Traditional microbiome studies rely on shotgun DNA sequencing, which loses all spatial context and information about functional interactions with the host. We recently developed a novel spatial sequencing technology called microDBIT (Spatial Co-profiling of Genome/Epigenome and Transcriptome) to simultaneously map the genomes, epigenomes, and transcriptomes of microbial and host cells within their spatial context. This approach can reveal the diverse states of the microbiome and brain tissue, and their interactions in gut tissue. microDBIT leverages deterministic barcoding in tissue for spatial omics profiling, allowing the identification of bacterial species and their activities by capturing their unique genomes and transcriptomes. Additionally, it can co-map host epigenomes and gene expression. microDBIT represents a flexible, multi-omics sequencing platform and will be the first to comprehensively map microbiome-brain interactions and the gut microenvironment of Parkinson’s disease.