Phylogenetic analysis of the genus Pediococcus, including Pediococcus claussenii sp. nov., a novel lactic acid bacterium isolated from beer

Abstract

Pediococci are found in foods and on plants and as beer-spoilage agents. The goal of the present study was to use the DNA sequences of the first three variable regions of the 165 rRNA gene, the 16S-23S rRNA internally transcribed spacer region sequence and approximately a third of the 60 kDa heat-shock protein gene to elucidate phylogenetic groupings within the genus Pediococcus. Phylogenetic trees were created with sequence data from 31 Pediococcus and three Lactobacillus isolates. Complete 16S rRNA gene sequences from selected Pediococcus isolates were also examined. The results were interpreted in relation to the currently accepted Pediococcus species. We found that, where previously done, speciation of many Pediococcus isolates is inaccurate. Also, one grouping of seven isolates did not include any currently recognized Pediococcus species type isolate. Our phylogenetic analyses support the conclusion that these seven isolates, all of brewing spoilage origin, belong to a novel species, for which the name Pediococcus claussenii sp. nov. is proposed (type strain P06(T0 = ATCC BAA-344(T) = DSM 14800(T)). Phylogenetic analysis has therefore helped to resolve problems surrounding species identification of Pediococcus isolates.

The genus Pediococcus

“…dextrinicus, all appear to demonstrate a close relationship and common ancestry of lactobacilli and pediococci. Data partially adapted from Simpson & Taguchi, 1995;Dobson et al, 2002;Holzapfel et al, 2006;Zhang et al, 2005;Franz et al, 2006;Liu et al, 2006;Tanasupawat et al, 2007;De Bruyne et al, 2008;Doi et al, 2009. The ability to ferment fructose, mannose and cellobiose was reported for all species. Although most species ferment maltose, Ped.…”

“…parvulus and Ped. siamensis are unable to do so (Simpson & Taguchi, 1995;Dobson et al, 2002). Rhamnose, melibiose, melezitose, raffinose, inulin, and α-methyl-D-glucoside are not readily fermented.…”

“…siamensis and Ped. stilesii (Simpson & Taguchi, 1995;Dobson et al, 2002) (Table 21.2). Starch and sorbitol are not fermented.…”

“…argentinicus and Ped. claussenii, ferment mannitol (Simpson & Taguchi, 1995;Dobson et al, 2002;De Bruyne et al, 2008). Variable results were recorded for the fermentation of trehalose, lactose, maltotriose, dextrin, glycerol, salicin and amygdalin (Simpson & Taguchi, 1995;Zhang et al, 2005;Liu et al, 2006;De Bruyne et al, 2008;Doi et al, 2009).…”

“…koreensis grows in up to 8% NaCl only. Data from Weiss (1992), Simpson and Taguchi (1995), Dobson et al (2002), Franz et al (2006) and Doi et al (2009). techniques used in the identification of pediococci include ribotyping, the analysis of profiles generated by intergenic spacer region (ISR) amplification, ISR restriction and ARDRA (amplified ribosomal DNA restriction analysis). Chenoll et al (2003) could not distinguish Lactobacillus strains from Pediococcus strains by ISR amplification patterns, but they were differentiated by ISR-DdeI restriction analyses.…”