Differentiation of Lactobacillus isolates from infant faeces by SDS-PAGE and rRNA-targeted oligonucleotide probes

Isolates of lactobacilli from infant faeces phenotypically characterized as Lactobacillus paracasei subsp. paracasei (six strains), Lact. rhamnosus (six strains), Lact. gasseri (three strains), Lact. acidophilus (one strain) and Lact. fermentum/reuteri (three strains) according to recent classification systems were subjected to SDS-PAGE of whole cell proteins and rRNA-targeted oligonucleotide probe hybridization, in order to confirm the phenotypic characterization and elucidate the exact taxonomic position of the three strains that had properties between fermentum and reuteri. Results suggested a good agreement between the phenotypic characterization, SDS-PAGE and rRNA-targeted oligonucleotide probe hybridization for strains of all species except for the Lact. fermentum/reuteri strains. Results obtained by rRNA probes suggested a possible phylogenetic relatedness of the strains to Lact. reuteri. Isolates from infant faeces with interesting probiotic properties could be used as components of fermented milk products.     

Antibiotic sensitivities in vitro of diverse spiroplasma strains associated with plants and insects

Fifteen spiroplasma strains, representing five serological subgroups classified in three distinct serogroups, and four strains unassigned to serogroups were examined for sensitivity to antibiotics. The data contribute to the characterization of spiroplasmas and enlarge comparisons between plant pathogenic strains and strains that are evidently a part of the normal epiphytic microflora.     

The Use of the A.P.I. Lactobacillus System for the Characterization of Pediococci

A commercially produced system for the identification of Lactobacillus , by which the reactions of concentrated cell suspensions towards 50 substrates may be determined, is useful for the characterization of strains of Pediococcus . Suitable conditions for inoculum preparation vary for slow and fast growing strains; the influence of cell concentration on the results is described. The reactions are classified in terms of their value for species characterization and the results are shown to agree well with those in other studies where classical procedures have been used.     

Evaluation of (GTG)<Subscript>5</Subscript>-PCR for rapid identification of <Emphasis Type="Italic">Streptococcus mutans</Emphasis>

Repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using the (GTG)(5) primer was applied for fast screening of bacterial strains isolated from dental plaque of early childhood caries (ECC)-affected children. A group of 29 Gram-positive bacteria was separated into a homogeneous cluster together with Streptococcus mutans reference strains and constituted an aberrant branch after the numerical analysis of (GTG)(5)-PCR fingerprints. Automated ribotyping with EcoRI restriction enzyme (RiboPrinter microbial characterization system) revealed high genetic heterogeneity among the tested group and proved to be a good tool for strain-typing purposes. Further characterization of the studied strains was achieved by extensive phenotyping and whole-cell protein fingerprinting and confirmed all the strains as S. mutans representatives. Obtained results showed rep-PCR fingerprinting with the (GTG)(5) primer to be a fast and reliable method for identification of S. mutans.     

A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background

In the analysis of complex traits, congenic strains are powerful tools because they allow characterization of a single locus in the absence of genetic variation throughout the remainder of the genome. Here, we report the construction and initial characterization of a genome-wide panel of congenic strains derived from the donor strain DBA/2J on the background strain C57BL/6J. For many strains, we have carried out high-density SNP genotyping to precisely map the congenic interval and to identify any contaminating regions. Certain strains exhibit striking variation in litter size and in the ratio of females to males. We illustrate the utility of the set by "Mendelizing" the complex trait of myocardial calcification. These 65 strains cover more than 95% of the autosomal genome and should facilitate the analysis of the many genetic trait differences that have been reported between these parental strains.     

Molecular Characterization of <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis> Strains Isolated from <Emphasis Type="Italic">Agave fourcroydes</Emphasis> (Lem.) in Yucatan,Mexico

The molecular characterization of 14 strains of Kluyveromyces marxianus isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico, was performed by AP-PCR analysis, PCR-RFLP of 5.8S-ITS, and complete NTS regions. A sequence analysis of the D1/D2 domain of the 26S rDNA was also carried out in six selected strains. The AP-PCR approach had the highest discrimination power for the molecular characterization of new henequen K. marxianus strains. PCR-RFLP of 5.8S-ITS regions did not reveal polymorphisms in this group of strains. The restriction enzyme digestion analysis of NTS region enables the separation among strains which coincides with ascospore shape groups. The molecular tools used in this article may be useful to confirm a preliminary screen of yeasts isolated from henequen without the use of growth characteristics or morpho-physiological tests.     

