Culture-independent analysis of diversity in microbial communities: pros and cons of the partial sequence-based profiling

Among the culture-independent techniques developed so far, DGGE/TGGE analysis of amplified 16S rRNA fragments is currently used to a great extent for the characterization of microbial consortia, due to its fast response and highly descriptive power. This approach relies on the separations of partial 16S rRNA gene amplicons targeting two specific hypervariable regions, namely V3 and V6-V8. Separation is followed by sequencing and identification of different bands based on BLAST comparisons. Some case studies are presented here concerning the identification of bacterial species and genera - belonging to different phyla such as Actinobacteria (Bifidobacterium, Rhodococcus), Firmicutes (Bacillus, Enterococcus, and Lactobacillus), Alphaproteobacteria (Sinorhizobium), Betaproteobacteria (Burkholderia), and Gammaproteobacteria (Pseudomonas) – all relevant to environmental and industrial biotechnology.