151
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Barai P, Kumar A, Mukherjee PP. Modeling of Mesoscale Variability in Biofilm Shear Behavior. PLoS One 2016; 11:e0165593. [PMID: 27806068 PMCID: PMC5091762 DOI: 10.1371/journal.pone.0165593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/16/2016] [Indexed: 12/24/2022] Open
Abstract
Formation of bacterial colonies as biofilm on the surface/interface of various objects has the potential to impact not only human health and disease but also energy and environmental considerations. Biofilms can be regarded as soft materials, and comprehension of their shear response to external forces is a key element to the fundamental understanding. A mesoscale model has been presented in this article based on digitization of a biofilm microstructure. Its response under externally applied shear load is analyzed. Strain stiffening type behavior is readily observed under high strain loads due to the unfolding of chains within soft polymeric substrate. Sustained shear loading of the biofilm network results in strain localization along the diagonal direction. Rupture of the soft polymeric matrix can potentially reduce the intercellular interaction between the bacterial cells. Evolution of stiffness within the biofilm network under shear reveals two regimes: a) initial increase in stiffness due to strain stiffening of polymer matrix, and b) eventual reduction in stiffness because of tear in polymeric substrate.
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Affiliation(s)
- Pallab Barai
- Department of Mechanical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Aloke Kumar
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
- * E-mail: (PPM); (AK)
| | - Partha P. Mukherjee
- Department of Mechanical Engineering, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (PPM); (AK)
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152
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Hassanpourfard M, Ghosh R, Thundat T, Kumar A. Dynamics of bacterial streamers induced clogging in microfluidic devices. LAB ON A CHIP 2016; 16:4091-4096. [PMID: 27713995 DOI: 10.1039/c6lc01055e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Using a microfabricated porous media mimic platform, we investigated the clogging dynamics of bacterial biomass that accumulated in the device due to the formation of bacterial streamers. Particularly, we found the existence of a distinct clogging front which advanced via pronounced 'stick-slip' of the viscoelastic bacterial biomass over the solid surface of the micro pillar. Thus, the streamer, the solid surface, and the background fluidic media defined a clear three-phase front influencing these advancing dynamics. Interestingly, we also found that once the clogging became substantial, contrary to a static homogenous saturation state, the clogged mimic exhibited an instability phenomena marked by localized streamer breakage and failure leading to extended water channels throughout the mimic. These findings have implications for design and fabrication of biomedical devices and membrane-type systems such as porous balloon catheters, porous stents and filtration membranes prone to bacteria induced clogging as well as understanding bacterial growth and proliferation in natural porous media such as soil and rocks.
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Affiliation(s)
- Mahtab Hassanpourfard
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Ranajay Ghosh
- Department of Mechanical and Aerospace Engineering, University of Central Florida, FL 32816, USA
| | - Thomas Thundat
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Aloke Kumar
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada.
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153
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Weiss N, Obied KETE, Kalkman J, Lammertink RG, van Leeuwen TG. Measurement of biofilm growth and local hydrodynamics using optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2016; 7:3508-3518. [PMID: 27699116 PMCID: PMC5030028 DOI: 10.1364/boe.7.003508] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 05/08/2023]
Abstract
We report on localized and simultaneous measurement of biofilm growth and local hydrodynamics in a microfluidic channel using optical coherence tomography. We measure independently with high spatio-temporal resolution the longitudinal flow velocity component parallel to the imaging beam and the transverse flow velocity component perpendicular to the imaging beam. Based on the measured velocities we calculate the shear-rates in the flow channel. We show the relation between the measured biofilm structure and flow velocities as biofilm growth progresses over the course of 48 hours.
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Affiliation(s)
- Nicolás Weiss
- Biomedical Engineering & Physics, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam,
The Netherlands
| | - Khalid El Tayeb El Obied
- Soft Matter, Fluidics and Interfaces, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede,
The Netherlands
| | - Jeroen Kalkman
- Department of Imaging Physics, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft,
The Netherlands
| | - Rob G.H. Lammertink
- Soft Matter, Fluidics and Interfaces, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede,
The Netherlands
| | - Ton G. van Leeuwen
- Biomedical Engineering & Physics, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam,
The Netherlands
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154
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Nonlinear deformation and localized failure of bacterial streamers in creeping flows. Sci Rep 2016; 6:32204. [PMID: 27558511 PMCID: PMC4997318 DOI: 10.1038/srep32204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
We investigate the failure of bacterial floc mediated streamers in a microfluidic device in a creeping flow regime using both experimental observations and analytical modeling. The quantification of streamer deformation and failure behavior is possible due to the use of 200 nm fluorescent polystyrene beads which firmly embed in the extracellular polymeric substance (EPS) and act as tracers. The streamers, which form soon after the commencement of flow begin to deviate from an apparently quiescent fully formed state in spite of steady background flow and limited mass accretion indicating significant mechanical nonlinearity. This nonlinear behavior shows distinct phases of deformation with mutually different characteristic times and comes to an end with a distinct localized failure of the streamer far from the walls. We investigate this deformation and failure behavior for two separate bacterial strains and develop a simplified but nonlinear analytical model describing the experimentally observed instability phenomena assuming a necking route to instability. Our model leads to a power law relation between the critical strain at failure and the fluid velocity scale exhibiting excellent qualitative and quantitative agreeing with the experimental rupture behavior.
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155
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Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging. Proc Natl Acad Sci U S A 2016; 113:E5337-43. [PMID: 27555592 DOI: 10.1073/pnas.1611494113] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli.
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156
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Bacteria Delay the Jamming of Particles at Microchannel Bottlenecks. Sci Rep 2016; 6:31471. [PMID: 27510611 PMCID: PMC4980593 DOI: 10.1038/srep31471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022] Open
Abstract
Clogging of channels by complex systems such as mixtures of colloidal and biological particles is commonly encountered in different applications. In this work, we analyze and compare the clogging mechanisms and dynamics by pure and mixture suspensions of polystyrene latex particles and Escherichia coli by coupling fluorescent microscopic observation and dynamic permeability measurements in microfluidic filters. Pure particles filtration leads to arches and deposit formation in the upstream side of the microfilter while pure bacteria form streamers in the downstream zone. When mixing particle and bacteria, an unexpected phenomenon occurs: the clogging dynamics is significantly delayed. This phenomenon is related to apparent “slippery” interactions between the particles and the bacteria. These interactions limit the arches formation at the channels entrances and favour the formation of dendritic structures on the pillars between the channels. When these dendrites are eroded by the flow, fragments of the deposit are dragged towards the channels entrances. However, these bacteria/particles clusters being lubricated by the slippery interactions are deformed and stretched by the shear thus facilitating their passage through the microchannels.
