Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping

We used rRNA FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of an active prophage with a sixth fluorophore. 

We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump.