An evaluation of chelex-based DNA purification protocols for the typing of lactic acid bacteria

Randomly-amplified microsatellite polymorphism for preliminary typing of lactic acid bacteria from Bryndza Cheese

A high-throughput, medium-discrimination method for preliminary typing and selecting non-identical isolates of lactic acid bacteria in cheeses was developed. RAMP, a PCR with one microsatellite-targeted and one random primer, was used for preliminary typing of 1119 isolates of lactic acid bacteria from Slovak Bryndza cheese. A total of 59 genotypes were identified based on RAMP profiles consisting of 12-23 DNA fragments of 150-3000 bp. For example, 18, 17, 13 and 7 different RAMP-types were identified in Lactobacillus brevis, L. plantarum, L. paracasei and L. fermentum, respectively. The method facilitated well reproducible, medium-discrimination typing of Lactobacillus spp. and Pediococcus spp. at a subspecies level and proved to be suitable for preliminary typing of lactic acid bacteria isolated from cheese.

Long-term Hg pollution-induced structural shifts of bacterial community in the terrestrial isopod (Porcellio scaber) gut

In previous studies we detected lower species richness and lower Hg sensitivity of the bacteria present in egested guts of Porcellio scaber (Crustacea, Isopoda) from chronically Hg polluted than from unpolluted environment. Basis for such results were further investigated by sequencing of 16S rRNA genes of mercury-resistant (Hgr) isolates and clone libraries. We observed up to 385 times higher numbers of Hgr bacteria in guts of animals from polluted than from unpolluted environment. The majority of Hgr strains contained merA genes. Sequencing of 16S rRNA clones from egested guts of animals from Hg-polluted environments showed elevated number of bacteria from Pseudomonas, Listeria and Bacteroidetes relatives groups. In animals from pristine environment number of bacteria from Achromobacter relatives, Alcaligenes, Paracoccus, Ochrobactrum relatives, Rhizobium/Agrobacterium, Bacillus and Microbacterium groups were elevated. Such bacterial community shifts in guts of animals from Hg-polluted environment could significantly contribute to P. scaber Hg tolerance.

Human TRAF3 adaptor molecule deficiency leads to impaired Toll-like receptor 3 response and susceptibility to herpes simplex encephalitis

Tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) functions downstream of multiple TNF receptors and receptors that induce interferon-α (IFN-α), IFN-β, and IFN-λ production, including Toll-like receptor 3 (TLR3), which is deficient in some patients with herpes simplex virus-1 encephalitis (HSE). Mice lacking TRAF3 die in the neonatal period, preventing direct investigation of the role of TRAF3 in immune responses and host defenses in vivo. Here, we report autosomal dominant, human TRAF3 deficiency in a young adult with a history of HSE in childhood. The TRAF3 mutant allele is loss-of-expression, loss-of-function, dominant-negative and associated with impaired, but not abolished, TRAF3-dependent responses upon stimulation of both TNF receptors and receptors that induce IFN production. TRAF3 deficiency is associated with a clinical phenotype limited to HSE resulting from the impairment of TLR3-dependent induction of IFN. Thus, TLR3-mediated immunity against primary infection by HSV-1 in the central nervous system is critically dependent on TRAF3.

Using oral microbial DNA analysis to identify expirated bloodspatter

Distinguishing expirated bloodstains (blood forced by airflow out of the nose, mouth or a chest wound) from impact spatter (blood from gunshots, explosives, blunt force trauma and/or machinery accidents) is an important challenge in forensic science. Streptococcal bacteria are only found in the human mouth and saliva. This study developed a polymerase chain reaction (PCR) method that detects DNA from these bacteria as a sensitive tool to detect the presence of saliva. The PCR method was very specific to human oral streptococci, with no PCR product being made from human DNA or DNA from other microbes that were tested. It was also very sensitive, detecting as little as 60 fg of target DNA. The PCR amplification gave product with 99 out of 100 saliva samples tested. PCR was not inhibited by the presence of blood and could detect target DNA in expirated bloodstains in a range of materials and for up to 92 days after deposit on cardboard or cotton fabric. In a blind trial, the PCR method was able to distinguish three mock forensic samples that contained expirated blood from four that did not. Our data show that bacteria present in the oral cavity can be detected in bloodstains that contain saliva and therefore can potentially be used as a marker in forensic work to distinguish mouth-expirated bloodstains from other types of bloodstains.

Lactobacillus plantarum bacteriophages isolated from Kefir grains: phenotypic and molecular characterization

Two greatly related Lactobacillus plantarum bacteriophages (named FAGK1 and FAGK2) were isolated from Kefir grains of different origins. Both phages belonged to the Siphoviridae family (morphotype B1) and showed similar dimensions for head and tail sizes. The host range of the two phages, using 36 strains as potential host strains, differed only in the phage reactivity against one of them. The phages showed latent periods of 30 min, burst periods of 80+/-10 min and burst size values of 11.0+/-1.0 PFU per infected cell as mean value. Identical DNA restriction patterns were obtained for both phages with PvuI, SalI, HindIII and MluI. The viral DNA apparently did not present extremes cos and the structural protein patterns presented four major bands (32.9, 35.7, 43.0 and 66.2 kDa). This study reports the first isolation of bacteriophages of Lb. plantarum from Kefir grains and adds further knowledge regarding the complex microbial community of this fermented milk.

Phage-resistance linked to cell heterogeneity in the commercial strain Lactobacillus delbrueckii subsp. lactis Ab1

The aim of this work was to study the relationship between the cell morphological heterogeneity and the phage-resistance in the commercial strain Lactobacillus delbrueckii subsp. lactis Ab1. Two morphological variants (named C and T) were isolated from this strain. Phage-resistant derivatives were isolated from them and the percentage of occurrence of confirmed phage-resistant cells was 0.001% of the total cellular population. Within these phage-resistant cell derivatives there were T (3 out of 4 total isolates) and C (1 out of 4 total isolates) variants. The study of some technological properties (e.g. proteolytic and acidifying activities) demonstrated that most of phage-resistant derivatives were not as good as the parental strain. However, for one derivative (a T variant), the technological properties were better than those of the parental strain. On the other hand, it was possible to determinate that the system of phage-resistance in the T variants was interference in adsorption step, with adsorption rates <15%. For the C variant derivative it was possible to demonstrate the presence of a restriction/modification system and, moreover, to determinate that this system could be Type I R/M.

Selective antimicrobial activity of maggots against pathogenic bacteria

Maggot therapy, also known as biosurgery, is an ancient method for the healing of chronic infected wounds. Although clinicians have reported on the beneficial activities of the Lucilia sericata larvae that have been used for healing chronic wounds, the selectivity of this therapy against the different pathogenic micro-organisms that are found in chronic wounds has never been analysed. In the present study, we have investigated the in vitro activities of larval excreta/secreta both against selected bacterial strains that frequently occur in chronically infected wounds, and against bacteria isolated directly from the larvae and their excreta/secreta. Additionally, the antibacterial activities were investigated in in vivo studies, by comparing bacterial diversity in wounds before and after the application of L. sericata larvae. In conclusion, larval therapy is highly recommended, particularly for the treatment of wounds infected with Gram-positive bacteria, like Staphylococcus aureus, but less so for wounds infected with Gram-negative bacteria, especially Proteus spp. and Pseudomonas spp. strains. Bacteria from the genus Vagococcus were resistant to the maggot excreta/secreta.

The use of a quantitative real-time polymerase chain reaction assay for identification and enumeration of Lactobacillus buchneri in silage

AIMS

To detect and quantify Lactobacillus buchneri in plant samples with the aid of polymerase chain reaction (PCR) methods.

METHODS AND RESULTS

DNA from silage samples spiked with different amounts of L. buchneri cells was isolated using a lysozyme/sodium dodecyl sulfate lysis and phenol/chloroform extraction method. The DNA served as a template for PCR amplification with primers specific for the bacterium. The primers were developed by comparison of 16S rDNA sequences from different lactic acid bacteria (LAB) and testing for specificity with 11 different strains of LAB. As few as 100 L. buchneri colony-forming units per gram of silage could be detected. Additionally, the technique was successfully applied to quantify the population of L. buchneri in two cultivars of corn with or without inoculation.

CONCLUSIONS

The PCR assay provided a specific and rapid tool for identifying and enumerating L. buchneri in silage samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of microbial inoculants for silage production is a safe and environment friendly practice, but the full potential of such additives can only be achieved with a better understanding of the fate and activity of the microbes involved. The current study describes a methodology to detect and enumerate L. buchneri, a micro-organism used as an inoculant.

