The micro-Petri dish, a million-well growth chip for the culture and high-troughput screening of microorganisms

Colin J. Ingham, Ad Sprenkels, Johan Bomer, Douwe Molenaar, Albert van den Berg, Johan E.T. van Hylckama Vlieg, Willem M. de Vos

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    Abstract

    A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 mu m, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolonly in 10,000. (iii) In screening for an enzyme-based, non-dominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without anti biotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of beta-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.
    Original languageEnglish
    Pages (from-to)18217-18222
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume104
    Issue number7/46
    DOIs
    Publication statusPublished - 13 Nov 2007

    Fingerprint

    Microorganisms
    Screening
    Recovery
    Throughput
    Microbiology
    Organophosphates
    beta-Galactosidase
    Multiplexing
    Metabolism
    Escherichia coli
    Plasmids
    Automation
    Genes
    Water
    Enzymes

    Cite this

    Ingham, Colin J. ; Sprenkels, Ad ; Bomer, Johan ; Molenaar, Douwe ; van den Berg, Albert ; van Hylckama Vlieg, Johan E.T. ; de Vos, Willem M. / The micro-Petri dish, a million-well growth chip for the culture and high-troughput screening of microorganisms. In: Proceedings of the National Academy of Sciences of the United States of America. 2007 ; Vol. 104, No. 7/46. pp. 18217-18222.
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    abstract = "A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 mu m, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolonly in 10,000. (iii) In screening for an enzyme-based, non-dominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without anti biotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of beta-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.",
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    The micro-Petri dish, a million-well growth chip for the culture and high-troughput screening of microorganisms. / Ingham, Colin J.; Sprenkels, Ad; Bomer, Johan; Molenaar, Douwe; van den Berg, Albert ; van Hylckama Vlieg, Johan E.T.; de Vos, Willem M.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 7/46, 13.11.2007, p. 18217-18222.

    Research output: Contribution to journalArticleAcademicpeer-review

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    AU - Ingham, Colin J.

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    AU - Bomer, Johan

    AU - Molenaar, Douwe

    AU - van den Berg, Albert

    AU - van Hylckama Vlieg, Johan E.T.

    AU - de Vos, Willem M.

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