Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis

Abstract

A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999 T , was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999 T (5CCUG 54535 T 5CRL 776 T ) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.Pediococci are homolactic acid-fermentative, non-motile, catalase-negative, facultative anaerobes of the family Lactobacillaceae. They inhabit fermentable-sugar-rich niches such as plant materials and fermented foods.Strains of the genus Pediococcus are used in the food industry as starter cultures for fermented meat or fish products and dairy products (Leroy & De Vuyst, 2004;Simpson & Taguchi, 1995). However, quality problems in beer and wine due to pediococci have also been reported (Renouf et al., 2007;Sakamoto & Konings, 2003). In the present study, we describe a novel species of the genus Pediococcus isolated from Argentinean fermented wheat flour. Despite their importance for the food industry, the correct identification of Pediococcus strains is complicated by their ambiguous response in traditional physiological tests and methods. Nowadays, speciation is based on habitat, DNA-DNA hybridizations and tolerance of temperature, pH and NaCl (Dobson et al., 2002;Garvie, 1974Garvie, , 1986. In this study, sequence analysis of the genes encoding the alpha subunits of phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase Abbreviations: FAFLP, fluorescent amplified fragment length polymorphism; LAB, lactic acid bacteria; T OR , temperature of optimal renaturation.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of LMG 23999T is AM709786. The accession numbers for the pheS, rpoA and atpA gene sequences reported in this paper are AM899805-AM899946, as indicated in Supplementary Fig. S2a-c.Supplementary figures showing a cluster analysis of whole cell protein profiles with a UPGMA dendrogram and additional neighbour-joining phylogenetic trees based on pheS, rpoA and atpA gene sequences are available with the online version of this paper. A supplementary table giving details of the genomes used for the design of primers rpo-21-F* and rpoA-23-R* is also provided.

The genus Pediococcus

“…Pediococcus dextrinicus is distantly related to the other species in the phylogenetic group (Collins et al, 1991) and has recently been reclassified to the genus Lactobacillus (Haakensen et al, 2009). With this reclassification, the genus Pediococcus is phylogenetically homogeneous, as also confirmed by multilocus sequence analysis based on several housekeeping genes (De Bruyne et al, 2008). After the report of Collins and co-workers, the Lb.…”

A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology

“…The species description was consulted when these sources were inconsistent (24)(25)(26)(27)(28)(29)(30). The assignment of the fermentation type of pediococci was based on the work of Franz et al (21) and the description of the species (31)(32)(33)(34)(35).…”

Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua

“…Quality and purity of the obtained DNA were checked by spectrophotometric measurements at 234, 260 and 280 nm (SpectraMax Plus384, Molecular Devices) and visually by electrophoresis of 5 ml DNA mixed with 2 ml loading dye (4 g sucrose and 2.5 mg bromophenol blue dissolved in 6 ml TE buffer) on a 1 % w/v agarose (Result LE General Purpose Agarose, BIOzym group) gel, run for 30 min at 100 V in 1 l TAE buffer (40 mM Tris/acetate, 1 mM EDTA, pH 8.0), flanked by a molecular-mass marker (SmartLadder, Eurogentec). 16S rRNA gene amplification, purification and sequencing were performed as described by De Bruyne et al (2008), using the following modifications. Sequencing reactions were purified using a BigDye XTerminator Purification kit according to the protocol of the supplier (Applied Biosystems).…”