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157
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Niepa THR, Hou L, Jiang H, Goulian M, Koo H, Stebe KJ, Lee D. Microbial Nanoculture as an Artificial Microniche. Sci Rep 2016; 6:30578. [PMID: 27476816 PMCID: PMC4967889 DOI: 10.1038/srep30578] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/04/2016] [Indexed: 02/02/2023] Open
Abstract
Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.
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Affiliation(s)
- Tagbo H R Niepa
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Likai Hou
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.,School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Hongyuan Jiang
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hyun Koo
- Department of Orthodontics, Pediatric Dentistry and Community Oral Health Divisions, University of Pennsylvania, PA19104, USA
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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158
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159
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Bocanegra Evans H, Gorumlu S, Aksak B, Castillo L, Sheng J. Holographic microscopy and microfluidics platform for measuring wall stress and 3D flow over surfaces textured by micro-pillars. Sci Rep 2016; 6:28753. [PMID: 27353632 PMCID: PMC4926118 DOI: 10.1038/srep28753] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 06/08/2016] [Indexed: 11/30/2022] Open
Abstract
Understanding how fluid flow interacts with micro-textured surfaces is crucial for a broad range of key biological processes and engineering applications including particle dispersion, pathogenic infections, and drag manipulation by surface topology. We use high-speed digital holographic microscopy (DHM) in combination with a correlation based de-noising algorithm to overcome the optical interference generated by surface roughness and to capture a large number of 3D particle trajectories in a microfluidic channel with one surface patterned with micropillars. It allows us to obtain a 3D ensembled velocity field with an uncertainty of 0.06% and 2D wall shear stress distribution at the resolution of ~65 μPa. Contrary to laminar flow in most microfluidics, we find that the flow is three-dimensional and complex for the textured microchannel. While the micropillars affect the velocity flow field locally, their presence is felt globally in terms of wall shear stresses at the channel walls. These findings imply that micro-scale mixing and wall stress sensing/manipulation can be achieved through hydro-dynamically smooth but topologically rough micropillars.
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Affiliation(s)
| | - Serdar Gorumlu
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States
| | - Burak Aksak
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States
| | - Luciano Castillo
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States
| | - Jian Sheng
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States
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160
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Chew SC, Kundukad B, Teh WK, Doyle P, Yang L, Rice SA, Kjelleberg S. Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers. SOFT MATTER 2016; 12:5224-5232. [PMID: 27191395 DOI: 10.1039/c5sm02755a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix.
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Affiliation(s)
- S C Chew
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore.
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161
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Stenosis triggers spread of helical Pseudomonas biofilms in cylindrical flow systems. Sci Rep 2016; 6:27170. [PMID: 27272623 PMCID: PMC4895183 DOI: 10.1038/srep27170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/13/2016] [Indexed: 01/18/2023] Open
Abstract
Biofilms are multicellular bacterial structures that adhere to surfaces and often endow the bacterial population with tolerance to antibiotics and other environmental insults. Biofilms frequently colonize the tubing of medical devices through mechanisms that are poorly understood. Here we studied the helicoidal spread of Pseudomonas putida biofilms through cylindrical conduits of varied diameters in slow laminar flow regimes. Numerical simulations of such flows reveal vortical motion at stenoses and junctions, which enhances bacterial adhesion and fosters formation of filamentous structures. Formation of long, downstream-flowing bacterial threads that stem from narrowings and connections was detected experimentally, as predicted by our model. Accumulation of bacterial biomass makes the resulting filaments undergo a helical instability. These incipient helices then coarsened until constrained by the tubing walls, and spread along the whole tube length without obstructing the flow. A three-dimensional discrete filament model supports this coarsening mechanism and yields simulations of helix dynamics in accordance with our experimental observations. These findings describe an unanticipated mechanism for bacterial spreading in tubing networks which might be involved in some hospital-acquired infections and bacterial contamination of catheters.
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162
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Hathroubi S, Mekni MA, Domenico P, Nguyen D, Jacques M. Biofilms: Microbial Shelters Against Antibiotics. Microb Drug Resist 2016; 23:147-156. [PMID: 27214143 DOI: 10.1089/mdr.2016.0087] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Biofilms are communities of aggregated bacterial cells embedded in a self-produced extracellular polymeric matrix. Biofilms are recalcitrant to antibiotic treatment and immune defenses and are implicated in many chronic bacterial and fungal infections. In this review, we provide an overview of the contribution of biofilms to persistent infections resistant to antibiotic treatment, the impact of multispecies biofilms on drug resistance and tolerance, and recent advances in the development of antibiofilm agents. Understanding the mechanisms of antibiotic resistance and tolerance in biofilms is essential for developing new preventive and therapeutic strategies and curbing drug resistance.
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Affiliation(s)
- Skander Hathroubi
- 1 Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal , Montréal, Canada
| | - Mohamed A Mekni
- 2 The National Bone Marrow Transplant Centre , UR12ES02, Faculty of Medicine, Tunis, Tunisia
| | | | - Dao Nguyen
- 4 Meakins Christie Laboratories, Department of Medicine, Research Institute of the McGill University Health Centre , Montréal, Canada
| | - Mario Jacques
- 1 Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal , Montréal, Canada
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163
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Hansen RH, Timm AC, Timm CM, Bible AN, Morrell-Falvey JL, Pelletier DA, Simpson ML, Doktycz MJ, Retterer ST. Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development. PLoS One 2016; 11:e0155080. [PMID: 27152511 PMCID: PMC4859483 DOI: 10.1371/journal.pone.0155080] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/24/2016] [Indexed: 12/26/2022] Open
Abstract
The structure and function of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment and the abundance of its community members. The complexity of this natural parameter space has made characterization of the key drivers of community development difficult. In order to facilitate these characterizations, we have developed a microwell platform designed to screen microbial growth and interactions across a wide variety of physical and initial conditions. Assembly of microbial communities into microwells was achieved using a novel biofabrication method that exploits well feature sizes for control of innoculum levels. Wells with incrementally smaller size features created populations with increasingly larger variations in inoculum levels. This allowed for reproducible growth measurement in large (20 μm diameter) wells, and screening for favorable growth conditions in small (5, 10 μm diameter) wells. We demonstrate the utility of this approach for screening and discovery using 5 μm wells to assemble P. aeruginosa colonies across a broad distribution of innoculum levels, and identify those conditions that promote the highest probability of survivial and growth under spatial confinement. Multi-member community assembly was also characterized to demonstrate the broad potential of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.
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Affiliation(s)
- Ryan H Hansen
- Kansas State University, Manhattan, Kansas, United States of America.,The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Andrea C Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Collin M Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Amber N Bible
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer L Morrell-Falvey
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dale A Pelletier
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Michael L Simpson
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Mitchel J Doktycz
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Scott T Retterer
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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164
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McNally L, Brown SP. Building the microbiome in health and disease: niche construction and social conflict in bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0298. [PMID: 26150664 PMCID: PMC4528496 DOI: 10.1098/rstb.2014.0298] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of ‘niche construction’. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.
