Sponge microbiome is an indicator of both natural and antropogenic stresses. In aquatic ecology, metagenomic approaches makes it possible to investigate complex microbial communities and their interactions within the host as well as with environment. A metagenomic study was performed among 4 different samples of healthy and diseased freshwater sponges belong to Lubomirskia baikalensis species collected from Baikal Lake, Bolshie Koty, Russia. The analysis of nucleotide composition of the 16S rRNAmetagenomic libraries will be carried out on an IlluminaMySeq sequencer. The PCR amplification of the V3-V4 16S rRNA ribosomal gene was used in this study. The primary analysis of NGS sequencing data, removal of short and chimeric sequences, clustering in OTUs (operational taxonomic units), assessment of biodiversity by calculating ACE, Chao1, and Shannon indices will be carried out using the Mothur v.1.22.0 program (http://www. mothur.org). The Pyrosequencing pipeline program (http://pyro.cme.msu.edu) will be used to determine species diversity and taxonomic composition and compare communities. Data cluster analysis will be performed using the Complete Linkage Clustering program, which is part of the Pyrosequencing pipeline. A comparative analysis of the metagenomes of diseased and healthy sponges showed that diseased sponges undergo a variety of nonspecific changes in the bacterial composition, in particular, an increase in the number of Flavobacteria and a decrease in Alphaproteobacteria and Saprospirae. The composition of the bacterial community is probably influenced by the type of sponge, as well as the degree of disease affection. The results contribute to understanding the nature of changes in symbiotic relationships during the development of discoloration syndrome in freshwater sponges.