The uses of AFLP for detecting DNA polymorphism, genotype identification and genetic diversity between yeasts isolated from Mexican agave-distilled beverages and from grape musts

AIMS: The objectives were to determine the variability and to compare the genetic diversity obtained using amplified fragment length polymorphism (AFLP) markers in analyses of wine, tequila, mezcal, sotol and raicilla yeasts. METHODS AND RESULTS: A molecular characterization of yeasts isolated from Mexican agave musts, has been performed by AFLP marker analysis, using reference wine strains from Italian and South African regions. CONCLUSIONS: A direct co-relation between genetic profile, origin and fermentation process of strains was found especially in strains isolated from agave must. In addition, unique molecular markers were obtained for all the strains using six combination primers, confirming the discriminatory power of AFLP markers. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of molecular characterization between yeasts isolated from different Mexican traditional agave-distilled beverages, which shows high genetic differences with respect to wine strains.     

Selection and characterization of transposon tagging mutants of<Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803 sensitive to high-light and oxidative Stresses

We compared several analytical tools to identify which were most applicable for the selection and characterization of specific transposon-tagged mutant strains ofSynechocystis sp. PCC 6803 that are sensitive to high light and oxidative stresses. Our primary parameter was the maximum photochemical efficiency of dark-adapted cells, a very sensitive factor that can be determined in a non-destructive manner. Using this as a tool for primary selection, we identified five mutant strains with different sensitivities to photoinhibition and photooxidation. For further characterization, we obtained data describing the absorption spectra for pigment contents, the 77K fluorescence spectra, non-photochemical quenching (as a down-regulation process), and the photosynthetic electron transfer rate. Based on these results, we were able to design a strategy for selecting mutants with specific phenotypes. Here, we also discuss the strengths and weaknesses of each selection and characterization tool.     

A comparison of the biological characteristics of EV71 C4 subtypes from different epidemic strains

The comparative analysis of the biological characterization and the genetic background study of EV71 circulating strains is commonly recognized as basic work necessary for development of an effective EV71 vaccine. In this study, we sequenced five EV71 circulating strains, isolated from Fuyang, Hefei, Kunming and Shenzhen city of China and named them FY-23, FY-22, H44, K9 and S1 respectively. The sequence alignment demonstrated their genotypes be C4. The genetic distance of the VP1 gene from these isolates suggested that they were highly co-related with genetic identity similar to other previously reported EV71 strains in China. Additionally, these strains were identified to display some obvious proliferation dynamics and plaque morphology when propagated in Vero cells. However, a distinctive difference in pathogenic ability in neonatal mice was found. Some differences in cross neutralization test &; immunogenic analysis were also found. All these results are related to the biological characterization of circulating EV71 strains in China and aid in the development of an EV71 vaccine in the future.     

Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes

Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality.     

Characterization of beta-lactam-resistant Bacteroides fragilis isolates by use of PCR fingerprinting

PCR fingerprinting was used for characterization of 35 beta-lactam-resistant Bacteroides fragilis strains isolated in Sweden and Hungary. Ten B. fragilis strains showed unique PCR fingerprints by use of the M13 core primer. Their main product was a DNA fragment with a length of 2000-bp which was absent in the other 25 strains and the reference strain B. fragilis ATCC 25285. The 2000-bp fragment from four imipenem-resistant strains gave rise to positive reactions in a specific PCR for detection of ccrA. Printed by the T3B primer, five B. fragilis strains, including the imipenem-resistant strains showed unique PCR fingerprints. The investigated imipenem-resistant strains produced carbapenem-hydrolysing metallo-beta-lactamases. The study indicates that the unique PCR fingerprinting profiles shown in highly beta-lactam resistant B. fragilis strains are correlated to antimicrobial resistance. The PCR fingerprinting technique is a useful tool for differentiation of Bacteroides fragilis strains with high-level beta-lactam resistance.     

