Fuente: WIPO "tomato" Provided herein are methods, compositions, and kits for determining the spatial location of target nucleic acids, including endogenous and exogenous target nucleic acids, in a biological sample using padlock probes and substrates with spatially barcoded capture probes. Also disclosed herein are methods for determining a presence and/or location of a microbe (e.g., archaea, fungi, bacteria) in a biological sample, e.g., by determining the presence and/or location of a microbial target nucleic acid in the biological sample.