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Research Article

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Jeremy J. Barr, Rita Auro, Nicholas Sam-Soon, Sam Kassegne, Gregory Peters, Natasha Bonilla, Mark Hatay, Sarah Mourtada, Barbara Bailey, Merry Youle, Ben Felts, Arlette Baljon, Jim Nulton, Peter Salamon, and Forest Rohwer
  1. aDepartment of Biology, San Diego State University, San Diego, CA 92182;
  2. bDepartment of Mechanical Engineering, San Diego State University, San Diego, CA 92182;
  3. cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
  4. dRainbow Rock, Ocean View, HI 96737;
  5. eDepartment of Physics, San Diego State University, San Diego, CA 92182

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PNAS November 3, 2015 112 (44) 13675-13680; first published October 19, 2015; https://doi.org/10.1073/pnas.1508355112
Jeremy J. Barr
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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  • For correspondence: jeremybarr85@gmail.com
Rita Auro
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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Nicholas Sam-Soon
bDepartment of Mechanical Engineering, San Diego State University, San Diego, CA 92182;
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Sam Kassegne
bDepartment of Mechanical Engineering, San Diego State University, San Diego, CA 92182;
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Gregory Peters
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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Natasha Bonilla
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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Mark Hatay
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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Sarah Mourtada
cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
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Barbara Bailey
cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
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Merry Youle
dRainbow Rock, Ocean View, HI 96737;
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Ben Felts
cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
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Arlette Baljon
eDepartment of Physics, San Diego State University, San Diego, CA 92182
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Jim Nulton
cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
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Peter Salamon
cDepartment of Mathematics, San Diego State University, San Diego, CA 92182;
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Forest Rohwer
aDepartment of Biology, San Diego State University, San Diego, CA 92182;
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  1. Edited by Sankar Adhya, National Institutes of Health, National Cancer Institute, Bethesda, MD, and approved September 22, 2015 (received for review April 28, 2015)

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Significance

Bacteriophages (phages) are viruses that infect and kill bacteria. Being inanimate, phages rely on diffusion to search for bacterial prey. Here we demonstrate that a phage that adheres weakly to mucus exhibits subdiffusive motion, not normal diffusion, in mucosal surfaces. Supporting theory and experiments revealed that subdiffusive motion increases bacterial encounter rates for phages when bacterial concentration is low. To the best of our knowledge, no other predator has been shown to effectively use a subdiffusive search mechanism. Mucosal surfaces are vulnerable to infection. Mucus-adherent phages reduce bacterial infection of lifelike mucosal surfaces more effectively than nonadherent phages. These findings provide a basis for engineering adherent phages to manipulate mucosal surface microbiomes for protection from infection and other purposes.

Abstract

Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4∆hoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4∆hoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4∆hoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage–host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.

  • BAM
  • virus
  • mucus
  • subdiffusion
  • search strategy

Footnotes

  • ↵1To whom correspondence should be addressed. Email: jeremybarr85{at}gmail.com.
  • Author contributions: J.J.B. and F.R. designed research; J.J.B., R.A., N.S.-S., G.P., N.B., and S.M. performed research; J.J.B., S.K., M.H., and B.B. contributed new reagents/analytic tools; J.J.B., B.F., A.B., J.N., and P.S. developed the mathematical model; J.J.B., B.F., A.B., J.N., P.S., and F.R. analyzed data; and J.J.B. and M.Y. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1508355112/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Phage subdiffusion in mucus increases encounters
Jeremy J. Barr, Rita Auro, Nicholas Sam-Soon, Sam Kassegne, Gregory Peters, Natasha Bonilla, Mark Hatay, Sarah Mourtada, Barbara Bailey, Merry Youle, Ben Felts, Arlette Baljon, Jim Nulton, Peter Salamon, Forest Rohwer
Proceedings of the National Academy of Sciences Nov 2015, 112 (44) 13675-13680; DOI: 10.1073/pnas.1508355112

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Phage subdiffusion in mucus increases encounters
Jeremy J. Barr, Rita Auro, Nicholas Sam-Soon, Sam Kassegne, Gregory Peters, Natasha Bonilla, Mark Hatay, Sarah Mourtada, Barbara Bailey, Merry Youle, Ben Felts, Arlette Baljon, Jim Nulton, Peter Salamon, Forest Rohwer
Proceedings of the National Academy of Sciences Nov 2015, 112 (44) 13675-13680; DOI: 10.1073/pnas.1508355112
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