| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Federal Research Centre for Nutrition and Food, Institute for Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
2 BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
Correspondence
Charles M. A. P. Franz
Charles.Franz{at}bfe.uni-karlsruhe.de
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
Published online ahead of print on 23 September 2005 as DOI 10.1099/ijs.0.63944-0.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of LMG 23082T is AJ973157.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
). Based on the phylogeny, P. dextrinicus is distantly related to the other pediococci (Dobson et al., 2002) and is also phenotypically distinguished from other Pediococcus species by the combination of the production of L(+) lactate as the end product of glucose metabolism and the production of CO2 from gluconate (Back, 1978; Simpson & Taguchi, 1995). Although P. dextrinicus is still a member of the genus, it has been suggested that it should be reclassified in the genus Lactobacillus (Collins et al., 1990; Dobson et al., 2002). In the present study, we describe a novel Pediococcus species, isolated from steeped white maize grains.
Strain LMG 23082T (=BFE 1652T=FAIR-E 180T) was isolated in 1997 in Lagos, Nigeria, from white maize grains, steeped for 3 days. Isolation and purification conditions were MRS agar (de Man et al., 1960) at 30 °C under aerobic conditions. Analogous cultivation conditions were used for further experiments, unless indicated otherwise.
Cell morphology was determined using phase-contrast microscopy. Cells of strain LMG 23082T were cocci, with a cell diameter of 1·2 µm. Cells occurred singly, in pairs or tetrads, the latter being typical for pediococci as a result of dividing alternately in two perpendicular directions (Simpson & Taguchi, 1995).
The phylogenetic position of strain LMG 23082T was determined by complete 16S rRNA gene sequence analysis as described by Vancanneyt et al. (2004) with the following modifications: PCR-amplified 16S rDNA was purified by using a NucleoFast 96 PCR Clean-up kit (Macherey-Nagel). Sequencing reactions were purified using a Montage SEQ96 Sequencing Reaction Clean-up kit (Millipore). Sample preparation was assisted using a Tecan Genesis Workstation 200 (Tecan). Electrophoresis of sequence reaction products was performed by using an ABI Prism 3100 Genetic Analyzer (Applied Biosystems). The 16S rRNA gene sequence (a continuous stretch of 1529 bp) and sequences of other pediococci, as well as Lactobacillus species belonging to the Lactobacillus/Pediococcus phylogenetic group which were retrieved from EMBL, were aligned and a phylogenetic tree was constructed by the neighbour-joining method using the BioNumerics software package, version 3.50 (Applied Maths). Unknown bases were discarded for the analyses. Bootstrapping analysis was undertaken to test the statistical reliability of the topology of the neighbour-joining tree using 500 bootstrap resamplings of the data (Fig. 1). Comparison of the sequence of strain LMG 23082T with deposited sequences available in the EMBL database revealed highest similarities with P. pentosaceus and P. acidilactici (sequence similarities of 98·2 and 97·5 %, respectively). Within the genus Pediococcus, the latter two taxa and P. claussenii occupy a distinct branch.
|
. Densitometric analysis, normalization and interpolation of protein profiles, and a numerical analysis were performed by using the GelCompar software package, versions 3.1 and 4.0, respectively (Applied Maths). A dendrogram confirmed that LMG 23082T constitutes a separate branch, distinct from its nearest phylogenetic neighbours, P. pentosaceus and P. acidilactici (Fig. 2).
|
; Torriani et al., 2001), pediococcal reference strains and LMG 23082T were also investigated using fluorescent amplified-fragment length polymorphism (FAFLP) fingerprinting of whole genomes. FAFLP fingerprinting was performed as described by Thompson et al. (2001) with the following modifications: EcoRI/TaqI was used as the restriction enzyme combination and the primer combination E01/T01 (both having an adenosine extension at the 3'-end) was applied for selective PCR. The resulting electrophoretic patterns were tracked and normalized using the GeneScan 3.1 software (Applera). Normalized tables of peaks, containing fragments of 50–536 bp, were transferred into the BioNumerics software package, version 3.5, and the computer-generated fingerprints were added to an existing database of FAFLP fingerprints of lactic acid bacteria at the BCCM/LMG Bacteria Collection. For numerical analysis, data between the 75- and 500-bp bands of the internal standard were used. Similarity was calculated using the Dice coefficient and clustering was done using the UPGMA algorithm. The FAFLP fingerprints of all strains were compared with reference profiles of lactic acid bacteria taxa as currently available in the database. FAFLP analysis revealed a separate branch for strain LMG 23082T (Fig. 3).