Selection and use of autochthonous multiple strain cultures for the manufacture of high-moisture traditional Mozzarella cheese

Lactobacillus plantarum 18A, Lactobacillus helveticus 2B, Lactobacillus delbrueckii subsp. lactis 20F, Streptococcus thermophilus 22C, Enterococcus faecalis 32C and Enterococcus durans 16E were the most acidifying strains within 146 isolates for natural whey starters. The effect of media and temperature on 2 autochthonous multiple strain cultures (AMSI: 18A, 2B, 20F and 22C, 32C and 16E and AMSII: 18A, 2B, 20F and 22C) was studied. Genomic analysis showed a constant cell numbers for AMSII during 16 days of propagation in whey milk. Mozzarella cheese was made by using AMSII, commercial starter (CS) or citric acid (DA). Compared to other cheeses, the DA had a lower level of protein, ash, Ca, free amino acids and a higher level of moisture. Based on confocal laser scanning microscopy analysis, AMSII cheese showed the lowest microstructural variations during the period of storage compared to other cheeses. All the sensory attributes were scored highest for AMSII cheese. ASMII extend the shelf-life to ca. 12-15 days instead of the 5-7 days of traditional high-moisture Mozzarella cheese.

Spontaneous Lactobacillus delbrueckii phage-resistant mutants with acquired bile tolerance

Three commercial phage-sensitive strains of Lactobacillus delbrueckii (strains Ab(1), YSD V and Ib(3)) and four spontaneous phage-resistant mutants (strains A(7), A(17), V(2) and I(39)) isolated from them, all with a probiotic potential previously demonstrated were studied for their tolerance of bile salts (ox gall). Minimal Inhibitory Concentrations (MICs) ranged from 0.30% to 0.35% (w/v) of ox gall. These strains were exposed to gradually increasing concentrations of ox gall with the aim of isolating bile resistant derivatives. Stable derivatives able to tolerate up to 0.9% of ox gall were obtained from L. delbrueckii Ab(1), as well as from its spontaneous phage-resistant mutants A(7) and A(17). Random Amplified Polymorphic DNA (RAPD-PCR) analysis revealed a strong genetic homology between the ox gall-tolerant derivatives and their respective non-adapted original strains. These derivatives maintained, in general, the phage resistance phenotype of the non-adapted strains, with only one exception (phage-resistant mutant A(7)). After progressive ox gall adaptation, the phage-resistant mutant A(7) also exhibited progressive reversion of the phage resistance phenotype. The derivative with the highest ox gall-acquired tolerance (A(7)(0.9)) became sensitive to the phage, but derivatives with low (A(7)(0.3)) and intermediate (A(7)(0.6)) ox gall-acquired tolerance retained phage resistance. The technological properties of ox gall derivatives were comparable to those of their respective parent strains. However, the cells of the former were smaller than those of the original strains. Finally, the tolerant derivatives grew faster in the presence of ox gall than the parent strains. Our results demonstrated that it was possible to obtain, by a natural selection strategy, probiotic strains with acquired ox gall-tolerance from three (L. delbrueckii Ab(1) and their phage-resistant mutants A(7) and A(17)) of seven tested strains. Since such derivatives keep both phage resistance and other useful technological properties, they could be used for production of functional foods.

Molecular identification and typing of natural whey starter cultures and microbiological and compositional properties of related traditional Mozzarella cheeses

Cell numbers of presumptive lactic acid bacteria varied markedly between 7 natural whey starter cultures (NWSC) used for producing traditional cows' milk Mozzarella cheeses in the Apulia region of Southern Italy. Taxonomic identification revealed a large diversity at species level, including mesophilic and thermophilic lactobacilli, lactococci, streptococci and enterococci. Randomly Amplified Polymorphic DNA (RAPD-PCR), analysis showed the biodiversity among the strains and, for lactobacilli, some relationships with provenience of the natural starter. Cell numbers of presumptive lactic acid bacteria in the corresponding Mozzarella cheeses were similar or higher than those found in the corresponding NWSC. RAPD-PCR analyses showed that most of the strains in cheese originated from the starter. The gross composition varied markedly between the 7 Mozzarella cheeses and ranged from 53-64% moisture, 17-23% protein, 13-20% fat and 0.50-1.61% salt. The values of pH for several samples were above 6.0. As shown by urea-PAGE of the pH 4.6-insoluble nitrogen fractions, cheese samples were characterized by differences in alpha(S1)- and beta-casein hydrolysis. Cheeses also differed with respect to secondary proteolysis as shown by Principal Component Analysis (PCA) of data from RP-HPLC of the pH 4.6-soluble, pH 4.6-70% ethanol-soluble and 70% ethanol-insoluble nitrogen fractions. These differences were attributed to the different microbial composition of the NWSC. Strain selection and optimization of a protocol for producing a natural whey starter culture to be used by dairy factories of the Apulia region appears to be a pre-requisite to standardize the major traits distinguishing this cheese variety.

