Spatial transcriptomics offers a glimpse of how microbiomes interact with their hosts.
Microbiome studies today depend heavily on DNA or RNA sequencing of microbial genetic material obtained from bulk environmental samples. These sequencing-based approaches erase all microbial spatial context information and do not capture bidirectional interactions between microbes and their host. The work of Giacomello and colleagues, and of Vickovic and colleagues, builds on recent methods for spatial transcriptomics that use RNA sequencing with arrayed reverse transcription oligo-dT primers tagged with position-specific barcodes3,4,5,6. The barcodes and complementary DNA copies of the RNA transcripts are recorded together by sequencing, which enables researchers to create a map of RNA transcript abundance as a function of location in the tissue. However, these methods are largely limited to capturing poly-A-tailed host messenger RNAs and are insensitive to microbial RNAs, which lack a poly-A-tail7.
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Competing interests
I.D.V. is a co-founder of Kanvas Biosciences. I.N. declares no competing interests.
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Ntekas, I., De Vlaminck, I. Spatial methods for microbiome–host interactions.
Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01996-1
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DOI: https://doi.org/10.1038/s41587-023-01996-1