|
for lactic acid bacteria. Total genomic DNA was isolated from the type strains of all recognized Pediococcus species according to the method of Pitcher et al. (1989), as modified by Björkroth & Korkeala (1996), relying on a combined lysozyme and mutanolysin treatment. DNA was amplified in 50 µl volumes containing 100 ng template DNA, 1x Taq DNA polymerase buffer (Amersham Pharmacia), 200 µM dNTPs, 50 pM primer, 4 % DMSO (Sigma) and 1·5 U Taq DNA polymerase (Amersham Pharmacia). PCR products were separated by electrophoresis and images were visualized and analysed as described by Kostinek et al. (2005) using the BioNumerics (version 2.5) software (Applied Maths). Groupings of the rep-PCR fingerprints were performed by using the Pearson product-moment correlation coefficient (r) and the UPGMA clustering algorithm (Sneath & Sokal, 1973). Using rep-PCR, LMG 23082T was clearly distinguished from the other type strains and had the closest, although not significant, match with P. inopinatus at a correlation level of r=0·61 (Fig. 4). It is not known whether the (GTG)5 sequence, which is highly repetitive on the chromosome of Escherichia coli (Versalovic et al., 1994) is indeed present and, if so, how often it would be present in the genomes of pediococci. Nevertheless, even if we assume that it is not, the resolution of the method would resemble a RAPD-PCR-type genotyping method. Therefore, in our study, as in the study of Gevers et al. (2001), the method was clearly suitable to discriminate among the pediococci at the species level.
|
as modified by Stackebrandt & Kandler (1979). The DNA base composition (G+C content) was determined from the thermal melting temperature (Tm) of DNA using a spectrophotometer (Varian Cary 100 Bio UV-Visible). DNA–DNA relatedness was determined spectrophotometrically from renaturation rates according to De Ley et al. (1970). DNA from LMG 23082T was hybridized with DNA of P. pentosaceus LMG 11488T and P. acidilactici LMG 11384T. A low reassociation value of 14·5 % was obtained with the type strain of P. acidilactici and 21 % with the type strain of P. pentosaceus, values that were well below the recommended 70 % cut-off value that indicates separate species (Wayne et al., 1987). The DNA G+C content of LMG 23082T was 38·0 mol%.
Phenotypic characterization was performed according to Schillinger & Lücke (1987). D(–)- and L(+)-lactate were determined from culture supernatants after 48 h of growth using an enzyme test kit (Roche Diagnostics). Maximum pH and NaCl tolerance were determined in MRS broth (Merck) after aerobic incubation for 5 days at 37 °C. The API 50 CHL identification system (bioMérieux) was used to determine the carbohydrate fermentation profile. Biochemical tests results are summarized in Table 1 and given in the species description below. LMG 23082T is distinguished from P. pentosaceus by its inability to produce acid from arabinose and lactose, from P. acidilactici by its inability to ferment xylose, and from P. claussenii by its ability to produce acid from galactose and DL-lactate from glucose (Table 1). Acid production from ribose distinguishes LMG 23082T from P. damnosus, P. inopinatus and P. parvulus. Unlike other pediococci, LMG 23082T grew at pH 9·0 (Table 1) and even at pH 9·6 (result not shown), a phenotypic characteristic which is commonly used to distinguish pediococci, lactococci and streptococci from enterococci (Weiss, 1991; Hardie & Whiley, 1997). The physiological and ecological significance of this alkaliphilic trait is not known, especially when considering that only one strain was isolated, which makes interpretations of such properties difficult. The maximum NaCl concentration for growth after 5 days of incubation was 8 %, a value which is higher than those reported for P. claussenii (5 %), P. damnosus (5 %) and P. dextrinicus (6 %), but lower than those for P. pentosaceus (10 %) and P. acidilactici (10 %) (Simpson & Taguchi, 1995; Holzapfel et al., 2005).
|
Description of Pediococcus stilesii sp. nov.