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Affiliation(s)
- Luke McNally
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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165
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Abstract
Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.
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166
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Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms. Appl Environ Microbiol 2016; 82:2424-2432. [PMID: 26873313 DOI: 10.1128/aem.03957-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/08/2016] [Indexed: 11/20/2022] Open
Abstract
Many bacteria form surface-attached communities known as biofilms. Due to the extreme resistance of these bacterial biofilms to antibiotics and mechanical stresses, biofilms are of growing interest not only in microbiology but also in medicine and industry. Previous studies have determined the extracellular polymeric substances present in the matrix of biofilms formed by Bacillus subtilis NCIB 3610. However, studies on the physical properties of biofilms formed by this strain are just emerging. In particular, quantitative data on the contributions of biofilm matrix biopolymers to these physical properties are lacking. Here, we quantitatively investigated three physical properties of B. subtilis NCIB 3610 biofilms: the surface roughness and stiffness and the bulk viscoelasticity of these biofilms. We show how specific biomolecules constituting the biofilm matrix formed by this strain contribute to those biofilm properties. In particular, we demonstrate that the surface roughness and surface elasticity of 1-day-old NCIB 3610 biofilms are strongly affected by the surface layer protein BslA. For a second strain,B. subtilis B-1, which forms biofilms containing mainly γ-polyglutamate, we found significantly different physical biofilm properties that are also differently affected by the commonly used antibacterial agent ethanol. We show that B-1 biofilms are protected from ethanol-induced changes in the biofilm's stiffness and that this protective effect can be transferred to NCIB 3610 biofilms by the sole addition of γ-polyglutamate to growing NCIB 3610 biofilms. Together, our results demonstrate the importance of specific biofilm matrix components for the distinct physical properties of B. subtilis biofilms.
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167
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Battin TJ, Besemer K, Bengtsson MM, Romani AM, Packmann AI. The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol 2016; 14:251-63. [DOI: 10.1038/nrmicro.2016.15] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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168
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Tierra G, Pavissich JP, Nerenberg R, Xu Z, Alber MS. Multicomponent model of deformation and detachment of a biofilm under fluid flow. J R Soc Interface 2016; 12:rsif.2015.0045. [PMID: 25808342 DOI: 10.1098/rsif.2015.0045] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A novel biofilm model is described which systemically couples bacteria, extracellular polymeric substances (EPS) and solvent phases in biofilm. This enables the study of contributions of rheology of individual phases to deformation of biofilm in response to fluid flow as well as interactions between different phases. The model, which is based on first and second laws of thermodynamics, is derived using an energetic variational approach and phase-field method. Phase-field coupling is used to model structural changes of a biofilm. A newly developed unconditionally energy-stable numerical splitting scheme is implemented for computing the numerical solution of the model efficiently. Model simulations predict biofilm cohesive failure for the flow velocity between [Formula: see text] and [Formula: see text] m s(-1) which is consistent with experiments. Simulations predict biofilm deformation resulting in the formation of streamers for EPS exhibiting a viscous-dominated mechanical response and the viscosity of EPS being less than [Formula: see text]. Higher EPS viscosity provides biofilm with greater resistance to deformation and to removal by the flow. Moreover, simulations show that higher EPS elasticity yields the formation of streamers with complex geometries that are more prone to detachment. These model predictions are shown to be in qualitative agreement with experimental observations.
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Affiliation(s)
- Giordano Tierra
- Mathematical Institute, Faculty of Mathematics and Physics, Charles University, 186 75 Prague 8, Czech Republic Department of Applied and Computational Mathematics and Statistics University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan P Pavissich
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Zhiliang Xu
- Department of Applied and Computational Mathematics and Statistics University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mark S Alber
- Department of Applied and Computational Mathematics and Statistics University of Notre Dame, Notre Dame, IN 46556, USA
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169
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Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc Natl Acad Sci U S A 2016; 113:E2066-72. [PMID: 26933214 DOI: 10.1073/pnas.1601702113] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.
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170
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Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics. Nat Rev Microbiol 2016; 13:761-75. [PMID: 26568072 DOI: 10.1038/nrmicro3567] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Motility is one of the most dynamic features of the microbial world. The ability to swim or crawl frequently governs how microorganisms interact with their physical and chemical environments, and underpins a myriad of microbial processes. The ability to resolve temporal dynamics through time-lapse video microscopy and the precise control of the physicochemical microenvironment afforded by microfluidics offer powerful new opportunities to study the many motility adaptations of microorganisms and thereby further our understanding of their ecology. In this Review, we outline recent insights into the motility strategies of microorganisms brought about by these techniques, including the hydrodynamic signature of microorganisms, their locomotion mechanics, chemotaxis, their motility near and on surfaces, swimming in moving fluids and motility in dense microbial suspensions.
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171
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Hol FJH, Rotem O, Jurkevitch E, Dekker C, Koster DA. Bacterial predator-prey dynamics in microscale patchy landscapes. Proc Biol Sci 2016; 283:20152154. [PMID: 26865299 PMCID: PMC4760159 DOI: 10.1098/rspb.2015.2154] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/18/2016] [Indexed: 01/22/2023] Open
Abstract
Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions.
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Affiliation(s)
- Felix J H Hol
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Or Rotem
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Daniel A Koster
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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173
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Schwarz-Schilling M, Aufinger L, Mückl A, Simmel FC. Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets. Integr Biol (Camb) 2016; 8:564-70. [PMID: 26778746 DOI: 10.1039/c5ib00301f] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Position-dependent gene expression in gradients of morphogens is one of the key processes involved in cellular differentiation during development. Here, we study a simple artificial differentiation process, which is based on the diffusion of genetic inducers within one-dimensional arrangements of 50 μm large water-in-oil droplets. The droplets are filled with either bacteria or cell-free gene expression systems, both equipped with genetic constructs that produce inducers or respond to them via expression of a fluorescent protein. We quantitatively study the coupled diffusion-gene expression process and demonstrate that gene expression can be made position-dependent both within bacteria-containing and cell-free droplets. By generating diffusing quorum sensing signals in situ, we also establish communication between artificial cell-free sender cells and bacterial receivers, and vice versa.
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Affiliation(s)
- M Schwarz-Schilling
- Technical University of Munich, Physics Department E14 and ZNN/WSI, Am Coulombwall 4a, 85748 Garching, Germany.
