Get access

Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity

Authors

  • Patrice Loisel,

    1. INRA-INRIA MERE Research Team, UMR Analyse des Systèmes et Biométrie, ENSAM Institut National de la Recherche Agronomique, Montpellier, France.
    Search for more papers by this author
  • Jérôme Harmand,

    1. INRA-INRIA MERE Research Team, UMR Analyse des Systèmes et Biométrie, ENSAM Institut National de la Recherche Agronomique, Montpellier, France.
    2. Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
    Search for more papers by this author
  • Olivier Zemb,

    1. Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
    2. Laboratoire Arago, Observatoire Océanologique, Centre National de la Recherche Scientifique, Institut National des Sciences de l’University, Université Paris VI, 66651 Banyuls-sur-Mer, France.
    Search for more papers by this author
  • Eric Latrille,

    1. Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
    Search for more papers by this author
  • Claude Lobry,

    1. INRA-INRIA MERE Research Team, UMR Analyse des Systèmes et Biométrie, ENSAM Institut National de la Recherche Agronomique, Montpellier, France.
    Search for more papers by this author
  • Jean-Philippe Delgenès,

    1. Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
    Search for more papers by this author
  • Jean-Jacques Godon

    Corresponding author
    1. Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
    Search for more papers by this author

*E-mail jean-jacques.godon@ensam.inra.fr; Tel. (+33) 4 68 42 51 54; Fax (+33) 4 68 42 51 60.

Summary

The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500 000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.

Ancillary