RT Journal Article SR Electronic T1 Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes JF bioRxiv FD Cold Spring Harbor Laboratory SP 2023.06.09.544291 DO 10.1101/2023.06.09.544291 A1 Grodner, Benjamin A1 Shi, Hao A1 Farchione, Owen A1 Vill, Albert C. A1 Ntekas, Ioannis A1 Diebold, Peter J. A1 Zipfel, Warren R. A1 Brito, Ilana L. A1 De Vlaminck, Iwijn YR 2023 UL http://biorxiv.org/content/early/2023/06/09/2023.06.09.544291.abstract AB The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.Competing Interest StatementH.S. is a co-founder at Kanvas Biosciences. I.D.V. is a member of the Scientific Advisory Board of Karius Inc., and GenDX and co-founder of Kanvas Biosciences. H.S. and I.D.V. are listed as inventors on patents related to multiplexed imaging methods.