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174
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Local and global consequences of flow on bacterial quorum sensing. Nat Microbiol 2016; 1:15005. [PMID: 27571752 DOI: 10.1038/nmicrobiol.2015.5] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/01/2015] [Indexed: 12/19/2022]
Abstract
Bacteria use a chemical communication process called quorum sensing (QS) to control collective behaviours such as pathogenesis and biofilm formation(1,2). QS relies on the production, release and group-wide detection of signal molecules called autoinducers. To date, studies of bacterial pathogenesis in well-mixed cultures have revealed virulence factors and the regulatory circuits controlling them, including the overarching role of QS(3). Although flow is ubiquitous to nearly all living systems(4), much less explored is how QS influences pathogenic traits in scenarios that mimic host environments, for example, under fluid flow and in complex geometries. Previous studies(5-7) have shown that sufficiently strong flow represses QS. Nonetheless, it is not known how QS functions under constant or intermittent flow, how it varies within biofilms or as a function of position along a confined flow, or how surface topography (grooves, crevices, pores) influence QS-mediated communication. We explore these questions using two common pathogens, Staphylococcus aureus and Vibrio cholerae. We identify conditions where flow represses QS and other conditions where QS is activated despite flow, including characterizing geometric and topographic features that influence the QS response. Our studies highlight that, under flow, genetically identical cells do not exhibit phenotypic uniformity with respect to QS in space and time, leading to complex patterns of pathogenesis and colonization. Understanding the ramifications of spatially and temporally non-uniform QS responses in realistic environments will be crucial for successful deployment of synthetic pro- and anti-QS strategies.
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175
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Photodynamic inactivation of antibiotic-resistant bacteria and biofilms by hematoporphyrin monomethyl ether. Lasers Med Sci 2015; 31:297-304. [PMID: 26719055 DOI: 10.1007/s10103-015-1859-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 12/17/2015] [Indexed: 01/03/2023]
Abstract
The worldwide increase in bacterial antibiotic resistance has led to a search for alternative antibacterial therapies. A promising approach to killing antibiotic-resistant bacteria is photodynamic antimicrobial chemotherapy, which uses light in combination with a photosensitizer to induce a phototoxic reaction. We evaluated the photodynamic inactivation (PDI) efficiency of hematoporphyrin monomethyl ether (HMME) on antibiotic-resistant bacteria and biofilms. HMME exhibited no significant dark toxicity and provided dose-dependent inactivation of antibiotic-resistant bacteria and biofilms. After incubation with 100-μM HMME and irradiation with 72-J cm(-2) white light, 4.19-7.59 log10 reductions in survival were achieved in planktonic suspension. Antibiotic-resistant strains were as susceptible to PDI in biofilms as in planktonic suspensions, but the inactivation of bacterial cells in biofilms was attenuated. In addition, gram-positive bacterial strains and biofilms were more susceptible than gram-negative strains and biofilms to the PDI effect of HMME. Thus, HMME is a promising photosensitizer for the treatment of infectious diseases caused by antibiotic-resistant bacteria, especially gram-positive bacteria.
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176
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Patteson AE, Gopinath A, Goulian M, Arratia PE. Running and tumbling with E. coli in polymeric solutions. Sci Rep 2015; 5:15761. [PMID: 26507950 PMCID: PMC4938119 DOI: 10.1038/srep15761] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/29/2015] [Indexed: 12/24/2022] Open
Abstract
Run-and-tumble motility is widely used by swimming microorganisms including numerous prokaryotic and eukaryotic organisms. Here, we experimentally investigate the run-and-tumble dynamics of the bacterium E. coli in polymeric solutions. We find that even small amounts of polymer in solution can drastically change E. coli dynamics: cells tumble less and their velocity increases, leading to an enhancement in cell translational diffusion and a sharp decline in rotational diffusion. We show that suppression of tumbling is due to fluid viscosity while the enhancement in swimming speed is mainly due to fluid elasticity. Visualization of single fluorescently labeled DNA polymers reveals that the flow generated by individual E. coli is sufficiently strong to stretch polymer molecules and induce elastic stresses in the fluid, which in turn can act on the cell in such a way to enhance its transport. Our results show that the transport and spread of chemotactic cells can be independently modified and controlled by the fluid material properties.
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Affiliation(s)
- A E Patteson
- Department of Mechanical Engineering &Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104
| | - A Gopinath
- Department of Mechanical Engineering &Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104.,School of Engineering, University of California Merced, Merced, CA 95343
| | - M Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - P E Arratia
- Department of Mechanical Engineering &Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104
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177
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Bacterial growth, detachment and cell size control on polyethylene terephthalate surfaces. Sci Rep 2015; 5:15159. [PMID: 26464114 PMCID: PMC4604555 DOI: 10.1038/srep15159] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/16/2015] [Indexed: 12/30/2022] Open
Abstract
In medicine and food industry, bacterial colonisation on surfaces is a common cause of infections and severe illnesses. However, the detailed quantitative information about the dynamics and the mechanisms involved in bacterial proliferation on solid substrates is still lacking. In this study we investigated the adhesion and detachment, the individual growth and colonisation, and the cell size control of Escherichia coli (E. coli) MG1655 on polyethylene terephthalate (PET) surfaces. The results show that the bacterial growth curve on PET exhibits the distinct lag and log phases, but the generation time is more than twice longer than in bulk medium. Single cells in the lag phase are more likely to detach than clustered ones in the log phase; clustered bacteria in micro-colonies have stronger adhesive bonds with surfaces and their neighbours with the progressing colonisation. We show that the cell size is under the density-dependent pathway control: when the adherent cells are at low density, the culture medium is responsible for coordinating cell division and cell size; when the clustered cells are at high population density, we demonstrate that the effect of quorum sensing causes the cell size decrease as the cell density on surfaces increases.
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178
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Wu F, Dekker C. Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology. Chem Soc Rev 2015; 45:268-80. [PMID: 26383019 DOI: 10.1039/c5cs00514k] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nanofabricated structures and microfluidic technologies are increasingly being used to study bacteria because of their precise spatial and temporal control. They have facilitated studying many long-standing questions regarding growth, chemotaxis and cell-fate switching, and opened up new areas such as probing the effect of boundary geometries on the subcellular structure and social behavior of bacteria. We review the use of nano/microfabricated structures that spatially separate bacteria for quantitative analyses and that provide topological constraints on their growth and chemical communications. These approaches are becoming modular and broadly applicable, and show a strong potential for dissecting the complex life of bacteria at various scales and engineering synthetic microbial societies.
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Affiliation(s)
- Fabai Wu
- Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Lorentzweg 1, 2628CJ Delft, The Netherlands.
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179
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Single gene locus changes perturb complex microbial communities as much as apex predator loss. Nat Commun 2015; 6:8235. [PMID: 26354365 PMCID: PMC4579780 DOI: 10.1038/ncomms9235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 07/30/2015] [Indexed: 02/08/2023] Open
Abstract
Many bacterial species are highly social, adaptively shaping their local environment through the production of secreted molecules. This can, in turn, alter interaction strengths among species and modify community composition. However, the relative importance of such behaviours in determining the structure of complex communities is unknown. Here we show that single-locus changes affecting biofilm formation phenotypes in Bacillus subtilis modify community structure to the same extent as loss of an apex predator and even to a greater extent than loss of B. subtilis itself. These results, from experimentally manipulated multitrophic microcosm assemblages, demonstrate that bacterial social traits are key modulators of the structure of their communities. Moreover, they show that intraspecific genetic variability can be as important as strong trophic interactions in determining community dynamics. Microevolution may therefore be as important as species extinctions in shaping the response of microbial communities to environmental change. Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al. show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator.
