The present invention relates to a method of typing a microbiome for having a desirable or undesirable signature, comprising analyzing the composition of the population of microorganisms in the microbiome based on taxonomic variation in the DNA sequence of the microbial 16S-23S rRNA internal transcribed spacer (ITS) regions in the genomic DNA of the microorganisms, wherein the sequences of conserved DNA regions comprised in the 16S and 23S rRNA sequences flanking said ITS region in the genome of the microorganisms comprise primer binding sites for amplification of the ITS regions.