Applicability of rep-PCR fingerprinting for identification of Lactobacillus species

Gevers, D

doi:10.1016/s0378-1097(01)00439-6

Cited by 219 publications

(335 citation statements)

References 12 publications

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“…Repetitive element sequence-based PCR (rep-PCR) using the single primer (GTG)5 or the primer pair REP1R-Dt (59-IIINCGNCGNCATCNGGC-39) and REP2R-Dt (59-IIINCGNCTTATCNGGCCTAC-39) was performed as described previously (Versalovic et al, 1994;Gevers et al, 2001 88-92 %, respectively, suggesting that the two isolates might represent distinct strains (Fig. 3a).…”

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confidence: 99%

Weissella uvarum sp. nov., isolated from wine grapes

Nisiotou¹,

Dourou²,

Filippousi³

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Two bacterial strains (B18BM42 T and B18NM6) were recovered during a study of bacterial diversity on wine grapes (Vitis vinifera L.) from the Nemea region in Greece. Phylogenetic analysis based on 16S rRNA gene sequences placed the two strains within the genus Weissella, and found them to be most closely related to Weissella minor NRIC 1625 T followed by Weissella viridescens NRIC 1536 T (99.1 and 98.9 % sequence similarity, respectively). The level of DNA-DNA relatedness between strains B18NM42 T and W. minor NRIC 1625 T or W. viridescens NRIC 1536 T was 31.9 and 35.0 %, respectively. The two novel strains could be genetically differentiated from their closest relatives by REA-PFGE (restriction enzyme analysis-pulse field gel electrophoresis), RAPD (randomly amplified polymorphic DNA) and rep-PC R analyses (repetitive sequence-based PCR). Physiological examination showed that the novel strains can be distinguished from phylogenetically related species by their ability to grow at 42 6C and by certain carbohydrate fermentations. Based on the evidence above, the affiliation of the two strains to a novel species with the proposed name Weissella uvarum sp. nov. is suggested. The type strain is B18NM42 T (5DSM 28060 T 5NCCB 100484 T ).

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confidence: 99%

Weissella uvarum sp. nov., isolated from wine grapes

Nisiotou¹,

Dourou²,

Filippousi³

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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“…Stability of the relationships was assessed by bootstrapping (1000 replicates). DNA fingerprinting using FAFLP, which included DNA extraction and purification (Gevers et al, 2001), FAFLP fingerprinting, data processing and numerical analysis , was performed by the BCCM TM / LMG (Belgian Coordinated Collections of Microorganisms/ Laboratorium voor Microbiologie from Universiteit Gent) Identification Service.…”

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confidence: 99%

Aeromonas bivalvium sp. nov., isolated from bivalve molluscs

Miñana-Galbis

Farfán

Fusté

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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A polyphasic study was performed to determine the taxonomic position of two Aeromonas strains, 665N and 868E T , isolated from bivalve molluscs, that could not be identified at the species level in a previous numerical taxonomy study. The DNA G+C content of these isolates was 62.3 and 62.6 mol%, respectively. Sequence analysis of the 16S rRNA gene showed that the two new strains were closely related to members of the genus Aeromonas. Fluorescence amplified fragment length polymorphism fingerprinting revealed that strains 665N and 868E T clustered together with a similarity of 78 % but did not cluster with any of the Aeromonas genomospecies. DNA-DNA hybridization experiments revealed a high level of relatedness between the two new isolates (76 %) but low levels of relatedness between these and phylogenetically most closely related Aeromonas genomospecies (30-44 %). Useful tests for the phenotypic differentiation of strains 665N and 868E T from other mesophilic Aeromonas species included those for gas from glucose, lysine decarboxylase, Voges-Proskauer reaction, acid from L-arabinose, hydrolysis of aesculin and utilization of L-lactate. On the basis of genotypic and phenotypic evidence, strains 665N and 868E T are considered to represent a novel species of the genus Aeromonas, for which the name Aeromonas bivalvium sp. nov. is proposed. The type strain is 868E T (=CECT 7113 T =LMG 23376 T ).Members of the genus Aeromonas, belonging to the class Gammaproteobacteria, are Gram-negative, non-spore-forming bacilli or coccobacilli, and are facultatively anaerobic, chemo-organotrophic, oxidase-and catalase-positive, resistant to the vibriostatic agent O/129 (2,4-diamino-6,7-diisopropylpteridine), generally motile by means of a single polar flagellum and are able to reduce nitrate to nitrite. Aeromonads are primarily aquatic, widespread in environmental habitats, frequently isolated from foods and often associated with aquatic animals, and some species are primary or opportunistic pathogens in invertebrates and vertebrates including humans (Martin-Carnahan & Joseph, 2005).At the time of writing, 17 Aeromonas species and 20 DNA-DNA hybridization groups (HGs) have been described: Aeromonas hydrophila (HG1), A. bestiarum (HG2), A. salmonicida (HG3), A. caviae (HG4), A. media (HG5), A. eucrenophila (HG6), A. sobria (HG7), A. veronii bv. Sobria (HG8/10), A. jandaei (HG9), A. veronii bv. Veronii (HG10/ 8), Aeromonas sp. HG11, A. schubertii (HG12), Aeromonas sp. group 501 (HG13), A. trota (HG14), A. allosaccharophila (HG15), A. encheleia (HG16), A. popoffii (HG17), A. culicicola (HG18), A. simiae (HG19) and A. molluscorum (HG20) (Pidiyar et al., 2002; Harf-Monteil et al., 2004; Miñana-Galbis et al., 2004;Martin-Carnahan & Joseph, 2005). In addition to the continuous description of novel species, the complexity of Aeromonas taxonomy results from the isolation of motile and non-motile, mesophilic and psychrophilic, pigmented and non-pigmented strains within several Aeromonas species (Altwegg et al., 1990;Martin-Carnahan & Joseph,...