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180
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Wolf J, Tang L, Rubnitz JE, Brennan RC, Shook DR, Stokes DC, Monagle P, Curtis N, Worth LJ, Allison K, Sun Y, Flynn PM. Monitoring Central Venous Catheter Resistance to Predict Imminent Occlusion: A Prospective Pilot Study. PLoS One 2015; 10:e0135904. [PMID: 26322512 PMCID: PMC4555832 DOI: 10.1371/journal.pone.0135904] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/27/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Long-term central venous catheters are essential for the management of chronic medical conditions, including childhood cancer. Catheter occlusion is associated with an increased risk of subsequent complications, including bloodstream infection, venous thrombosis, and catheter fracture. Therefore, predicting and pre-emptively treating occlusions should prevent complications, but no method for predicting such occlusions has been developed. METHODS We conducted a prospective trial to determine the feasibility, acceptability, and efficacy of catheter-resistance monitoring, a novel approach to predicting central venous catheter occlusion in pediatric patients. Participants who had tunneled catheters and were receiving treatment for cancer or undergoing hematopoietic stem cell transplantation underwent weekly catheter-resistance monitoring for up to 12 weeks. Resistance was assessed by measuring the inline pressure at multiple flow-rates via a syringe pump system fitted with a pressure-sensing transducer. When turbulent flow through the device was evident, resistance was not estimated, and the result was noted as "non-laminar." RESULTS Ten patients attended 113 catheter-resistance monitoring visits. Elevated catheter resistance (>8.8% increase) was strongly associated with the subsequent development of acute catheter occlusion within 10 days (odds ratio = 6.2; 95% confidence interval, 1.8-21.5; p <0.01; sensitivity, 75%; specificity, 67%). A combined prediction model comprising either change in resistance greater than 8.8% or a non-laminar result predicted subsequent occlusion (odds ratio = 6.8; 95% confidence interval, 2.0-22.8; p = 0.002; sensitivity, 80%; specificity, 63%). Participants rated catheter-resistance monitoring as highly acceptable. CONCLUSIONS In this pediatric hematology and oncology population, catheter-resistance monitoring is feasible, acceptable, and predicts imminent catheter occlusion. Larger studies are required to validate these findings, assess the predictive value for other clinical outcomes, and determine the impact of pre-emptive therapy. TRIAL REGISTRATION Clinicaltrials.gov NCT01737554.
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Affiliation(s)
- Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Rachel C. Brennan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - David R. Shook
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Dennis C. Stokes
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Paul Monagle
- Department of Haematology, Royal Children’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nigel Curtis
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Leon J. Worth
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Kim Allison
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yilun Sun
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Patricia M. Flynn
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
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181
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Chang CB, Wilking JN, Kim SH, Shum HC, Weitz DA. Monodisperse Emulsion Drop Microenvironments for Bacterial Biofilm Growth. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3954-61. [PMID: 25959709 DOI: 10.1002/smll.201403125] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/13/2015] [Indexed: 05/20/2023]
Abstract
In this work, microfluidic technology is used to rapidly create hundreds of thousands of monodisperse double and triple emulsion drops that serve as 3D microenvironments for the containment and growth of bacterial biofilms. The size of these drops, with diameters from tens to hundreds of micrometers, makes them amenable to rapid manipulation and analysis. This is demonstrated by using microscopy to visualize cellular differentiation of Bacillus subtilis biofilm communities within each drop and the bacterial biofilm microstructure. Biofilm growth is explored upon specific interfaces in double and triple emulsions and upon negative and positive radii of curvature. Biofilm attachment of matrix and flagella mutants is studied as well as biofilms of Pseudomonas aeruginosa. This is the first demonstration of biofilms grown in microscale emulsion drops, which serve as both templates and containers for biofilm growth and attachment. These microenvironments have the potential to transform existing high-throughput screening methods for bacterial biofilms.
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Affiliation(s)
- Connie B Chang
- School of Engineering and Applied Science, Department of Physics Harvard University, Cambridge, MA, 02138, USA
- Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, 59717, USA
| | - James N Wilking
- School of Engineering and Applied Science, Department of Physics Harvard University, Cambridge, MA, 02138, USA
- Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, 59717, USA
| | - Shin-Hyun Kim
- School of Engineering and Applied Science, Department of Physics Harvard University, Cambridge, MA, 02138, USA
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Ho Cheung Shum
- School of Engineering and Applied Science, Department of Physics Harvard University, Cambridge, MA, 02138, USA
- Department of Mechanical Engineering, The University of Hong Kong, China
| | - David A Weitz
- School of Engineering and Applied Science, Department of Physics Harvard University, Cambridge, MA, 02138, USA
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182
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Bacterial floc mediated rapid streamer formation in creeping flows. Sci Rep 2015; 5:13070. [PMID: 26278133 PMCID: PMC4538384 DOI: 10.1038/srep13070] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/16/2015] [Indexed: 12/01/2022] Open
Abstract
One of the central puzzles concerning the interaction of low Reynolds number fluid transport with bacterial biomass is the formation of filamentous structures called streamers. In this manuscript, we report our discovery of a new kind of low Re bacterial streamers, which appear from pre-formed bacterial flocs. In sharp contrast to the biofilm-mediated streamers, these streamers form over extremely small timescales (less than a second). Our experiments, carried out in a microchannel with micropillars rely on fluorescence microscopy techniques to illustrate that floc-mediated streamers form when a freely-moving floc adheres to the micropillar wall and gets rapidly sheared by the background flow. We also show that at their inception the deformation of the flocs is dominated by recoverable large strains indicating significant elasticity. These strains subsequently increase tremendously to produce filamentous streamers. Interestingly, we find that these fully formed streamers are not static structures and show viscous response at time scales larger than their formation time scales. Finally, we show that such novel streamer formation can lead to rapid clogging of microfluidic devices.
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183
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Persat A, Nadell CD, Kim MK, Ingremeau F, Siryaporn A, Drescher K, Wingreen NS, Bassler BL, Gitai Z, Stone HA. The mechanical world of bacteria. Cell 2015; 161:988-997. [PMID: 26000479 DOI: 10.1016/j.cell.2015.05.005] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 10/23/2022]
Abstract
In the wild, bacteria are predominantly associated with surfaces as opposed to existing as free-swimming, isolated organisms. They are thus subject to surface-specific mechanics, including hydrodynamic forces, adhesive forces, the rheology of their surroundings, and transport rules that define their encounters with nutrients and signaling molecules. Here, we highlight the effects of mechanics on bacterial behaviors on surfaces at multiple length scales, from single bacteria to the development of multicellular bacterial communities such as biofilms.