The applicability of the time/temperature superposition principle to brain tissue

This paper deals with the mechanical characterization of brain tissue which behaves as a viscoelastic material. We focus on the linear viscoelastic behavior, which should apply for small strains at any strain rate, and demonstrate the applicability of the time/temperature superposition principle. This principle allows the opportunity to extend the range of shear rates for which the material is characterized, and makes the results applicable to impact conditions. This characterization of the linear behavior forms the basis for a further nonlinear characterization of the tissue.     

Prevalence of verotoxin-producing Escherichia coli (VTEC) and E. coli O157:H7 in French pork

AIMS: To determination the prevalence of VTEC in pork products and the surrounding environment of the pork plant (slaughterhouse and cutting plant), and characterization of the VTEC strains isolated (virulence genes and serotype). METHODS AND RESULTS: Among the 2146 carcass and pork samples and 876 environmental samples (swabs of surfaces or materials), 328 (15%) and 170 (19%) were PCR-positive for stx genes respectively. VTEC strains were recovered from positive samples by colony hybridization or immunoconcentration, serotyped and genetically characterized. Strains of E. coli O157:H7 were not isolated from 3 uidA-positive samples detected by PCR. The VTEC isolates did not harbour eae, ehx and uidA genes. CONCLUSIONS: Pigs and pork meat may contain VTEC strains but characterization of the strains based on virulence factors showed that the potential danger of pork meat appears to be low since although all strains harboured a stx gene, they did not have other virulence genes. SIGNIFICANCE OF THE STUDY: General hygiene measures appear to be sufficient and specific hygiene measures for VTEC are not necessary at this time. The porcine VTEC strains isolated in our study probably do not present a hazard.     

Genetic composition of the recombinant congenic strains

For the study of biological phenomena influenced by multiple genes in mice, the Recombinant Congenic Strains (RCS) have been developed. An RCS series comprises approximately 20 homozygous strains, each of which contains on average 87.5% genes of a common background strain and 12.5% of a common donor strain. In an RCS series, non-linked genes involved in the control of a multigenic trait become distributed into different recombinant congenic strains. In this way a multigenic trait is transformed into a series of single gene traits in which each gene can be studied individually. For the ability to use the strength of the recombinant congenic strains system to its full extent, a thorough genetic characterization is indispensable. We have typed the CcS/Dem and OcB/Dem series for 611 and 550 markers, respectively. This results in a genetic characterization sufficient to detect most donor strain genes. In addition, we report the genetic characterization of the HcB/Dem and HcB(N4)/Dem series. Strains of the latter series contain on average 6.25% of the donor strain genome. Both series have been typed for 130 markers. All the typing data have been deposited in the Mouse Genome Database at The Jackson Laboratory. Received: 11 July 1995 / Accepted: 18 August 1995     

Genotypic analysis of strains of mutans streptococci by pulsed-field gel electrophoresis

The species and serotypes of various strains of S. mutans and S. sobrinus were characterized by pulsed-field gel electrophoresis after the genomic DNA from the various strains had been digested with five restriction enzymes (EcoR I, Xba I, Hind III, Sfi I and BssH II) separately. Among these restriction enzymes, BssH II was very useful for the characterization of species and serotypes and, in particular, digestion discriminated between serotypes d and g. The restriction patterns obtained from the genomic DNA of isolates isolated from children's saliva were essentially identical to those from the genomic DNA of the standard laboratory strains. Patterns of BssH II digests of the genomic DNA of 10 isolates identified as S. sobrinus were characteristic of serotype g of the standard laboratory strains. Our results indicate that digestion with BssH II and subsequence analysis by pulsed-field gel electrophoresis should be useful for the characterization of species and serotypes and for epidemiological studies of mutans streptococci.     

