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Identification of lactobacilli by pheS and rpoA gene sequence analyses

¹ Department of Biology and Biotechnology, Faculty of Sciences, An-Najah National University, Nablus, Palestine
² Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
³ BCCM^TM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
⁴ Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure links 653, Ghent 9000, Belgium
⁵ Bioinformatics and Evolutionary Genomics, Ghent University/VIB, Technologiepark 927, Ghent 9052, Belgium

Correspondence
Sabri M. Naser
Sabri-Naser{at}najah.edu

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are AM087677–AM087773, AM263502–AM263510, AM157783–AM157787, AM168426–AM168429, AM159098–AM159099, AM236139–AM236143, AM284176–AM284250, AM694185, AM694187 (pheS partial gene sequences) and AM087774–AM087869, AM263511–AM263518, AM157775, AM157777–AM157780, AM168431–AM168433, AM236144–AM236148, AM284251–AM284315, AM694186, AM694188 (rpoA partial gene sequences).

Neighbour-joining phylogenetic trees constructed using the pheS and rpoA gene sequences of the type strains of species of the genus Lactobacillus are available with the online version of this paper.

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