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Affiliation(s)
- Alexandre Persat
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Carey D Nadell
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | | | - Francois Ingremeau
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Albert Siryaporn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Ned S Wingreen
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA.
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184
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Parvinzadeh Gashti M, Bellavance J, Kroukamp O, Wolfaardt G, Taghavi SM, Greener J. Live-streaming: Time-lapse video evidence of novel streamer formation mechanism and varying viscosity. BIOMICROFLUIDICS 2015; 9:041101. [PMID: 26339304 PMCID: PMC4529438 DOI: 10.1063/1.4928296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 07/29/2015] [Indexed: 05/12/2023]
Abstract
Time-lapse videos of growing biofilms were analyzed using a background subtraction method, which removed camouflaging effects from the heterogeneous field of view to reveal evidence of streamer formation from optically dense biofilm segments. In addition, quantitative measurements of biofilm velocity and optical density, combined with mathematical modeling, demonstrated that streamer formation occurred from mature, high-viscosity biofilms. We propose a streamer formation mechanism by sudden partial detachment, as opposed to continuous elongation as observed in other microfluidic studies. Additionally, streamer formation occurred in straight microchannels, as opposed to serpentine or pseudo-porous channels, as previously reported.
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Affiliation(s)
| | | | - Otini Kroukamp
- Department of Chemistry and Biology, Ryerson University , Toronto, Canada
| | - Gideon Wolfaardt
- Department of Microbiology, Stellenbosch University , Stellenbosch, South Africa
| | | | - Jesse Greener
- Département de Chimie, Université Laval , Québec, Canada
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185
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Weiss N, van Leeuwen TG, Kalkman J. Simultaneous and localized measurement of diffusion and flow using optical coherence tomography. OPTICS EXPRESS 2015; 23:3448-59. [PMID: 25836201 DOI: 10.1364/oe.23.003448] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report on the simultaneous and localized measurement of the diffusion coefficient and flow velocity based on the normalized autocorrelation function using optical coherence tomography (OCT). Our results on a flowing suspension of polystyrene spheres show that the flow velocity and the diffusion coefficient can be reliably estimated in a regime determined by the sample diffusivity, the local flow velocity, and the Gaussian beam waist. We experimentally demonstrate that a smaller beam waist results in an improvement of the velocity sensitivity at the expense of the precision and accuracy of the estimation of the diffusion coefficient. Further, we show that the decay of the OCT autocorrelation function due to flow depends only on the Gaussian beam waist irrespective of the sample position with respect to the focus position.
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186
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Espeso DR, Carpio A, Einarsson B. Differential growth of wrinkled biofilms. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022710. [PMID: 25768534 DOI: 10.1103/physreve.91.022710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Biofilms are antibiotic-resistant bacterial aggregates that grow on moist surfaces and can trigger hospital-acquired infections. They provide a classical example in biology where the dynamics of cellular communities may be observed and studied. Gene expression regulates cell division and differentiation, which affect the biofilm architecture. Mechanical and chemical processes shape the resulting structure. We gain insight into the interplay between cellular and mechanical processes during biofilm development on air-agar interfaces by means of a hybrid model. Cellular behavior is governed by stochastic rules informed by a cascade of concentration fields for nutrients, waste, and autoinducers. Cellular differentiation and death alter the structure and the mechanical properties of the biofilm, which is deformed according to Föppl-Von Kármán equations informed by cellular processes and the interaction with the substratum. Stiffness gradients due to growth and swelling produce wrinkle branching. We are able to reproduce wrinkled structures often formed by biofilms on air-agar interfaces, as well as spatial distributions of differentiated cells commonly observed with B. subtilis.
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Affiliation(s)
- D R Espeso
- Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - A Carpio
- Departamento de Matematica Aplicada, Universidad Complutense, Madrid 28040, Spain
| | - B Einarsson
- Center for Complex and Nonlinear Science, UC Santa Barbara, California 93106, USA
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187
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Li S, Stone HA, Murphy CT. A microfluidic device and automatic counting system for the study of C. elegans reproductive aging. LAB ON A CHIP 2015; 15:524-31. [PMID: 25407755 PMCID: PMC4277648 DOI: 10.1039/c4lc01028k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The nematode Caenorhabditis elegans (C. elegans) is an excellent model to study reproductive aging because of its short life span, its cessation of reproduction in mid-adulthood, and the strong conservation of pathways that regulate longevity. During its lifetime, a wild-type C. elegans hermaphrodite usually lays about 200-300 self-fertilized hatchable eggs, which mainly occurs in the first three to five days of adulthood. Here, we report the development of a microfluidic assay and a real-time, automatic progeny counting system that records progeny counting information from many individual C. elegans hermaphrodites. This system offers many advantages compared to conventional plate assays. The flow of non-proliferating bacteria not only feeds the worms but also flushes the just-hatched young progeny through a filter that separates mothers from their offspring. The progeny that are flushed out of the chamber are detected and recorded using a novel algorithm. In our current design, one device contains as many as 16 individual chambers. Here we show examples of real-time progeny production information from wild-type (N2) and daf-2 (insulin receptor) mutants. We believe that this system has the potential to become a powerful, high time-resolution tool to study the detailed reproduction of C. elegans.
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Affiliation(s)
- Siran Li
- Lewis-Sigler Institute for integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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188
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Paquet-Mercier F, Karas A, Safdar M, Aznaveh NB, Zarabadi M, Greener J. Development and calibration of a microfluidic biofilm growth cell with flow-templating and multi-modal characterization. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:1557-62. [PMID: 25570268 DOI: 10.1109/embc.2014.6943900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the development of a microfluidic flow-templating platform with multi-modal characterization for studies of biofilms and their precursor materials. A key feature is a special three inlet flow-template compartment, which confines and controls the location of biofilm growth against a template wall. Characterization compartments include Raman imaging to study the localization of the nutrient solutions, optical microscopy to quantify biofilm biomass and localization, and cyclic voltammetry for flow velocity measurements. Each compartment is tested and then utilized to make preliminary measurements.
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189
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Karimi A, Karig D, Kumar A, Ardekani AM. Interplay of physical mechanisms and biofilm processes: review of microfluidic methods. LAB ON A CHIP 2015; 15:23-42. [PMID: 25385289 PMCID: PMC4261921 DOI: 10.1039/c4lc01095g] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Bacteria in natural and artificial environments often reside in self-organized, integrated communities known as biofilms. Biofilms are highly structured entities consisting of bacterial cells embedded in a matrix of self-produced extracellular polymeric substances (EPS). The EPS matrix acts like a biological 'glue' enabling microbes to adhere to and colonize a wide range of surfaces. Once integrated into biofilms, bacterial cells can withstand various forms of stress such as antibiotics, hydrodynamic shear and other environmental challenges. Because of this, biofilms of pathogenic bacteria can be a significant health hazard often leading to recurrent infections. Biofilms can also lead to clogging and material degradation; on the other hand they are an integral part of various environmental processes such as carbon sequestration and nitrogen cycles. There are several determinants of biofilm morphology and dynamics, including the genotypic and phenotypic states of constituent cells and various environmental conditions. Here, we present an overview of the role of relevant physical processes in biofilm formation, including propulsion mechanisms, hydrodynamic effects, and transport of quorum sensing signals. We also provide a survey of microfluidic techniques utilized to unravel the associated physical mechanisms. Further, we discuss the future research areas for exploring new ways to extend the scope of the microfluidic approach in biofilm studies.