Characterization of Italian cheeses ripened under nonconventional conditions

Four Italian cheeses (Casciotta di Urbino, Barricato San Martino, Vento d'Estate, and Ubriaco di Raboso) nonconventionally ripened under different plant materials (walnut leaves, herbs, hay, and wine by-products, respectively) were compared for compositional, microbiological, biochemical, and volatile profile characteristics. Mean values for gross composition were rather similar. Because primary starters were not used for manufacture, the endogenous lactic acid bacteria were mainly present (7.0 to 9.0 log10 cfu/g). Except for Lactobacillus paracasei and Leuconostoc mesenteroides, which were commonly identified in 3 cheeses, Lactococcus lactis, Enterococcus sanguinicola, Lactobacillus brevis, Enterococcus durans/Enterococcus faecium, Lactobacillus plantarum, and Weissella cibaria/Weissella confusa were variously found in the 4 cheeses. Random amplification of polymorphic DNA-PCR analysis showed the biodiversity among the strains, and the species of lactobacilli were in part grouped according to their origin. As shown by the principal component analysis of reverse-phase fast protein liquid chromatography data for the pH 4.6-soluble fractions and by the determination of free AA, the secondary proteolysis of Barricato San Martino and Vento d'Estate mainly differed from the other 2 cheeses. Purge-and-trap and solid-phase microextraction were coupled with gas chromatography-mass spectrometry to determine volatile compounds. Vento d'Estate showed the highest levels of almost all chemical classes, and Casciotta di Urbino was characterized by a very low level of volatile components. Esters, ketones, and terpenes were the chemical classes that mainly differentiated the cheeses. Several volatile compounds seemed to be released directly from the plant materials used for ripening, especially terpenes for Vento d'Estate cheese. The lowest level of volatile free fatty acids was found in Casciotta d'Urbino, in which rennet paste was not used during manufacture. The highest concentration of free fatty acids, especially butyric and caproic acids, was found in Vento d'Estate cheese.

Phage-resistant mutants of Lactobacillus delbrueckii may have functional properties that differ from those of parent strains

Three commercial phage sensitive Lactobacillus delbrueckii strains (identified as Ab(1), YSD V and Ib(3)), and four spontaneous phage-resistant mutants isolated from them were tested for their capacity to activate the gut mucosal immune response in mice, as indicated by the numbers of IgA-producing cells. Random Amplified Polymorphic DNA (RAPD) analysis revealed a strong genetic homology between the sensitive strains and their respective derivatives. The phage-resistant mutants exhibited high levels of phage resistance, elevated stability of this phenotype and technological properties comparable to those of their respective parent strains. The tolerance to acidic conditions, bile salts and lysozyme was strain dependent and total cell viability losses as a result of exposure to all three stresses ranged from 2.0 to 3.7 log units. All the strains were highly resistant to a simulated gastric solution of pH 3, while significant additional losses in cell viability were observed when acid treated cells were exposed to bile salts and lysozyme. BALB/c mice received pure cultures of Lb. delbrueckii sensitive and phage-resistant strains for 2, 5 or 7 consecutive days. The ability of the parent strains to activate the small intestine immune response was preserved or enhanced in phage-resistant mutants. The maximal proliferation of IgA(+) cells was observed at day 5 or 7, depending on the strain. Mutants isolated in this study using natural selection strategies had improved phage resistance, adequate technological properties and satisfactory gut mucosal immunostimulation ability, and so would be good candidates for industrial applications in functional foods.