Allelopathic activity among Cyanobacteria and microalgae isolated from Florida freshwater habitats

We evaluated allelopathic interactions between strains of Cyanobacteria and green algae isolated from south and central Florida. Allelopathy, including inhibition or stimulation of growth, was assessed by cocultivation of each of the isolated strains, as well as by evaluation of extracts prepared from the isolates. All of the strains of Cyanobacteria, and four of the six isolates of green algae, showed some allelopathic activity (i.e. inhibition or stimulation of the growth of other strains). Of these, the most pronounced activity was observed for the cyanobacterial isolate Fischerella sp. strain 52-1. In the cocultivation experiments this cyanobacterium inhibited the growth of all tested green algae and Cyanobacteria. The crude lipophilic extracts from Fischerella sp. strain 52-1 isolated from both the biomass and the culture liquid inhibited photosynthesis of the green alga Chlamydomonas sp. in a concentration- and time-dependent manner and caused extensive loss of ultrastructural cell organization. Preliminary chemical characterization of compounds extracted from Fischerella sp. strain 52-1 indicated the presence of indole alkaloids, and further characterization has confirmed that these compounds belong to the hapalindoles previously isolated from other species of Fischerella and related genera. Further chemical characterization of these compounds, and further investigation of their apparent role in allelopathy is ongoing.     

Use of an enzyme-linked lectinsorbent assay to monitor the shift in polysaccharide composition in bacterial biofilms

An enzyme-linked lectinsorbent assay (ELLA) was developed for quantification and characterization of extracellular polysaccharides produced by 1- and 4-day biofilms of 10 bacterial strains isolated from food industry premises. Peroxidase-labeled concanavalin A (ConA) and wheat germ agglutinin (WGA) were used, as they specifically bind to saccharide residues most frequently encountered in biofilms matrices: D-glucose or D-mannose for ConA and N-acetyl-D-glucosamine or N-acetylneuraminic acid for WGA. The ELLA applied to 1- and 4-day biofilms colonizing wells of microtiter plates was able to detect that for Stenotrophomonas maltophilia and to a lesser extent Staphylococcus sciuri, the increase in production of exopolysaccharides over time was not the same for sugars binding with ConA and those binding with WGA. Differences in extracellular polysaccharides produced were observed among strains belonging to the same species. These results demonstrate that ELLA is a useful tool not only for rapid characterization of biofilm extracellular polysaccharides but also, in studies of individual strains, for detection of changes over time in the proportion of the exopolysaccharidic component within the polymeric matrix.     

MORPHOLOGY AND NUTRITION OF PANDORINA UNICOCCA SP. NOV.1,2

Eleven strains of Pandorina unicocca sp. nov. were studied for morphological characterization. The species was delimited by having cells which contain a single basal pyrenoid and by colonies which have cells separate from each other in the colonial envelope. A defined medium was developed for 4 strains of P. unicocca and the nutritional requirements of these strains were examined. All 4 strains were capable of completely autotrophic growth and they could utilize nitrate, ammonium, or urea as nitrogen sources. Optimum growth was nuts attained at pH 8.0.     

Evaluation of intra-specific diversities in Oenococcus oeni through analysis of genomic and expressed DNA

In winemaking Oenococcus (O.) oeni is the most frequent species of lactic acid bacteria (LAB) associated with malolactic fermentation (MLF). Several studies have demonstrated that O. oeni is a quite homogeneous species and strains are difficult to differentiate especially when isolates from the same region are analyzed. In this study, the molecular biodiversity of O. oeni isolated from wines of the same region (Aglianico produced in Basilicata Region, Southern Italy) was evaluated with the aim of designing a molecular approach for discrimination and characterization of the isolates at the strain level. Three molecular techniques were applied: random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), restriction endonucleases analysis-pulsed field gel electrophoresis (REA-PFGE) and differential display PCR (DD-PCR). The results obtained by RAPD-PCR confirmed the difficulty in differentiating isolates. By means of REA-PFGE a higher polymorphism, often related to the origin (winery) of strains, was revealed. However, on analyzing strains isolated from the same winery, only in some cases was more than one REA-PFGE pattern obtained. By analyzing dendrograms constructed on the basis of DD-PCR profiles differentiation of strains isolated from the same winery, in some cases, could be accomplished. The reliability of the DD-PCR in the differentiation of closely related strains suggests that this method could represent an alternative and/or additional tool to other molecular methods, such as REA-PFGE, for fine characterization of oenococcal strains.