Social lives of bacteria as revealed through CLASI-FISH

Abstract

The spatial organization of microbiomes illuminates their structure, function, and relationship to their host. Using fluorescence spectral imaging to discriminate up to 16 fluorophores and using combinations of probes to generate unique spectral signatures, combinatorial labeling and spectral imaging-fluorescence in situ hybridization (CLASI-FISH) has been deployed to analyze spatial organization in oral, gut, and marine microbiomes. In dental plaque, imaging revealed the structural role of Corynebacterium matruchotii in organizing the plaque biofilm and revealed previously unrecognized complexity in dental plaque corncob structures. Tongue dorsum biofilms showed a patchy organization around a core of host epithelial cells projecting from the tongue surface, with anaerobes located near the core and oxygen-tolerant taxa near the surface. Taxa that are prominent in these tongue dorsum communities can reduce nitrate to nitrite and thus may play an important role in human nitrate metabolism. In contrast with the highly structured organization of oral biofilms, analysis of the gut microbiome by CLASI-FISH showed a mixed community, indicating that the rate of mixing in the gut is high enough to overcome the tendency of bacterial replication to generate single-taxon patches. Application of CLASI-FISH to blades of kelp showed a dense biofilm with clusters of cocci near the kelp surface, bacteria invading the kelp tissue, and rod-shaped and filamentous bacteria extending into the water column. Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host–microbiome interaction.