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Affiliation(s)
- A. Karimi
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - D. Karig
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
| | - A. Kumar
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada AB T6G 2G8
| | - A. M. Ardekani
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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190
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Formation and post-formation dynamics of bacterial biofilm streamers as highly viscous liquid jets. Sci Rep 2014; 4:7126. [PMID: 25410423 PMCID: PMC4237988 DOI: 10.1038/srep07126] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/30/2014] [Indexed: 11/09/2022] Open
Abstract
It has been recently reported that in presence of low Reynolds number (Re ≪ 1) transport, preformed bacterial biofilms, several hours after their formation, may degenerate in form of filamentous structures, known as streamers. In this work, we explain that such streamers form as the highly viscous liquid states of the intrinsically viscoelastic biofilms. Such “viscous liquid” state can be hypothesized by noting that the time of appearance of the streamers is substantially larger than the viscoelastic relaxation time scale of the biofilms, and this appearance is explained by the inability of a viscous liquid to withstand external shear. Further, by identifying the post formation dynamics of the streamers as that of a viscous liquid jet in a surrounding flow field, we can interpret several unexplained issues associated with the post-formation dynamics of streamers, such as the clogging of the flow passage or the exponential time growth of streamer dimensions. Overall our manuscript provides a biophysical basis for understanding the evolution of biofilm streamers in creeping flows.
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191
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Hol FJH, Dekker C. Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science 2014; 346:1251821. [PMID: 25342809 DOI: 10.1126/science.1251821] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spatial structure of natural habitats strongly affects bacterial life, ranging from nanoscale structural features that individual cells exploit for surface attachment, to micro- and millimeter-scale chemical gradients that drive population-level processes. Nanofabrication and microfluidics are ideally suited to manipulate the environment at those scales and have emerged as powerful tools with which to study bacteria. Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities. This toolbox is beginning to elucidate disparate bacterial phenomena-including aging, electron transport, and quorum sensing-and enables the dissection of environmental communities through single-cell genomics. A more intimate integration of microfluidics, nanofabrication, and microbiology will enable further exploration of bacterial life at the smallest scales.
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Affiliation(s)
- Felix J H Hol
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands.
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192
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Vega NM, Gore J. Collective antibiotic resistance: mechanisms and implications. Curr Opin Microbiol 2014; 21:28-34. [PMID: 25271119 DOI: 10.1016/j.mib.2014.09.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 09/10/2014] [Accepted: 09/10/2014] [Indexed: 12/17/2022]
Abstract
In collective resistance, microbial communities are able to survive antibiotic exposures that would be lethal to individual cells. In this review, we explore recent advances in understanding collective resistance in bacteria. The population dynamics of 'cheating' in a system with cooperative antibiotic inactivation have been described, providing insight into the demographic factors that determine resistance allele frequency in bacteria. Extensive work has elucidated mechanisms underlying collective resistance in biofilms and addressed questions about the role of cooperation in these structures. Additionally, recent investigations of 'bet-hedging' strategies in bacteria have explored the contributions of stochasticity and regulation to bacterial phenotypic heterogeneity and examined the effects of these strategies on community survival.
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Affiliation(s)
- Nicole M Vega
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeff Gore
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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193
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Mendis N, Lin YR, Faucher SP. Comparison of virulence properties of Pseudomonas aeruginosa exposed to water and grown in rich broth. Can J Microbiol 2014; 60:777-81. [PMID: 25352257 DOI: 10.1139/cjm-2014-0519] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can infect susceptible patients suffering from cystic fibrosis, immunosuppression, and severe burns. Nosocomial- and community-acquired infection is likely due to contact with water sources contaminated with P. aeruginosa. Most of what is known about the virulence properties of P. aeruginosa was derived from studies using fairly rich broths, which do not represent conditions found in water, such as low nutrient concentrations. Here, we compare biofilm production, invasion of epithelial cells, cytotoxicity, and pyocyanin production of P. aeruginosa in water with P. aeruginosa grown in rich broth. Since tap water is variable, we used a defined water medium, Fraquil, to ensure reproducibility of the results. We found that P. aeruginosa does not readily form biofilm in Fraquil. Pseudomonas aeruginosa is equally able to attach to and invade epithelial cells but is more cytotoxic after incubation in water for 30 days than when it is grown in rich broth. Moreover, P. aeruginosa produces less pyocyanin when exposed to water. Our results show that P. aeruginosa seems to have different properties when exposed to water than when grown in rich broth.
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Affiliation(s)
- Nilmini Mendis
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada
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194
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Beirão S, Fernandes S, Coelho J, Faustino MAF, Tomé JPC, Neves MGPMS, Tomé AC, Almeida A, Cunha A. Photodynamic inactivation of bacterial and yeast biofilms with a cationic porphyrin. Photochem Photobiol 2014; 90:1387-96. [PMID: 25112506 DOI: 10.1111/php.12331] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/05/2014] [Indexed: 12/26/2022]
Abstract
The efficiency of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetra-iodide (Tetra-Py(+)-Me) in the photodynamic inactivation of single-species biofilms of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans and mixed biofilms of S. aureus and C. albicans was evaluated. The effect on the extracellular matrix of P. aeruginosa was also assessed. Irradiation with white light up to an energy dose of 64.8 J cm(-2) in the presence of 20 μm of Tetra-Py(+)-Me caused significant inactivation in all single-species biofilms (3-6 log reductions), although the susceptibility was attenuated in relation to planktonic cells. In mixed biofilms, the inactivation of S. aureus was as efficient as in single-species biofilms but the susceptibility of C. albicans decreased. In P. aeruginosa biofilms, a reduction of 81% in the polysaccharide content of the matrix was observed after treatment with a 20 μm PS concentration and a total light dose of 64.8 J cm(-2). The results show that the Tetra-Py(+)-Me causes significant inactivation of the microorganisms, either in biofilms or in the planktonic form, and demonstrate that polysaccharides of the biofilm matrix may be a primary target of photodynamic damage.
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Affiliation(s)
- Sandra Beirão
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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195
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Abstract
Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.
