The invention comprises a substrate for detection of micro-organisms, wherein said substrate comprises a set of molecular markers linked, optionally with linker molecules or moeieties, 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. Said substrate preferably is used for the detection of Bacillus anthracis. Alternatively, the invention is directed to a substrate for detection of micro-organisms, more specifically P. aeruginosa, wherein said substrate comprises a set of molecular markers linked, optionally with linker molecules or moeities to a tri- tetra or pentapeptide consisting of glycine amino acids.; The invention further comprises methods for detection of micro-organisms, specifically Bacillus anthracis and Pseudomonas aeruginosa, with the substrates of the invention and use of the substrate(s) in such a method.