The feasibility of storing ovarian tumor cells on databasing paper: establishing a library of ovarian cancer DNA

The purpose of this study was to assess the feasibility of establishing a library of ovarian cancer nucleic acids using paper matrix by: 1) confirming the stability of DNA stored on paper matrix over a prolonged period of time, 2) determining the amount of genetic material required for storage, and 3) establishing the stability of RNA. Tumor tissue from 66 patients with ovarian cancer was collected intraoperatively, frozen, and dissociated with collagenase and trypsin. A cell suspension was then prepared and spotted onto the paper. The numbers of cells that were stored on the paper were counted using a hemocytometer. The cell suspension was serially diluted and spotted on the paper matrix until the minimum cell number that can be stored and produce a PCR product was determined. PCR, STR genotyping and direct sequencing were performed on tissue stored on the paper matrix. FTA® paper was used as RNA template, and RT PCR converted the RNA to cDNA. Ten to 50 mg of ovarian cancer tissue was stored on FTA® paper. We stored 7 × 104cells on ISOcode® paper and 18 × 104cells on FTA® and obtained extractable DNA. PCR analysis on cards with DNA stored 18 months ago enabled us to establish the stability of DNA after storage. RNA was stable for 6 months when stored on FTA® cards. Since genetic material is extractable from the paper matrices after passage of time, it could be a suitable medium for the storage of genetic material in cancer tissue banks.

Identification of genetic differences between two clinical isolates of Streptococcus mutans by suppression subtractive hybridization

Streptococcus mutans is generally considered to be the principal aetiological agent for dental caries. Phenotypic variation in strains is often associated with differences in gene content, so the isolation of DNA fragments from these genes or associated regions is illuminating. The S. mutans strains 9-1 and 9-2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. Genomic DNA of strain 9-1 was used as the tester, and that of 9-2 was used as the driver. Suppression subtractive hybridization (SSH) was applied between the tester and the driver DNAs. The subtractive products were cloned into a pCR2.1 vector. Clone libraries representing sequence differences were obtained. The subtractive fragments that were found specifically in strain 9-1 but not in strain 9-2 were identified by dot blotting and then sequenced. BLASTn and BLASTx sequence homology analyses were subsequently performed. Twenty-seven sequences were found in the genome of strain 9-1 that were not in 9-2. Among them, three revealed no homology to published nucleotide sequences while the remaining sequences showed 81-100% homology to known genes of S. mutans strain UA159. These sequences are involved in competence development, signal transduction and transcriptional regulation, repairing stress damage, transport, carbohydrate catabolism, biochemical synthesis, or unknown functions. Differences exist in the genomes of different S. mutans isolates. SSH is effective in screening for S. mutans strain specific DNA sequences.

Comparison of the Compositional, Microbiological, Biochemical, and Volatile Profile Characteristics of Nine Italian Ewes’ Milk Cheeses

Nine Italian ewes' milk cheeses were compared for compositional, microbiological, biochemical, and volatile profile characteristics. Mean values for the gross composition were rather similar among cheeses. The lowest pH values were found for cheeses that used primary starters. At the end of ripening, cheeses made from raw milk contained >6.0 log10 cfu/g of nonstarter lactic acid bacteria. Several species of lactobacilli were identified, but Lactobacillus plantarum and Lactobacillus paracasei were dominant. Random amplified polymorphic DNA-PCR analysis showed the biodiversity among the strains, and in several cases a relationship with the cheese of provenance. Cheeses differed mainly for secondary proteolysis, as shown by the principal component analysis applied to reversed-phase fast protein liquid chromatography data of the pH 4.6-soluble fractions and by determination of the free AA. A total of 113 volatile components were identified in the Italian Pecorino cheeses by solid-phase microextraction coupled with gas chromatography-mass spectrometry analysis. The volatile profiles of the 9 cheeses differed significantly. Quantitatively, alcohols were the most abundant chemical class for some cheeses, whereas ketones were the most abundant for other cheeses. Esters and carboxylic acids were largely found. Specific volatile components seemed to distinguish specific cheeses.

Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases

About a thousand lactic acid bacteria (LAB) isolated from dairy products, especially cheeses, were identified and typed by species-specific PCR and RAPD-PCR, respectively. RAPD-PCR profiles, which were obtained by using the M13 sequence as a primer, allowed us to implement a large database of different fingerprints, which were analysed by BioNumerics software. Cluster analysis of the combined RAPD-PCR fingerprinting profiles enabled us to implement a library, which is a collection of library units, which in turn is a selection of representative database entries. A library unit, in this case, can be considered to be a definable taxon. The strains belonged to 11 main RAPD-PCR fingerprinting library units identified as Lactobacillus casei/paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus helveticus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus brevis, Enterococcus faecium, Enterococcus faecalis, Streptococcus thermophilus and Lactococcus lactis. The possibility to routinely identify newly typed, bacterial isolates by consulting the library of the software was valued. The proposed method could be suggested to refine previous strain identifications, eliminate redundancy and dispose of a technologically useful LAB strain collection. The same approach could also be applied to identify LAB strains isolated from other food ecosystems.

