Abstract
In this paper, the methods and devices used to confine, observe and characterize the growth of bacteria on an agar based nutrient media are described. Selected strain E. coli MG1655 [1, 2] was successfully inoculated in a confinement structure composed of a microchannel (7 μm × 60 μm × 6.345 mm) with two culture chambers of 3 mm in diameter on both ends. The microchannel was fabricated on a standard microscope glass slide using a mask-less photolithographic technique and chemical etching. Isolation and manipulation of the confined bacteria was achieved by means of a custom designed 3D printed test cell. Observation was performed on an optical transmission microscope enhanced with a customized automation system. Growth characterization was performed by calculating the surface area colonized by the bacteria through image processing and analysis. The discussion focuses on the comparison of the growth rate within the confinement structure compared to traditional cell counting methods and the description of an observed, but inconsistent, scouting behavior. Finally, we discuss on the possible uses of the reported work and extend a call for introducing this system in current bacteriology research.
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Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B.L., Mori, H.: Highly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110. Mol. Syst. Biol. 2 (2006)
Sezonov, G., Joseleau-Petit, D., D’Ari, R.: Escherichia coli physiology in Luria-Bertani broth. J. Bacteriol. 189, 8746–8749 (2007)
Hol, F.J.H., Dekker, C.: Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science 346, 1251821 (2014). doi:10.1126/science.1251821
Weibel, D.B., Diluzio, W.R., Whitesides, G.M.: Microfabrication meets microbiology. Nat. Rev. Microbiol. 5, 209–218 (2007). doi:10.1038/nrmicro1616
Norman, T.M., Lord, N.D., Paulsson, J., Losick, R.: Memory and modularity in cell-fate decision making. Nature 503, 481–486 (2013)
Biondi, S.A., Quinn, J.A., Goldfine, H.: Random motility of swimming bacteria in restricted geometries. AIChE J. 44, 1923–1929 (1998). doi:10.1002/aic.690440822
Frymier, P.D., Ford, R.M.: Analysis of bacterial swimming speed approaching a solid–liquid interface. AIChE J. 43, 1341–1347 (1997). doi:10.1002/aic.690430523
Lauga, E., DiLuzio, W.R., Whitesides, G.M., Stone, H.A.: Swimming in circles: motion of bacteria near solid boundaries. Biophys. J. 90, 400–412 (2006). doi:10.1529/biophysj.105.069401
Ramia, M., Tullock, D.L., Phan-Thien, N.: The role of hydrodynamic interaction in the locomotion of microorganisms. Biophys. J. 65, 755–778 (1993). doi:10.1016/S0006-3495(93)81129-9
Ko, H., Lee, J.S., Jung, C.-H., Choi, J.-H., Kwon, O.-S., Shin, K.: Actuation of digital micro drops by electrowetting on open microfluidic chips fabricated in photolithography. J. Nanosci. Nanotechnol. 14, 5894–5897 (2014)
Gao, J., Manard, B.T., Castro, A., Montoya, D.P., Xu, N., Chamberlin, R.M.: Solid-phase extraction microfluidic devices for matrix removal in trace element assay of actinide materials. Talanta 167, 8–13 (2017). doi:10.1016/j.talanta.2017.01.080
Fukuba, T., Yamamoto, T., Naganuma, T., Fujii, T.: Microfabricated flow-through device for DNA amplification—towards in situ gene analysis. Chem. Eng. J. 101, 151–156 (2004)
Benhamed, S., Guardiola, F.A., Mars, M., Esteban, M.Á.: Pathogen bacteria adhesion to skin mucus of fishes. Vet. Microbiol. 171, 1–12 (2014). doi:10.1016/j.vetmic.2014.03.008
Cortés, M.E., Bonilla, J.C., Sinisterra, R.D.: Biofilm formation, control and novel strategies for eradication. Sci. Against Microb. Pathog. Commun. Curr. Res. Technol. Adv. 2, 896–905 (2011)
Toy, L.W., Macera, L.: Evidence-based review of silver dressing use on chronic wounds. J. Am. Acad. Nurse Pract. 23, 183–192 (2011)
Yue, I.C., Poff, J., Cortés, M.E., Sinisterra, R.D., Faris, C.B., Hildgen, P., Langer, R., Shastri, V.P.: A novel polymeric chlorhexidine delivery device for the treatment of periodontal disease. Biomaterials 25, 3743–3750 (2004)
Kirillov, A.: AForge.NET (2006)
van der Valk, F.M., Verweij, S.L., Zwinderman, K.A.H., Strang, A.C., Kaiser, Y., Marquering, H.A., Nederveen, A.J., Stroes, E.S.G., Verberne, H.J., Rudd, J.H.F.: Thresholds for arterial wall inflammation quantified by 18F-FDG PET imaging: implications for vascular interventional studies. JACC Cardiovasc. Imaging 9, 1198–1207 (2016). doi:10.1016/j.jcmg.2016.04.007
Osma, J.F., Toca-Herrera, J.L., Rodríguez-Couto, S.: Environmental, scanning electron and optical microscope image analysis software for determining volume and occupied area of solid-state fermentation fungal cultures. Biotechnol. J. 6, 45–55 (2011). doi:10.1002/biot.201000256
Noor, R., Islam, Z., Munshi, S.K., Rahman, F.: Influence of temperature on Escherichia coli growth in different culture media. J. Pure Appl. Microbiol. 7, 899–904 (2013)
Lopez-Barbosa, N., Segura, C., Osma, J.F.: Electro-immuno sensors: current developments and future trends. Int. J. Biosens. Bioelectron. 2, 1–6 (2017). doi:10.15406/ijbsbe.2017.02.00010
Lopez-Barbosa, N., Gamarra, J.D., Osma, J.F.: The future point-of-care detection of disease and its data capture and handling. Anal. Bioanal. Chem. (2016). doi:10.1007/s00216-015-9249-2
Lopez-Barbosa, N., Osma, J.F.: Biosensors: migrating from clinical to environmental industries. Biosens. J. (2016). doi:10.4172/2090-4967.100e106
Costerton, J.W., Stewart, P.S., Greenberg, E.P.: Bacterial biofilms: a common cause of persistent infections. Science 284, 1318–1322 (1999)
Satpathy, S., Sen, S.K., Pattanaik, S., Raut, S.: Review on bacterial biofilm: an universal cause of contamination. Biocatal. Agr. Biotechnol. 7, 56–66 (2016). doi:10.1016/j.bcab.2016.05.002
Hernández, C.A., Gaviria, L.N., Segura, S.M., Osma, J.F.: Concept design for a novel confined-bacterial-based biosensor for water quality control. In: 2013 Pan American Health Care Exchanges, pp. 1–3 (2013). doi:10.1109/PAHCE.2013.6568257
Acknowledgements
The authors thank the cleanroom facilities from the Department of Electrical and Electronics Engineering at Universidad de los Andes for the financial support. Claudia Camila Barrera Garzón for her help during the bacteria culturing with traditional techniques and important insights during the design stage. The group of Biophysics, specially to David Camilo Durán Chaparro, from the Physics Department of the Universidad de los Andes, for providing us with the E. coli strain, their support and facilities.
Finally, Cesar A. Hernandez thanks Colciencias for their support through doctoral scholarship PDBCNal 567.
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In this work, there are no potential conflicts between or related to any author.
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Hernandez, C.A., Lopez-Barbosa, N., Segura, C.C., Osma, J.F. (2017). High Definition Method for Imaging Bacteria in Microconfined Environments on Solid Media. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_64
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