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Affiliation(s)
- Roberto Rusconi
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; , ,
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196
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Hassanpourfard M, Sun X, Valiei A, Mukherjee P, Thundat T, Liu Y, Kumar A. Protocol for biofilm streamer formation in a microfluidic device with micro-pillars. J Vis Exp 2014. [PMID: 25178035 DOI: 10.3791/51732] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Several bacterial species possess the ability to attach to surfaces and colonize them in the form of thin films called biofilms. Biofilms that grow in porous media are relevant to several industrial and environmental processes such as wastewater treatment and CO2 sequestration. We used Pseudomonas fluorescens, a Gram-negative aerobic bacterium, to investigate biofilm formation in a microfluidic device that mimics porous media. The microfluidic device consists of an array of micro-posts, which were fabricated using soft-lithography. Subsequently, biofilm formation in these devices with flow was investigated and we demonstrate the formation of filamentous biofilms known as streamers in our device. The detailed protocols for fabrication and assembly of microfluidic device are provided here along with the bacterial culture protocols. Detailed procedures for experimentation with the microfluidic device are also presented along with representative results.
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Affiliation(s)
| | - Xiaohui Sun
- Department of Civil and Environmental Engineering, University of Alberta
| | - Amin Valiei
- Department of Chemical and Material Engineering, University of Alberta
| | | | - Thomas Thundat
- Department of Chemical and Material Engineering, University of Alberta
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta
| | - Aloke Kumar
- Department of Mechanical Engineering, University of Alberta;
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197
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Aznaveh NB, Safdar M, Wolfaardt G, Greener J. Micropatterned biofilm formations by laminar flow-templating. LAB ON A CHIP 2014; 14:2666-72. [PMID: 24722812 DOI: 10.1039/c4lc00084f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a microfluidic device capable of patterning linear biofilm formations using a flow templating approach. We describe the design considerations and fabrication methodology of a two level flow-templating micro-bioreactor (FT-μBR), which generates a biofilm growth stream surrounded on 3 sides by a growth inhibiting confinement stream. Through a combination of experiments and simulations we comprehensively evaluate and exploit control parameters to manipulate the biofilm growth template stream dimensions. The FT-μBR is then used to grow biofilm patterns with controllable dimensions. A proof-of-principle study using the device demonstrates its utility in conducting biofilm growth rate measurements under different shear stress environments. This opens the way for quantitative studies into the effects of the local shear environment on biofilm properties and for the synthesis of a new generation of functional biomaterials with controllable properties.
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Affiliation(s)
- Nahid Babaei Aznaveh
- Département de Chimie, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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198
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Chew SC, Kundukad B, Seviour T, van der Maarel JRC, Yang L, Rice SA, Doyle P, Kjelleberg S. Dynamic remodeling of microbial biofilms by functionally distinct exopolysaccharides. mBio 2014; 5:e01536-14. [PMID: 25096883 PMCID: PMC4128364 DOI: 10.1128/mbio.01536-14] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 07/07/2014] [Indexed: 12/24/2022] Open
Abstract
Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. Importance: Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical and industrial settings. One of the defining features of a biofilm is its extracellular matrix. The matrix has a heterogeneous structure and is formed from a secretion of various biopolymers, including proteins, extracellular DNA, and polysaccharides. It is generally known to interact with biofilm cells, thus affecting cell physiology and cell-cell communication. Despite the fact that the matrix may comprise up to 90% of the biofilm dry weight, how the matrix properties affect biofilm structure, maturation, and interspecies interactions remain largely unexplored. This study reveals that bacteria can use specific extracellular polymers to modulate the physical properties of their microenvironment. This in turn impacts biofilm structure, differentiation, and interspecies interactions.
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Affiliation(s)
| | - Binu Kundukad
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
| | - Thomas Seviour
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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199
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Kim MK, Drescher K, Pak OS, Bassler BL, Stone HA. Filaments in curved streamlines: Rapid formation of Staphylococcus aureus biofilm streamers. NEW JOURNAL OF PHYSICS 2014; 16:065024. [PMID: 25484614 PMCID: PMC4255984 DOI: 10.1088/1367-2630/16/6/065024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biofilms are surface-associated conglomerates of bacteria that are highly resistant to antibiotics. These bacterial communities can cause chronic infections in humans by colonizing, for example, medical implants, heart valves, or lungs. Staphylococcus aureus, a notorious human pathogen, causes some of the most common biofilm-related infections. Despite the clinical importance of S. aureus biofilms, it remains mostly unknown how physical effects, in particular flow, and surface structure influence biofilm dynamics. Here we use model microfluidic systems to investigate how environmental factors, such as surface geometry, surface chemistry, and fluid flow affect biofilm development in S. aureus. We discovered that S. aureus rapidly forms flow-induced, filamentous biofilm streamers, and furthermore if surfaces are coated with human blood plasma, streamers appear within minutes and clog the channels more rapidly than if the channels are uncoated. To understand how biofilm streamer filaments reorient in flows with curved streamlines to bridge the distances between corners, we developed a mathematical model based on resistive force theory of slender filaments. Understanding physical aspects of biofilm formation in S. aureus may lead to new approaches for interrupting biofilm formation of this pathogen.
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Affiliation(s)
| | - Knut Drescher
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - On Shun Pak
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Howard A. Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544
- Corresponding author:
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200
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Karande R, Halan B, Schmid A, Buehler K. Segmented flow is controlling growth of catalytic biofilms in continuous multiphase microreactors. Biotechnol Bioeng 2014; 111:1831-40. [PMID: 24729096 DOI: 10.1002/bit.25256] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 01/20/2023]
Abstract
Biofilm reactors are often mass transfer limited due to excessive biofilm growth, impeding reactor performance. Fluidic conditions play a key role for biofilm structural development and subsequently for overall reactor performance. Continuous interfacial forces generated by aqueous-air segmented flow are controlling biofilm structure and diminish mass transfer limitations in biofilm microreactors. A simple three step method allows the formation of robust biofilms under aqueous-air segmented flow conditions: a first-generation biofilm is developing during single phase flow, followed by the introduction of air segments discarding most of the established biofilm. Finally, a second-generation, mature biofilm is formed in the presence of aqueous-air segments. Confocal laser scanning microscopy experiments revealed that the segmented flow supports the development of a robust biofilm. This mature biofilm is characterized by a three to fourfold increase in growth rate, calculated from an increase in thickness, a faster spatial distribution (95% surface coverage in 24 h), and a significantly more compact structure (roughness coefficient <1), as compared to biofilms grown under single phase flow conditions. The applicability of the concept in a segmented flow biofilm microreactor was demonstrated using the epoxidation of styrene to (S)-styrene oxide (ee > 99.8%) catalyzed by Pseudomonas sp. strain VLB120ΔC cells in the mono-species biofilm. The limiting factor affecting reactor performance was oxygen transfer as the volumetric productivity rose from 11 to 46 g L tube (-1) day(-1) after increasing the air flow rate. In summary, different interfacial forces can be applied for separating cell attachment and adaptation resulting in the development of a robust catalytic biofilm in continuous microreactors.
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Affiliation(s)
- Rohan Karande
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, Dortmund, 44227, Germany
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