InSituMicroSeq: 3D reconstruction of microbial communities through in situ sequencing

● Current techniques for studying microorganisms in their natural environment lack resolution to recover the complex spatial features of microbial communities, which are essential to unveil microbial interactions.

● In InSituMicroSeq, I propose to merge microscopy imaging and DNA sequencing technologies to create the first spatial maps of combined taxonomic and functional features of microbial communities in 3D.

● The key idea is to design barcodes attached to hybridisation probes that are then in situ sequenced (i.e., under the microscope rather than in a sequencer) to inform about hundreds of spatially referenced taxonomic and functional features of microorganisms.

● This technology will be showcased by 3D-reconstructing, for the first time, the gut microbiome of an entire gut section of an animal, namely the honey bee.

● Successful development of this technology will open new avenues on how microbial communities are studied, and will enable addressing ecological questions that are currently hidden due to technological limitations.