Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness
Tài liệu tham khảo
Donlan, 2002, Biofilms: microbial life on surfaces, Emerg Infect Dis, 8, 881, 10.3201/eid0809.020063
Yin, 2019, Biofilms: the microbial “protective clothing” in extreme environments, Int J Mol Sci, 20, 3423, 10.3390/ijms20143423
Cont, 2020, Biofilms deform soft surfaces and disrupt epithelia, Elife, 9, 10.7554/eLife.56533
Mimura, 2000, Reaction–diffusion modelling of bacterial colony patterns, Phys Stat Mech Appl, 282, 283, 10.1016/S0378-4371(00)00085-6
Tokita, 2009, Pattern formation of bacterial colonies by escherichia coli, J Phys Soc Jpn, 78, 10.1143/JPSJ.78.074005
Fei, 2020, Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates, Proc Natl Acad Sci USA, 117, 7622, 10.1073/pnas.1919607117
Bryers, 2008, Medical biofilms, Biotechnol Bioeng, 100, 1, 10.1002/bit.21838
Song, 2014, Stiffness of cross-linked poly (dimethylsiloxane) affects bacterial adhesion and antibiotic susceptibility of attached cells, Langmuir, 30, 10354, 10.1021/la502029f
Kolewe, 2015, Fewer bacteria adhere to softer hydrogels, ACS Appl Mater Interfaces, 7, 19562, 10.1021/acsami.5b04269
Song, 2017, How bacteria respond to material stiffness during attachment: a role of escherichia coli flagellar motility, ACS Appl Mater Interfaces, 9, 22176, 10.1021/acsami.7b04757
Saha, 2013, Influence of polyelectrolyte film stiffness on bacterial growth, Biomacromolecules, 14, 520, 10.1021/bm301774a
Grant, 2014, The role of mechanical forces in the planar-to-bulk transition in growing escherichia coli microcolonies, J R Soc Interface, 11, 10.1098/rsif.2014.0400
Paliy, 2007, Growth of e. coli bl21 in minimal media with different gluconeogenic carbon sources and salt contents, Appl Microbiol Biotechnol, 73, 1169, 10.1007/s00253-006-0554-8
Shehata, 1971, Effect of nutrient concentration on the growth of escherichia coli, J Bacteriol, 107, 210, 10.1128/jb.107.1.210-216.1971
Bauchop, 1960, The growth of micro-organisms in relation to their energy supply, Microbiology, 23, 457, 10.1099/00221287-23-3-457
Kandemir, 2018, Mechanical interactions between bacteria and hydrogels, Sci Rep, 8, 1, 10.1038/s41598-018-29269-x
Witten, 1983, Diffusion-limited aggregation, Phys Rev B, 27, 5686, 10.1103/PhysRevB.27.5686
Fujikawa, 1991, Bacterial fractal growth in the concentration field of nutrient, J Phys Soc Jpn, 60, 88, 10.1143/JPSJ.60.88
Beyenal, 2000, Combined effect of substrate concentration and flow velocity on effective diffusivity in biofilms, Water Res, 34, 528, 10.1016/S0043-1354(99)00147-5
Díaz-Pascual, 2021, Spatial alanine metabolism determines local growth dynamics of escherichia coli colonies, Elife, 10, 10.7554/eLife.70794
Wolfsberg, 2018, Metabolism in dense microbial colonies: 13c metabolic flux analysis of e. coli grown on agar identifies two distinct cell populations with acetate cross-feeding, Metab Eng, 49, 242, 10.1016/j.ymben.2018.08.013
Benomar, 2015, Nutritional stress induces exchange of cell material and energetic coupling between bacterial species, Nat Commun, 6, 1, 10.1038/ncomms7283
Massol-Deyá, 1995, Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater, Appl Environ Microbiol, 61, 769, 10.1128/aem.61.2.769-777.1995
Tolker-Nielsen, 2000, Spatial organization of microbial biofilm communities, Microb Ecol, 40, 75, 10.1007/s002480000057
Birjiniuk, 2014, Single particle tracking reveals spatial and dynamic organization of the escherichia coli biofilm matrix, New J Phys, 16, 10.1088/1367-2630/16/8/085014
Rooney, 2020, Intra-colony channels in e. coli function as a nutrient uptake system, ISME J, 14, 2461, 10.1038/s41396-020-0700-9
