Spatiotemporally resolved tools for analyzing gut microbiota

The gut microbiota is a hidden vital organ closely related to human health. Its spatial patterns and dynamics influence processes and functions including microbial colonization, community stability, host-microbe interactions, host metabolism, immune regulation, and neurodevelopment, but are not measurable via traditional techniques such as culturing, sequencing, and mass spectrometry, thus remaining largely unexplored. Here, we highlight emerging techniques such as spatially resolved sequencing and in vivo imaging, enabling the acquisition of spatial organizations and dynamic information of the gut microbiome, and discuss their contributions to our understanding of the gut microbiota including physiological activities, symbiotic functions, and spatial organization rearrangement under diverse physiological and pathological statuses, which provide new views for diet and clinical treatment via managing the gut microbiota.