Pediococcus stilesii (stile'si.i. N.L. gen. n. stilesii named in honour of Prof. emerit. Michael E. Stiles, a food microbiologist who specialized in food preservation with bacteriocinogenic lactic acid bacteria).
Cells are cocci, 0·6–1·2 µm in diameter. They are Gram-positive, non-motile, do not form spores and occur singly, in pairs or in tetrads. Colonies are white, smooth and circular with a convex elevation and an entire margin. Acid is produced from glucose, ribose, galactose, fructose, mannose, N-acetylglucosamine, amygdalin, arbutin, aesculin, salicin, cellobiose, maltose, gentiobiose and tagatose. Acid is not produced from glycerol, erythritol, D-arabinose, L-arabinose, D-xylose, L-xylose, adonitol, methyl 
-D-xylopyranoside, sorbose, rhamnose, dulcitol, inositol, mannitol, sorbitol, methyl 
-D-mannopyranoside, methyl -D-glucopyranoside, lactose, melibiose, sucrose, trehalose, inulin, melezitose, raffinose, starch, glycogen, xylitol, turanose, lyxose, D-fucose, L-fucose, D-arabitol, L-arabitol, potassium gluconate, potassium 2-ketogluconate or potassium 5-ketogluconate. The G+C content of the DNA is 38·0 mol%.
The type strain is LMG 23082T (=BFE 1652T=FAIR-E 180T=CCUG 51290T), isolated from white maize grains.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Björkroth, J. & Korkeala, H. (1996). Evaluation of Lactobacillus sake contamination in vacuum-packaged sliced cooked meat products by ribotyping. J Food Prot 59, 398–401.
Collins, M. D., Williams, A. M. & Wallbanks, S. (1990). The phylogeny of Aerococcus and Pediococcus as determined by 16S rRNA sequence analysis: description of Tetragenococcus gen. nov. FEMS Microbiol Lett 70, 255–262.[CrossRef]
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[Medline]
de Man, J. C., Rogosa, M. & Sharpe, M. E. (1960). A medium for the cultivation of lactobacilli. J Appl Bacteriol 23, 130–135.
Dobson, C. M., Deneer, H., Lee, S., Hemmingsen, S., Glaze, S. & Ziola, B. (2002). Phylogenetic analysis of the genus Pediococcus, including Pediococcus claussenii sp. nov., a novel lactic acid bacterium isolated from beer. Int J Syst Evol Microbiol 52, 2003–2010.[Abstract]
Felis, G. E., Torriani, S. & Dellaglio, F. (2005). Reclassification of Pediococcus urinaeequi (ex Mees 1934) Garvie 1988, as Aerococcus urinaeequi comb. nov. Int J Syst Evol Microbiol 55, 1325–1327.
Gancheva, A., Pot, B., Vanhonacker, K., Hoste, B. & Kersters, K. (1999). A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species. Syst Appl Microbiol 22, 573–585.[Medline]
Gevers, D., Huys, G. & Swings, J. (2001). Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205, 31–36.[CrossRef][Medline]
Hardie, J. M. & Whiley, R. A. (1997). Classification and overview of the genera Streptococcus and Enterococcus. J Appl Microbiol Symp Suppl 83, 1S–11S.
Holzapfel, W. H., Franz, C. M. A. P., Ludwig, W., Back, W. & Dicks, L. M. T. (2005). Genera Pediococcus and Tetragenococcus. In The Prokaryotes, 3rd edn, An Evolving Electronic Resource for the Microbiological Community, release 3.15. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer. http://link.springer-ny.com/link/service/books/10125/
Kostinek, M., Specht, I., Edward, V. A., Schillinger, U., Hertel, C., Holzapfel, W. H. & Franz, C. M. A. P. (2005). Diversity and technological properties of predominant lactic acid bacteria from fermented cassava used for the preparation of Gari, a traditional African food. Syst Appl Microbiol 28, 527–540.[CrossRef][Medline]
Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.
Pitcher, D. G., Saunders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151–156.
