Abstract Sponge diseases occur globally and the resulting reduction of sponge populations has negative effects on other organisms within the ecosystems due to loss of nutrient enrichment and loss of bioremediation. In Lake Baikal, the predominate sponge species Lubomirskia baicalensis is currently being infected with an unidentified pathogen resulting in a sharp decline in population. The current hypothesis is that the recent increase in methane concentration in the lake has caused dysbiosis within the bacterial community of L. baicalensis resulting in the disease outbreak. In this study we investigated the changes in the bacterial community between healthy and sick sponges using 16S bacterial profiling targeting veritable regions 3-5. Here we present data that the bacterial communities of the healthy sponge samples were significantly different from sick samples and several poorly classified organisms were identified by Indicator Species Analysis as significant. Organisms identified from the sick samples classified within taxonomic units that contain acidophilic bacteria which suggest pH may play a role. There was also an observed decrease in the number of identified methyltropic bacteria present in the sick sponge samples compared to the healthy.