Hobley L, Harkins C, MacPhee CE, Stanley-Wall NR. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol Rev. 2015;39:649–69.
Nadell CD, Drescher K, Foster KR. Spatial structure, cooperation and competition in biofilms. Nat Rev Microbiol. 2016;14:589.
Flemming H-C, Wuertz S. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol. 2019;17:247–60.
Costerton JW, Cheng KJ, Geesey GG, Ladd TI, Nickel JC, Dasgupta M, et al. Bacterial biofilms in nature and disease. Annu Rev Microbiol. 1987;41:435–64.
Bixler GD, Bhushan B. Biofouling: lessons from nature. Philos Trans R Soc Math Phys Eng Sci. 2012;370:2381–417.
Chaves Simões L, Simões M. Biofilms in drinking water: problems and solutions. RSC Adv. 2013;3:2520–33.
Percival SL, Suleman L, Vuotto C, Donelli G. Healthcare-associated infections, medical devices and biofilms: risk, tolerance and control. J Med Microbiol. 2015;64:323–34.
Roberts AEL, Kragh KN, Bjarnsholt T, Diggle SP. The limitations of in vitro experimentation in understanding biofilms and chronic infection. J Mol Biol. 2015;427:3646–61.
Carvalho G, Balestrino D, Forestier C, Mathias J-D. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? Npj Biofilms Microbiomes. 2018;4:6.
Costerton J. Introduction to biofilms. Int J Antimicrob Agents. 1999;11:217–21.
Serra DO, Richter AM, Klauck G, Mika F, Hengge R. Microanatomy at cellular resolution and spatial order of physiological differentiation in a bacterial biofilm. mBio. 2013;4:e00103–13.
Ghanbari A, Dehghany J, Schwebs T, Müsken M, Häussler S, Meyer-Hermann M. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms. Sci Rep. 2016;6:32097.
Sheraton MV, Yam JKH, Tan CH, Oh HS, Mancini E, Yang L, et al. Mesoscopic energy minimization drives pseudomonas aeruginosa biofilm morphologies and consequent stratification of antibiotic activity based on cell metabolism. Antimicrob Agents Chemother. 2018;62:e02544–17.
Libicki SB, Salmon PM, Robertson CR. The effective diffusive permeability of a nonreacting solute in microbial cell aggregates. Biotechnol Bioeng. 1988;32:68–85.
Hunt SM, Werner EM, Huang B, Hamilton MA, Stewart PS. Hypothesis for the role of nutrient starvation in biofilm detachment. Appl Environ Microbiol. 2004;70:7418–25.
Stewart PS. Diffusion in biofilms. J Bacteriol. 2003;185:1485–91.
Guélon T, Mathias J-D, Deffuant G. Influence of spatial structure on effective nutrient diffusion in bacterial biofilms. J Biol Phys. 2012;38:573–88.
Rudge TJ, Steiner PJ, Phillips A, Haseloff J. Computational modeling of synthetic microbial biofilms. ACS Synth Biol. 2012;1:345–52.
Rudge TJ, Federici F, Steiner PJ, Kan A, Haseloff J. Cell polarity-driven instability generates self-organized, fractal patterning of cell layers. ACS Synth Biol. 2013;2:705–14.
Blanchard AE, Lu T. Bacterial social interactions drive the emergence of differential spatial colony structures. BMC Syst Biol. 2015;9:59. https://doi.org/10.1186/s12918-015-0188-5.
Smith WPJ, Davit Y, Osborne JM, Kim W, Foster KR, Pitt-Francis JM. Cell morphology drives spatial patterning in microbial communities. Proc Natl Acad Sci. 2017;114:E280–6.
Goldschmidt F, Regoes RR, Johnson DR. Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations. ISME J. 2017;11:2112.
Jauffred L, Vejborg RM, Korolev KS, Brown S, Oddershede LB. Chirality in microbial biofilms is mediated by close interactions between the cell surface and the substratum. ISME J. 2017;11:1688.
Eriksen RS, Svenningsen SL, Sneppen K, Mitarai N. A growing microcolony can survive and support persistent propagation of virulent phages. Proc Natl Acad Sci. 2018;115:337–42.
Xiao J, Hara AT, Kim D, Zero DT, Koo H, Hwang G. Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface. Int J Oral Sci. 2017;9:74–9.
Liu J, Martinez-Corral R, Prindle A, Dong-yeon DL, Larkin J, Gabalda-Sagarra M, et al. Coupling between distant biofilms and emergence of nutrient time-sharing. Science. 2017;356:638–42.
Kempes CP, Okegbe C, Mears-Clarke Z, Follows MJ, Dietrich LEP. Morphological optimization for access to dual oxidants in biofilms. Proc Natl Acad Sci. 2014;111:208–13.
Jo J, Cortez KL, Cornell WC, Price-Whelan A, Dietrich LE. An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence. 2017;30:e30205.
Wilking JN, Zaburdaev V, De Volder M, Losick R, Brenner MP, Weitz DA. Liquid transport facilitated by channels in Bacillus subtilis biofilms. Proc Natl Acad Sci. 2013;110:848–52.
Asally M, Kittisopikul M, Rue P, Du Y, Hu Z, Cagatay T, et al. Localized cell death focuses mechanical forces during 3D patterning in a biofilm. Proc Natl Acad Sci. 2012;109:18891–6.
Stoodley P, Debeer D, Lewandowski Z. Liquid flow in biofilm systems. Appl Environ Microbiol. 1994;60:2711–6.