Pot, B., Vandamme, P. & Kersters, K. (1994). Analysis of electrophoretic whole-organism protein fingerprints. In Chemical Methods in Prokaryotic Systematics, pp. 493–521. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
Schillinger, U. & Lücke, F.-K. (1987). Identification of lactobacilli from meat and meat products. Food Microbiol 4, 199–208.[CrossRef]
Simpson, W. J. & Taguchi, H. (1995). The genus Pediococcus, with notes on the genera Tetragenococcus and Aerococcus. In The Genera of Lactic Acid Bacteria, pp. 125–172. Edited by B. J. B. Wood & W. H. Holzapfel. London: Blackie Academic & Professional.
Sneath, P. H. A. & Sokal, R. R. (1973). Numerical Taxonomy: the Principles and Practice of Numerical Classification. San Francisco: W. H. Freeman.
Stackebrandt, E. & Kandler, O. (1979). Taxonomy of the genus Cellulomonas, based on phenotypic characters and deoxyribonucleic acid-deoxyribonucleic acid homology and proposal of seven neotype strains. Int J Syst Bacteriol 29, 273–282.
Thompson, F. L., Hoste, B., Vandemeulebroecke, K. & Swings, J. (2001). Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism. Syst Appl Microbiol 24, 520–538.[CrossRef][Medline]
Torriani, S., Clementi, F., Vancanneyt, M., Hoste, B., Dellaglio, F. & Kersters, K. (2001). Differentiation of Lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP. Syst Appl Microbiol 24, 554–560.[CrossRef][Medline]
Vancanneyt, M., Mengaud, J., Cleenwerck, I., Hoste, B., Dawyndt, P., Degivry, M. C., Ringuet, D., Janssens, D. & Swings, J. (2004). Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988. Int J Syst Evol Microbiol 54, 551–556.
Versalovic, J., Schneider, M., de Bruijn, F. J. & Lupski, J. R. (1994). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5, 25–40.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Weiss, N. (1991). The genera Pediococcus and Aerococcus. In The Prokaryotes, 2nd edn, vol. 2, pp. 1502–1507. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer. New York: Springer.
This article has been cited by other articles:
|
|
 |
|
  I. Cleenwerck, M. De Wachter, A. Gonzalez, L. De Vuyst, and P. De Vos Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii Int J Syst Evol Microbiol, July 1, 2009; 59(7): 1771 - 1786. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Doi, Y. Nishizaki, Y. Fujino, T. Ohshima, S. Ohmomo, and S. Ogata Pediococcus lolii sp. nov., isolated from ryegrass silage Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1007 - 1010. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Haakensen, C. M. Dobson, J. E. Hill, and B. Ziola Reclassification of Pediococcus dextrinicus (Coster and White 1964) Back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacillus Int J Syst Evol Microbiol, March 1, 2009; 59(3): 615 - 621. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. De Bruyne, N. Camu, L. De Vuyst, and P. Vandamme Lactobacillus fabifermentans sp. nov. and Lactobacillus cacaonum sp. nov., isolated from Ghanaian cocoa fermentations Int J Syst Evol Microbiol, January 1, 2009; 59(1): 7 - 12. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. De Bruyne, N. Camu, K. Lefebvre, L. De Vuyst, and P. Vandamme Weissella ghanensis sp. nov., isolated from a Ghanaian cocoa fermentation Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2721 - 2725. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. De Bruyne, C. M. A. P. Franz, M. Vancanneyt, U. Schillinger, F. Mozzi, G. F. de Valdez, L. De Vuyst, and P. Vandamme Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2909 - 2916. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Cleenwerck, A. Gonzalez, N. Camu, K. Engelbeen, P. De Vos, and L. De Vuyst Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2180 - 2185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Nielsen, U. Schillinger, C. M. A. P. Franz, J. Bresciani, W. Amoa-Awua, W. H. Holzapfel, and M. Jakobsen Lactobacillus ghanensis sp. nov., a motile lactic acid bacterium isolated from Ghanaian cocoa fermentations Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1468 - 1472. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Cleenwerck, N. Camu, K. Engelbeen, T. De Winter, K. Vandemeulebroecke, P. De Vos, and L. De Vuyst Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1647 - 1652. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Liu, B. Zhang, H. Tong, and X. Dong Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar. Int J Syst Evol Microbiol, October 1, 2006; 56(Pt 10): 2405 - 2408. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
