Regarding the genotypic characterisation of the strains isolated,
a combination of ITS- and rep-PCR was shown to be a suitable
method for characterisation at species and in some cases subspecies
level. Use of these typing methods in combination with
gene sequencing of strains representative of specific rep-PCR
clusters was effective for accurate identification. Amplification
and sequencing of the pheS, rpoA and rpoB genes provided more
discriminatory information in identifying LAB and Bacillus isolates
compared to use of 16S rRNA gene sequences alone and provide a
rapid, reliable tool for bacterial identification without the need for
further phenotypic characterisation.