McConnell G, Trägaardh J, Amor R, Dempster J, Reid E, Amos WB. A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout. eLife. 2016;5:e18659.
McConnell G, Amos WB. Application of the Mesolens for subcellular resolution imaging of intact larval and whole adult Drosophila. J Microsc. 2018;270:252–8.
Schniete J, Franssen A, Dempster J, Bushell TJ, Amos WB, McConnell G. Fast optical sectioning for widefield fluorescence mesoscopy with the mesolens based on HiLo microscopy. Sci Rep. 2018;8:16259.
Elbing KL, Brent R. Recipes and tools for culture of Escherichia coli. Curr Protoc Mol Biol. 2019;125:e83.
Dempster J, Wokosin DL, McCloskey KD, Girkin JM, Gurney AM. WinFluor: an integrated system for the simultaneous recording of cell fluorescence images and electrophysiological signals on a single computer system. Br J Pharm. 2002;137:146.
Lambertsen L, Sternberg C, Molin S. Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins. Environ Microbiol. 2004;6:726–32.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.
Drescher K, Dunkel J, Nadell CD, van Teeffelen S, Grnja I, Wingreen NS, et al. Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc Natl Acad Sci. 2016;113:E2066–72.
Yan J, Sharo AG, Stone HA, Wingreen NS, Bassler BL. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging. Proc Natl Acad Sci. 2016;113:E5337–43.
Hartmann R, Singh PK, Pearce P, Mok R, Song B, Díaz-Pascual F, et al. Emergence of three-dimensional order and structure in growing biofilms. Nat Phys. 2019;15:251–6.
Lagree K, Desai JV, Finkel JS, Lanni F. Microscopy of fungal biofilms. Curr Opin Microbiol. 2018;43:100–7.
Xiao J, Hara AT, Kim D, Zero DT, Koo H, Hwang G. Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface. Int J Oral Sci. 2017;9:74–9.
Thomsen H, Benkovics G, Fenyvesi É, Farewell A, Malanga M, Ericson MB. Delivery of cyclodextrin polymers to bacterial biofilms—an exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy. Int J Pharm. 2017;531:650–7.
Shemesh H, Goertz DE, van der Sluis LWM, de Jong N, Wu MK, Wesselink PR. High frequency ultrasound imaging of a single-species biofilm. J Dent. 2007;35:673–8.
Vaidya K, Osgood R, Ren D, Pichichero ME, Helguera M. Ultrasound imaging and characterization of biofilms based on wavelet de-noised radiofrequency data. Ultrasound Med Biol. 2014;40:583–95.
Xi C, Marks D, Schlachter S, Luo W, Boppart SA. High-resolution three-dimensional imaging of biofilm development using optical coherence tomography. J Biomed Opt. 2006;11:034001.
Wagner M, Taherzadeh D, Haisch C, Horn H. Investigation of the mesoscale structure and volumetric features of biofilms using optical coherence tomography. Biotechnol Bioeng. 2010;107:844–53.
Leite de Andrade MC, Soares de Oliveira MA, Santos F, de AG, dos, Ximenes Vilela P, de B, et al. A new approach by optical coherence tomography for elucidating biofilm formation by emergent Candida species. PLoS ONE. 2017;12:e0188020.
Drury WJ, Characklis WG, Stewart PS. Interactions of 1 μm latex particles with Pseudomonas aeruginosa biofilms. Water Res. 1993;27:1119–26.
Xu H, Dauparas J, Das D, Lauga E, Wu Y. Self-organization of swimmers drives long-range fluid transport in bacterial colonies. Nat Commun. 2019;10:1792.
Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, et al. Artificial symmetry-breaking for morphogenetic engineering bacterial colonies. ACS Synth Biol. 2017;6:256–65.
Wimpenny JWT, Coombs JP. Penetration of oxygen into bacterial colonies. Microbiology. 1983;129:1239–42.
Peters AC, Wimpenny JWT, Coombs JP. Oxygen profiles in, and in the agar beneath, colonies of Bacillus cereus, Staphylococcus albus and Escherichia coli. J Gen Microbiol. 1987;133:1257–63.
Jeanson S, Floury J, Gagnaire V, Lortal S, Thierry A. Bacterial colonies in solid media and foods: a review on their growth and interactions with the micro-environment. Front Microbiol. 2015;6:1284.
Hwang G, Liu Y, Kim D, Sun V, Aviles-Reyes A, Kajfasz JK, et al. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure. Sci Rep. 2016;6:32841.
Webb JS, Thompson LS, James S, Charlton T, Tolker-Nielsen T, Koch B, et al. Cell death in Pseudomonas aeruginosa biofilm development. J Bacteriol. 2003;185:4585–92.
Moscona AA. Aggregation of sponge cells: cell-linking macromolecules and their role in the formation of multicellular systems. In Vitro. 1967;3:13–21.
Lavrov AI, Kosevich IA. Sponge cell reaggregation: mechanisms and dynamics of the process. Russ J Dev Biol. 2014;45:205–23.
Jolivet-Gougeon A, Bonnaure-Mallet M. Biofilms as a mechanism of bacterial resistance. Drug Disco Today Technol. 2014;11:49–56.
Oliveira NM, Martinez-Garcia E, Xavier J, Durham WM, Kolter R, Kim W, et al. Biofilm formation as a response to ecological competition. PLoS Biol. 2015;13:e1002191.
Source: Ecology - nature.com
