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How to get more out of molecular fingerprints: practical tools for microbial ecology
Author(s) -
Marzorati Massimo,
Wittebolle Lieven,
Boon Nico,
Daffonchio Daniele,
Verstraete Willy
Publication year - 2008
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2008.01572.x
Subject(s) - biology , microbial ecology , temperature gradient gel electrophoresis , microbial population biology , terminal restriction fragment length polymorphism , ecology , 16s ribosomal rna , molecular ecology , computational biology , fingerprint (computing) , genetics , community structure , evolutionary biology , restriction fragment length polymorphism , gene , polymerase chain reaction , artificial intelligence , bacteria , computer science , population , demography , sociology
Summary Community‐level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single‐strand conformation polymorphism (SSCP), length heterogeneity‐PCR (LH‐PCR), terminal‐restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting‐independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range‐weighted richness ( Rr ) reflecting the carrying capacity of the system, (ii) the dynamics ( Dy ) reflecting the specific rate of species coming to significance, and (iii) functional organization ( Fo ), defined through a relation between the structure of a microbial community and its functionality. These Rr , Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.