Environmental pH is a key modulator of Staphylococcus aureus biofilm development under predation by the virulent phage phiIPLA-RODI


Previous work had shown that, in some Staphylococcus aureus strains, low concentrations of the virulent phage vB_SauM_phiIPLA-RODI (phiIPLA-RODI) promoted the formation of DNA-rich biofilms, whose cells exhibited significant transcriptional differences compared to an uninfected control. This study aimed to dissect the sequence of events leading to these changes. Analysis of phage propagation throughout biofilm development revealed that the number of phage particles increased steadily up to a certain point and then declined. This partial phage inactivation seemed to be a consequence of medium acidification due to glucose fermentation by the bacterium. Computer simulation of phage–host dynamics during biofilm development showed how even small differences in pH evolution can affect the outcome of phage infection. An acidic pH, together with successful phage propagation, was also necessary to observe the phage-associated changes in biofilm architecture and in the transcriptional profile of the bacterial population. Altogether, this study shows how the dynamics between phage and host can be tightly coordinated through an environmental cue, even in the context of a complex biofilm population.

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Fig. 1: Analysis of the propagation and inactivation of bacteriophage phiIPLA-RODI during biofilm development of S. aureus IPLA1 and the potential role of pH in phage inactivation.
Fig. 2: Biofilm development under predation with an initial MOI of 10−5 of phage phiIPLA-RODI (10 PFU/well) in TSB-7 for 24 h at 37 °C.
Fig. 3: Output of the optimized phiIPLA-RODI infection model for different starting phage concentrations (10 and 100 PFU/well) in the biofilm and the planktonic phase when the lowest possible pH value was set at 4.75, 5.0, 5.5, or 5.9.
Fig. 4: Output of the optimized phiIPLA-RODI infection model for different starting phage concentrations (10, 100, 1000, 104, and 105 PFU/well) in the biofilm and the planktonic phase when the starting pH value was set at 6 and the lowest pH value reached during growth was set at 5.
Fig. 5: Impact of phage predation on biofilm formation and elimination of S. aureus.
Fig. 6: Schematic summary of the effect of phiIPLA-RODI infection on S. aureus gene expression under different conditions.


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We would like to thank Dr. J.R. Penadés and Dr. N. Quiles-Puchalt (University of Glasgow, UK) for sending strain RN450, Dr. C. Wolz (University of Tübingen, Germany) for sending strains Newman, Newman-86 and Newman-86-199, and A. Toledo-Arana (Instituto de Agrobiotecnología, CSIC-Universidad Pública de Navarra, Spain) for strain ISP479r. Also special thanks to three anonymous reviewers for their helpful comments and suggestions. This study was funded by grants PCIN-2017-001 (AEI/FEDER, UE), Proyecto Intramural CSIC 201770E016, and IDI/2018/000119 (Asturias Innovation 2018-2020, Principado de Asturias, Spain and FEDER/EU).

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Fernández, L., Gutiérrez, D., García, P. et al. Environmental pH is a key modulator of Staphylococcus aureus biofilm development under predation by the virulent phage phiIPLA-RODI. ISME J (2020). https://doi.org/10.1038/s41396-020-00778-w

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