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Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodologic…
2001
ABSTRACT Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extracti…
Comparison of different primer sets for use in Automated Ribosomal Intergenic Spacer Analysis of complex bacterial communities.
2004
ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxi…
Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure
2006
ABSTRACT In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg ≥ Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the “hump-backed” relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, an…
Polyphasic taxonomic characterization of Lactobacillus rossiae isolates from Belgian and Italian sourdoughs reveals intraspecific heterogeneity.
2009
Abstract (GTG) 5 -PCR fingerprinting and pheS sequence analysis of 18 Lactobacillus rossiae isolates, mainly originating from Belgian and Italian artisan sourdoughs, revealed intraspecies grouping as evidenced by the delineation of three and two subgroups, respectively. On the other hand, 16S rRNA and rpoA gene sequence analysis and DNA–DNA hybridizations supported the accommodation of all isolates in a single species. No correlation between genetic and phenotypic heterogeneity was observed. Collectively, these data do not warrant taxonomic division of L. rossiae . On the other hand, the considerable differences in intraspecies sequence variation of L. rossiae isolates displayed by the pheS…
Epidemiology ofSalmonella typhimurium: ribosomal DNA analysis of strains from human and animal sources
1993
SUMMARYSalmonella typhimuriumis the most frequently identified serovar ofSalmonellain Italy. This serovar is characterized by the widespread dissemination among human and non-human sources of phenotypically and genetically well-differentiated clones.In this study 457 strains ofS. typhimuriumisolated in Italy in the years 1982–91 from human and animal sources were submitted to characterization by the rDNA fingerprinting technique. Application of this typing method, after digestion of chromosomal DNA withHincII endonuclease, confirmed the greatest genetic differentiation of clones ofS. typhimurium, allowing reliable identification of 45 rDNA patterns linked into 9 major clusters. rDNA pattern…
rRNA probing of chromosomal DNA of epidemic and sporadic isolates of Salmonella enterica subsp. Enterica serovar kottbus from Northern and Southern I…
1990
Fifty-two strains of Salmonella enterica subsp. enterica serovar Kottbus, identified at the Centres of Enterobacteriaceae of Northern and Southern Italy, were investigated by molecular genetic methods. Thirteen isolates were recovered during two food-poisoning outbreaks that occurred in May 1987 in Lombardy. The rDNA gene restriction patterns, obtained by probing endonuclease cleaved chromosomal DNA with photobiotin labeled Escherichia coli rRNA, revealed some heterogeneity among strains isolated from Southern Italy, whereas Northern Italy isolates exhibited virtually identical banding patterns.
rDNA fingerprinting as a tool in epidemiological analysis of Salmonella typhi infections
1991
SUMMARYCharacterization of 169 strainsof Salmonella typhiof phage types C1, C4, D1and D9isolated in 1975–88 was carried out by rDNA gene restriction pattern analysis. Twenty-four isolates had been recovered during four large waterbone outbreaks in the last 20 years in Sicily; 145 strains, isolated from apparently sporadic cases of infection in Southern Italy in the same period of time, were also examined.Application of rRNA–DNA hybridization technique after digestion of chromosomal DNA withClaI showed the identity of patterns of the epidemic strains of phage types C1and D1, confirming attribution of the outbreaks to single bacterial clones. Patterns of the two available strains of lysotype …
Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques.
2005
Abstract The possibility of using PCR for rapid identification of food-borne Staphylococcus aureus isolates was evaluated as an alternative to the API-Staph system. A total of 158 strains, 15 S. aureus , 12 other staphylococcal species, and 131 isolates recovered from 164 food samples were studied. They were phenotypically characterized by API-Staph profiles and tested for PCR amplification with specific primers directed to thermonuclease ( nuc ) and enterotoxin ( sea to see ) genes. Disagreement between the PCR results and API-Staph identification was further assessed by the analysis of randomly amplified polymorphic DNA (RAPD) profiles obtained with three universal primers (M13, T3, and T…
16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine.
2003
Lactic acid bacteria (LAB) are found in a great variety of habitats, including grape must and wines. There is a close relationship between the species of LAB which develop during fermentation and the eventual quality of the wine. For these reasons analytical techniques allowing fast and reliable identification of wine LAB are needed. In this work a simple and accurate protocol for identifying species of LAB isolated from grape must and wine is presented. This protocol is based on the amplification, directly from colony, of 16S rDNA and later digestion with one of the following restriction enzymes BfaI, MseI and AluI. A sequential use of the three enzymes is proposed to simplify LAB wine ide…
Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes
2006
AbstractImprinted genes are expressed from only one allele in a parent-of-origin-specific manner. We here describe a systematic approach to identify novel imprinted genes using quantification of allele-specific expression by Pyrosequencing, a highly accurate method to detect allele-specific expression differences. Sixty-eight candidate imprinted transcripts mapping to known imprinted chromosomal regions were selected from a recent expression profiling study of uniparental mouse embryos and analyzed. Three novel imprinted transcripts encoding putative non-protein-coding RNAs were identified on the basis of parent-of-origin-specific monoallelic expression in E11.5 (C57BL/6 × Cast/Ei)F1 and in…