McConnell, 2016, A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout, Elife, 5, 10.7554/eLife.18659
Chen, 2003, Impact of carbon and nitrogen conditions on e. coli surface thermodynamics, Colloids Surf B Biointerfaces, 28, 135, 10.1016/S0927-7765(02)00143-1
Warren, 2019, Spatiotemporal establishment of dense bacterial colonies growing on hard agar, Elife, 8, 10.7554/eLife.41093
Wimpenny, 1979, The growth and form of bacterial colonies, Microbiology, 114, 483
Gingichashvili, 2021, Topography and expansion patterns at the biofilm-agar interface in bacillus subtilis biofilms, Microorganisms, 9, 84, 10.3390/microorganisms9010084
Yan, 2019, Mechanical instability and interfacial energy drive biofilm morphogenesis, Elife, 8, 10.7554/eLife.43920
Nijjer, 2021, Mechanical forces drive a reorientation cascade leading to biofilm self-patterning, Nat Commun, 12, 1, 10.1038/s41467-021-26869-6
Qin, 2020, Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy, Science, 369, 71, 10.1126/science.abb8501
Serra, 2021, Bacterial multicellularity: the biology of escherichia coli building large-scale biofilm communities, Annu Rev Microbiol, 75, 269, 10.1146/annurev-micro-031921-055801
Yao, 2012, Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in escherichia coli, Proc Natl Acad Sci USA, 109, E2561, 10.1073/pnas.1209742109
Chanson, 2004
Batchelor, 2000
Waldrop, 2014, Biofilm growth has a threshold response to glucose in vitro, Clin Orthop Relat Res, 472, 3305, 10.1007/s11999-014-3538-5
Pirt, 1967, A kinetic study of the mode of growth of surface colonies of bacteria and fungi, Microbiology, 47, 181
Chen, 2014, Two-dimensionality of yeast colony expansion accompanied by pattern formation, PLoS Comput Biol, 10, 10.1371/journal.pcbi.1003979
Chacón, 2018, The spatial and metabolic basis of colony size variation, ISME J, 12, 669, 10.1038/s41396-017-0038-0
Yang, 2017, Influence of physical effects on the swarming motility of pseudomonas aeruginosa, Biophys J, 112, 1462, 10.1016/j.bpj.2017.02.019
Reshes, 2008, Timing the start of division in e. coli: a single-cell study, Phys Biol, 5, 10.1088/1478-3975/5/4/046001
Ju, 2001, Individual-based modelling of biofilms, Microbiology, 147, 2897, 10.1099/00221287-147-11-2897
Alpkvist, 2006, Three-dimensional biofilm model with individual cells and continuum eps matrix, Biotechnol Bioeng, 94, 961, 10.1002/bit.20917
Lardon, 2011, idynomics: next-generation individual-based modelling of biofilms, Environ Microbiol, 13, 2416, 10.1111/j.1462-2920.2011.02414.x
Xavier, 2005, A framework for multidimensional modelling of activity and structure of multispecies biofilms, Environ Microbiol, 7, 1085, 10.1111/j.1462-2920.2005.00787.x
Yan, 2016, Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging, Proc Natl Acad Sci USA, 113, E5337, 10.1073/pnas.1611494113
Hartmann, 2019, Emergence of threedimensional order and structure in growing biofilms, Nat Phys, 15, 251, 10.1038/s41567-018-0356-9
Drescher, 2016, Architectural transitions in vibrio cholerae biofilms at single-cell resolution, Proc Natl Acad Sci USA, 113, E2066, 10.1073/pnas.1601702113
Lambertsen, 2004, Mini-tn7 transposons for site-specific tagging of bacteria with fluorescent proteins, Environ Microbiol, 6, 726, 10.1111/j.1462-2920.2004.00605.x
Elbing, 2019, Recipes and tools for culture of escherichia coli, Curr Protoc Mol Biol, 125, e83, 10.1002/cpmb.83
Schniete, 2018, Fast optical sectioning for widefield fluorescence mesoscopy with the mesolens based on hilo microscopy, Sci Rep, 8, 1, 10.1038/s41598-018-34516-2
Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nat Methods, 9, 676, 10.1038/nmeth.2019
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