Substrates for detecting microorganisms are provided, wherein the substrate comprises a set of molecular markers linked, optionally with linker molecules or moieties, to a di-, or tripeptide consisting of amino acids X1 and X2, or X1, X2 and X3, in which one of them, for example, X1, is a D-amino acid and the others, for example, X2 and X3, may be any D- or L-amino acid. The substrate preferably is used for the detection of Bacillus anthracis. Also provided are substrates for detecting Pseudomonas aeruginosa, wherein the substrate comprises a set of molecular markers linked, optionally with linker molecules or moieties to a tri-, tetra-, or pentapeptide consisting of glycine amino acids. The invention further comprises methods for detecting microorganisms, specifically B. anthracis and P. aeruginosa, with the substrates of the invention and use of the substrate(s) in such a method.