16S-ARDRA, a Tool for Identification of Lactic Acid Bacteria Isolated from Grape Must and Wine

Rodas, Ana; Ferrer, Sergi; Pardo, Isabel

doi:10.1078/072320203322497446

Cited by 162 publications

(117 citation statements)

References 37 publications

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“…The unclear identification of isolates, which clustered together in both dendrograms with the collection strains of the L. casei group, reflects the contentious taxonomic position of L. casei and related species. Our findings are in line with the results reported by Rodas et al (2003). Another limitation of our method is that we were not able to distinguish L. johnsonii from L. gasseri and L. plantarum from L. paraplantarum.…”

Section: Salivarius D D D/nd -Differentiated/not Differentiated Bysupporting

confidence: 81%

“…The restriction with aluI yielded unique clusters for the species L. brevis, L. salivarius, L. rham(2003) Rodas et al (2003). Some of the differences between in silico and experimental results can be explained by possible punctual errors in the sequences previously reported to the GenBank database and resulting in the disappearance of the restriction sites.…”

Section: Resultsmentioning

confidence: 89%

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Differentiation of Lactobacillus species by ARDRA

Kšicová¹,

Dušková²,

Karpíšková³

2013

Czech J. Food Sci.

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Kšicová † K., Dušková M., Karpíšková R. (2013): Differentiation of Lactobacillus species by ARDRA. Czech J. Food Sci., 31: 180-188.The Lactobacillus species by 16S Amplified Ribosomal DNA Restriction Analysis (16S-ARDRA) was identified. Lactobacilli are bacteria often found in foodstuffs of both animal and vegetable origins. On one hand, they play an important role in the food spoilage and, on the other hand, they are used as starter cultures in food fermentation processes. The species-specific identification by traditional biochemical methods is time consuming and not always fully effective. Therefore, more efficient techniques are searched for. We focused on rapid identification of Lactobacillus isolates from different habitats. Forty-nine collection strains and isolates belonging to the genus Lactobacillus were discriminated. ARDRA was carried out with two restriction endonucleases. For the comparison of similarity, the Jaccard coefficient and clustering by the unweighted pair group method with arithmetic averages (UPGMA) were used. The percentages of similarity between profiles varied from 22% to 100% (aluI) and from 27% to 100% (MspI). This method proved applicable to the differentiation of 10 species.

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Section: Salivarius D D D/nd -Differentiated/not Differentiated Bysupporting

confidence: 81%

Section: Resultsmentioning

confidence: 89%

Differentiation of Lactobacillus species by ARDRA

Kšicová¹,

Dušková²,

Karpíšková³

2013

Czech J. Food Sci.

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“…16S-ARDRA (amplified rDNA restriction analysis), ISR (internal spacer region) analysis, RAPD (randomly amplified polymorphic DNA) analysis and ribotyping were used to characterize this strain genotypically, as described previously (Rodas et al, 2003(Rodas et al, , 2005Chenoll et al, 2006). Strain IMCC1736 T could be differentiated from the reference strains by RAPD and ribotyping profiles, but not by the other techniques based on ribosomal gene analysis.…”

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confidence: 99%

Lactobacillus aquaticus sp. nov., isolated from a Korean freshwater pond

Mañes-Lázaro

Song

Pardo

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A Lactobacillus strain, IMCC1736 T , was isolated recently from a Korean freshwater pond following an extensive study of the microbial community in this ecosystem. Its 16S rRNA gene was sequenced and phylogenetic analysis placed this strain within the Lactobacillus salivarius group, closely related to Lactobacillus satsumensis NRIC 0604 T , with 97.9 % sequence similarity. In the present work, the taxonomic status of strain IMCC1736 T has been re-evaluated. It was characterized phylogenetically, genotypically and phenotypically and, based on DNA-DNA hybridization values, this strain represents a novel Lactobacillus species. Strain IMCC1736 T can be differentiated genotypically from its closest relatives by randomly amplified polymorphic DNA analysis and ribotyping patterns; phenotypically, it can be distinguished by its inability to grow in 5 % NaCl and at pH 3.3 and by certain carbohydrate fermentations. Strain IMCC1736 T is Grampositive, catalase-negative and microaerophilic. Cells are motile rods and show homofermentative metabolism. The name Lactobacillus aquaticus sp. nov. is proposed, with strain IMCC1736 T (5CECT 7355 T 5DSM 21051 T ) as the type strain.