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“…The isolates were grown for up to 2 days at 30 u C on tryptic soy broth (TSB; Difco) containing 1.5 % agar (Oxoid). DNA isolation and electrophoresis were done according to Gevers et al (2001) and rep-PCR was carried out with the primer set BOXAIR according to Versalovic et al (1994). Band patterns analysed using the Pearson product moment coefficient and the UPGMA clustering algorithm with Bionumerics software (Applied Maths) were compared with a database composed of type and reference strains representing species that are common on the surfaces of smear-ripened cheeses (data not shown).…”

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confidence: 99%

Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses

Bora

Vancanneyt

Gelsomino

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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Seven Gram-positive, coryneform bacteria with virtually identical whole-organism protein patterns were isolated from the surface of smear-ripened cheeses. Representatives of these strains were the subject of a polyphasic study designed to establish their taxonomic status. The organisms formed a distinct branch in the Microbacteriaceae 16S rRNA gene tree and were most closely related to members of the genus Agrococcus, sharing sequence similarities of 95.4-98.7 %. The chemotaxonomic profiles of the strains were consistent with their classification in the genus Agrococcus. The combined genotypic and phenotypic data show that the isolates should be classified in the genus Agrococcus as representatives of a novel species. The name Agrococcus casei sp. nov. is proposed for this taxon. Isolate R-17892t2 T (=DSM 18061 T =LMG 22410 T ) is the type strain of Agrococcus casei sp. nov.The complex consortium of micro-organisms found on the surfaces of smear-ripened cheeses includes major populations of coryneform bacteria (catalase-positive irregular rods and cocci), staphylococci (catalase-positive cocci) and yeasts (Valdés-Stauber et al., 1997;Carnio et al., 1999;Bockelmann & Hoppe-Seyler, 2001). Until recently, cheese coryneform bacteria were assigned to groups based on a few subjectively weighted morphological and staining properties (Piton-Malleret & Gorrieri, 1992;Eliskases-Lechner & Ginzinger, 1995). Such studies have been replaced by polyphasic taxonomic investigations, which show that the coryneform component of smear-ripened cheeses contains members of novel taxa, as exemplified by the isolation and description of Corynebacterium casei and Microbacterium gubbeenense from the surface of Gubbeen cheese (Brennan et al., 2001a(Brennan et al., , b, 2002 and Arthrobacter arilaitensis and Arthrobacter bergerei from diverse French smear-ripened cheeses (Irlinger et al., 2005). The present study was designed to determine the taxonomic status of a homogeneous group of coryneform bacteria isolated from smear-ripened cheeses and presumptively assigned to the genus Agrococcus.The genus Agrococcus was proposed by Groth et al. (1996) for two Gram-positive, coryneform bacteria that could be distinguished from members of other genera classified in the family Microbacteriaceae using genotypic and phenotypic criteria. The genus currently contains four species with validly described names: Agrococcus baldri Zlamala et al. The phylogenetic positions of the four representative cheese isolates were determined by 16S rRNA gene sequence analysis. Biomass from growth in brain-heart infusion broth (BHI; Difco) for 5 days at 30 uC was checked for purity, harvested by centrifugation, washed in NaCl/EDTA buffer (0.1 M EDTA, 0.1 M NaCl, pH 8.0) and stored at 220 u C until required. Genomic DNA was extracted as described by Sambrook & Russell (2001) and used as a template for PCR amplification and sequencing following the procedure of Kim et al. (1998). The resultant almost complete 16S rRNA gene sequences (1466-1470 nt) were manually aligned ...

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Applicability of rep-PCR fingerprinting for identification of Lactobacillus species

Cited by 219 publications

References 12 publications

Weissella uvarum sp. nov., isolated from wine grapes

Weissella uvarum sp. nov., isolated from wine grapes

Aeromonas bivalvium sp. nov., isolated from bivalve molluscs

Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses

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