Independent cultivation methods are used to characterize microbial diversity in mixed samples derived from industrial processes or natural environments.
These approaches include analyzing the structure and dynamics of populations through genetic fingerprints (Denaturing Gradient Gel Electrophoresis – DGGE) or characterizing the composition of the microbiota by extracting the total genomic DNA directly from the sample and amplifying the marker gene (ribosomal RNA 16S for bacteria and ITS – Internal Transcribed Spacer region for fungi). In the first case, the sequences obtained from the amplification (amplicons) are separated on a gel with a denaturing gradient and the obtained fingerprint reflects the complexity of the microbial community and allows to follow changes in populations along a spatial or temporal gradient. In the second case, the amplicons are submitted to large-scale sequencing and the comparison of the sequences obtained with databases allows to identify the genera present and to characterize the microbial composition of the sample.