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, <em>Veillonella, Streptococcus, Corynebacterium, Lautropia, </em>and <em>Neisseria</em>, each with a different fluorophore, and we used MGE-FISH to stain the <em>termL</em> 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.