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“…Amplified rDNA restriction analysis (16S-ARDRA), analysis of the 16S-23S rDNA intergenic spacer region (ISR), random amplification of polymorphic DNA (RAPD) profiling and ribotyping were applied to characterize these strains genotypically, as described previously (Rodas et al, 2003(Rodas et al, , 2005Chenoll et al, 2006). Strain 203 T could be differentiated from the reference strains by using RAPD and ribotyping profiles.…”

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confidence: 99%

“…All of them, as well as wine isolate 203 T , were grown in MRS broth (Scharlab) supplemented with 0.5 g L-cysteine hydrochloride l 21 (mMRS) under the conditions described by Rodas et al (2003).…”

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confidence: 99%

Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must

Mañes-Lázaro

Ferrer

Rodas

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A Lactobacillus strain, designated 203 T , previously isolated from Bobal grape must was characterized phylogenetically, genotypically and phenotypically in order to establish whether it represents a novel species. On the basis of the 16S rRNA gene sequence, strain 203 T was shown to belong to the genus Lactobacillus, falling within the Lactobacillus alimentariusLactobacillus farciminis group and being closely related to the type strains of L. alimentarius, Lactobacillus kimchii and Lactobacillus paralimentarius. DNA-DNA hybridization results confirmed the separate status of strain 203 T at the species level. To establish the similarities and differences between 203 T and the three aforementioned closest species, the following methods were used: amplified rDNA restriction analysis, analysis of the 16S-23S rDNA intergenic spacer region, random amplification of polymorphic DNA (RAPD) profiling, ribotyping, carbohydrate fermentation and physiological tests. Strain 203 T could be differentiated genetically using RAPD analysis and ribotyping. Phenotypically, it can be distinguished from its closest relatives by its ability to grow at pH 3.3, by gas production from gluconate and by certain carbohydrate fermentations. On the basis of these data, strain 203 T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus bobalius sp. nov. is proposed. The type strain is 203 T (5CECT 7310 T 5DSM 19674 T ).Eighteen different species of the genus Lactobacillus have been reported to be involved in the winemaking process (Chalfan et al., 1977;Costello et al., 1983;Davis et al., 1986;Lafon-Lafourcade, 1983;Lafon-Lafourcade et al., 1983;Maret & Sozzi, 1977, 1979 Ribéreau-Gayon et al., 2000b;Rodas et al., 2005;Wibowo et al., 1985). In recent years, three of them have been described as novel species, namely Lactobacillus kunkeei (Edwards et al., 1998), Lactobacillus nagelii (Edwards et al., 2000) and Lactobacillus vini (Rodas et al., 2006). Wine lactobacilli are sometimes considered as spoilage organisms since they can produce acetic acid and/ or off-flavours Wibowo et al., 1985;Fleet, 1993;Sponholz, 1993) and biogenic amines (Lonvaud Funel, 2001; Ribéreau-Gayon et al., 2000a;Landete et al., 2005).In an earlier study, Rodas et al. (2005) carried out an extensive polyphasic analysis using genotypic and phenotypic methods to characterize 170 lactobacilli isolated from musts and wines. The dendrogram built by comparing the results obtained from the different techniques showed that strain 203 T did not cluster with any of the reference species of the genus Lactobacillus. An analysis of 16S rRNA gene sequence similarity showed that strain 203 T was most closely related to the type strains of Lactobacillus kimchii (99.3 %), Lactobacillus paralimentarius (97.8 %) and Lactobacillus alimentarius (98.2 %). However, the study results did not confirm whether strain 203 T represented a novel species or not.The phylogenetic, genotypic and phenotypic characterization of isolate 203 T and its closest phylogenetic relati...

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16S-ARDRA, a Tool for Identification of Lactic Acid Bacteria Isolated from Grape Must and Wine

Cited by 162 publications

References 37 publications

Differentiation of Lactobacillus species by ARDRA

Differentiation of Lactobacillus species by ARDRA

Lactobacillus aquaticus sp. nov., isolated from a Korean freshwater pond

Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must

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