Results/Conclusions: The phyla e.g. Actinobacteria, Gammaproteobacteria, Firmicutes, Betaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Bacteroidetes were found as the representatives of freshwater bacterial groups whose identities were established by the excising and sequencing DGGE bands and comparing the 16S rDNA sequences with those available in GenBank. Relatively the number of Deltaproteobacteria, Cyanobacteriaig, and Actinobacteria was very low. The phyla Betaproteobacteria, Firmicutes, and Bacteroidetes were present with Gammaproteobacteria in maximum cases. With varying degrees of identity, the Escherichia-Shigella group, Bacillus sp., Verminephrobacter sp., Acidovorax sp., Streptococcus sp., Synechococcus sp., Arthrobacter sp., Shewanella sp., Acinetobacter sp., Flavobacterium sp., Aeromonas sp., Bacteroides sp., Polaromonas sp., Vibrio sp., Staphylococcus sp., Yersinia sp., Pelobacter sp., Alkalilimnicola sp., Pseudomonas sp., and some uncultured bacterial sequences were identified. The Escherichia-Shigella group was present in almost all the representative samples. Significant correlation was found between the four genes ial, virA, ipaBCD, and ipaH specific for Shigella spp., and enteroinvasive E. coli. Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes were always present with these four genes. There was no such relationship between the E. coli specific genes lt1, stx1, and bfp relative to the presence of the phyla. The total community of E. coli, and Shigella spp. could not be detected due to specific enrichment used in this investigation. The identified community is a reflection of the partial community. This might help recovery of Shigella spp. from environmental samples hither to difficult to isolate culturally.