Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes

Area of Science:

• Microbiology and Microbial Ecology
• Genetics and Genomics
• Biofilm Research

Background:

• Mobile genetic elements (MGEs) drive the dissemination of crucial traits, such as antimicrobial resistance (AMR), among bacterial populations.
• Current methodologies are insufficient for spatially mapping MGEs and identifying their hosts within complex microbial communities, hindering research into gene transfer dynamics.

Purpose of the Study:

• To develop and apply a novel technique for simultaneous spatial visualization of MGEs and bacterial taxa in microbial communities.
• To investigate the spatial distribution of bacteriophage and AMR plasmids and their host bacteria in human oral biofilms.

Main Methods:

• Combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH.
• Enabled simultaneous visualization and spatial mapping of MGEs (bacteriophage, AMR plasmids) and their bacterial hosts.

Main Results:

• Successfully spatially mapped bacteriophage and AMR plasmids, identifying their specific host taxa within human oral biofilms.
• Observed distinct clustering of AMR plasmids and prophage in close proximity to dense populations of host bacteria.
• Data indicate that spatial heterogeneity of bacterial taxa influences MGE distribution, with clusters potentially arising from horizontal gene transfer hotspots or strain expansion.

Conclusions:

• The developed FISH-based approach allows for unprecedented spatial resolution in studying MGEs and their hosts within biofilms.
• Findings highlight the importance of spatial structure in driving MGE distribution and gene transfer within bacterial communities.
• This methodology provides a powerful tool to advance the study of antimicrobial resistance spread and phage ecology in complex microbial environments.