Highly polymorphic and modular extragenic (h.p.m.e.) markers within specific taxa of microorganisms and use thereof for their differentiation, identification and quantification

A Method to identify and quantify a target microorganism with a Highly Polymorphic and Modular Extragenic (HPME) marker, said H.P.M.E. being a microbial genome sequence characterized by a length of less than or equal to 2000 bp, said HPME having detectable means attached hereto, said detectable means being selected from the group consisting of an adaptor, a probe, a reporter molecule, fluorescein, FAM, HEX, NED, TAMRA, R6G, JOE, VIC, Cyanine dyes, AlexFluor® and quantum dots and comprising two genetic elements, said two genetic elements being each an Open Reading Frame coding for a protein selected from the group consisting of the genes mleA, mleR, tkt, grpE and hrcA;

• wherein said two genetic elements are separated by a noncoding nucleotide sequence, said noncoding nucleotide sequence being a promoter region and wherein said two genetic elements are—the gene mleA coding for the Malolactic enzyme and the gene mleR coding for the mleA transcriptional regulator, belonging to the LysR-type transcriptional regulator family, namely H.P.M.E. mleA-mleR marker, for the identification and quantification of microorganisms within the Lactobacillales order;
• the gene tkt coding for the Transketolase enzyme and the gene hrcA coding for the HrcA transcriptional regulator, namely H.P.M.E. tkt-hrcA marker, for the identification and quantification of microorganisms within the Bifidobacterium family;
• and/or
• the gene grpE coding for the Heat Shock Protein GrpE and the gene hrcA coding for the HrcA transcriptional regulator, namely H.P.M.E. hrcA-grpE marker, for the identification and quantification of microorganisms within the Bacillus family.