Despite the battery of human spaceflight data from NASA, ESA, and other missions, our understanding of the biology of spaceflight is still incomplete and spans only a few dozen individuals. Current data has shown that spaceflight causes changes in cell signaling, immune function, and tissue regulation, but such alterations could be better understood with more modern molecular methods. To help address this gap in knowledge, the Inspiration4 mission (deployed on the SpaceX Dragon Capsule) leveraged genome, epigenome, transcriptome, proteome, microbiome, metabolome, exosome, telomere, single-cell V(D)J immunophenotyping, and epitope profiling for the astronauts, as well as single-nucleus, multiome sequencing and multi-omicspatial mapping (human and microbial). Nanostring were able to clearly dissect the gene expression changes from spaceflight occurring at the single-cell level, particularly for concomitant chromatin (scATAC-seq) and expression (scRNA-seq) changes for macrophages, neutrophils, and CD4 T-cells, and they also mapped the first-ever in vivo human-microbial interaction maps from spaceflight (on the NanoString GeoMx® Digital Spatial Profiling platform). The single-cell data showed that interleukin-6 (IL-6) was elevated in flight and post-flight, which is consistent with the response to zero gravity seen in other crew members. Also, their metagenome data showed a “blending” of the skin microbiome for the crew within the first two days of the mission (Shannon and beta-diversity down by 0.2), particularly with rapid transfer of Caulobacter soli and other commensal species, indicating a rapid transfer of skin flora to other crew in the confines of the Dragon space capsule.