilm thickness was set equal to Wmax = 80 μm, pseudo steady-state solutions were obtained after only 50 h of simulation (Fig. 3a). Oxygen was quickly depleted throughout most of the biofilm, except near the biofilm-air interface where an aerobic region was established as observed experimentally [81]. Similarly, glucose was rapidly depleted in all regions except near the tissue-biofilm interface where a glucose rich region was maintained. S. aureus was predicted to quickly establish dominance throughout the biofilm due to its higher local growth rates, especially in the anaerobic region. Initially acetate and succinate levels increased but thereafter they were predicted to decrease due to metabolite removal at the tissue-biofilm boundary. Lactate levels were predicted to remain high throughout the biofilm due to S. aureus synthesis in the anaerobic region and diffusion into the aerobic region. As in the single species biofilms, multispecies biofilm spatial profiles obtained after 1000 h of simulation (Fig. 3b) were characterized by the presence of a glucose rich, anaerobic region near the tissue-biofilm interface and a glucose depleted, aerobic region near the biofilm-air interface. S. aureus was predicted to be dominant throughout the biofilm, especially in the anaerobic region, while P. aeruginosa was predicted to be present only in the aerobic region. Byproduct profiles were similar to those obtained for the S. aureus single species biofilm (see Fig. 2b) with high lactate levels, low acetate levels and no succinate production. We attributed this behavior to partitioning of P. aeruginosa to the aerobic region where the synthesis of byproducts was substantially reduced.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12918-016-0334-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus