Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity.
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.
Loisel
Patrice
P
INRA-INRIA MERE Research Team, UMR Analyse des Systèmes et Biométrie, ENSAM Institut National de la Recherche Agronomique, Montpellier, France.
Harmand
Jérôme
J
Zemb
Olivier
O
Latrille
Eric
E
Lobry
Claude
C
Delgenès
Jean-Philippe
JP
Godon
Jean-Jacques
JJ
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics*; D003627:Data Interpretation, Statistical; D004591:Electrophoresis, Polyacrylamide Gel; D005243:Feces / Q000382:microbiology; D018807:Polymorphism, Single-Stranded Conformational; D013552:Swine
D004269:DNA, Bacterial