Typing of Mutans Streptococci by Arbitrarily Primed PCR in Patients Undergoing Orthodontic Treatment

The aim of this study was to clarify the genotypic stability of mutans streptococci (MS) longitudinally during orthodontic treatment. Plaque samples were obtained from the supragingival smooth surface of the upper right teeth at four stages: prior to and after 1, 3 and 6 months of orthodontic treatment. Levels of total viable count, total streptococci and MS in dental plaque of 17 patients were recorded. Streptococci isolated from dental plaque samples were identified as MS on the basis of their morphological and biochemical properties. DNA was prepared from 713 strains of MS and the strains were then identified with polymerase chain reaction (PCR) again. Arbitrarily primed PCR (AP-PCR) fingerprinting was applied in determining the genotypes of MS. The results indicated that levels of total viable count, total streptococci and MS increased significantly after the fixed appliances were bonded. A maximum of 3 different genotypes were found in an individual. All the genotypes were found again after the application of the fixed appliances in 17 patients. A new AP-PCR typing pattern was found after the application of fixed appliances for 1 month in patient 1. That strain was not detected either prior to or after 3, or 6 months of treatment. The result indicated that the MS clones were very stable during orthodontic treatment.

Soluble transition metals cause the pro-inflammatory effects of welding fumes in vitro

Epidemiological studies have consistently reported a higher incidence of respiratory illnesses such as bronchitis, metal fume fever (MFF), and chronic pneumonitis among welders exposed to high concentrations of metal-enriched welding fumes. Here, we studied the molecular toxicology of three different metal-rich welding fumes: NIMROD 182, NIMROD c276, and COBSTEL 6. Fume toxicity in vitro was determined by exposing human type II alveolar epithelial cell line (A549) to whole welding fume, a soluble extract of fume or the "washed" particulate. All whole fumes were significantly toxic to A549 cells at doses >63 microg ml(-1) (TD 50; 42, 25, and 12 microg ml(-1), respectively). NIMROD c276 and COBSTEL 6 fumes increased levels of IL-8 mRNA and protein at 6 h and protein at 24 h, as did the soluble fraction alone, whereas metal chelation of the soluble fraction using chelex beads attenuated the effect. The soluble fraction of all three fumes caused a rapid depletion in intracellular glutathione following 2-h exposure with a rebound increase by 24 h. In addition, both nickel based fumes, NIMROD 182 and NIMROD c276, induced significant reactive oxygen species (ROS) production in A549 cells after 2 h as determined by DCFH fluorescence. ICP analysis confirmed that transition metal concentrations were similar in the whole and soluble fractions of each fume (dominated by Cr), but significantly less in both the washed particles and chelated fractions. These results support the hypothesis that the enhanced pro-inflammatory responses of welding fume particulates are mediated by soluble transition metal components via an oxidative stress mechanism.

Extracción de adn con resina chelex en el análisis de la amplificación oncogénica en carcinomas de cabeza y cuello

DNA extraction from tissues can be the most laborious and complex step in amplifying DNA by PCR when phenol-choroform procedure is used. We compare this lengthy, slow and expensive extraction method with other two based in the use of Chelex-100 resin. This chelating resin has been applied for extracting DNA from different tissues to use with the PCR. These procedures are simple, rapid and do not require multiple steps. In this study we compared DNA extraction from 30 head and neck squamous cell carcinomas (HNSCC) using organic solvent precipitation, Chelex 100 resin with and without proteinase K pretreatment. The results show that proteinase K-Chelex 100 procedure is as efficient as the phenol-chloroform one.

Molecular typing of Lactobacillus delbrueckii of dairy origin by PCR-RFLP of protein-coding genes

Thirty-five strains of Lactobacillus delbrueckii subsp. lactis and subsp. bulgaricus isolated from dairy products were typed by restriction fragment length polymorphism (RFLP) of protein-coding genes. The strains were analysed by RFLP of PCR amplified, infragenic fragments of the following housekeeping genes: beta-galactosidase, lactose permease, and proline dipeptidase. Sequencing of the variable regions of the 16S rDNA was then performed on a reduced number of strains. PCR-RFLP analysis evidenced wide strain heterogeneity. Strains were grouped into genotypes according to both subspecies assignment and infra-species genetic polymorphism. This polymorphism was related to the presence of microbial groups within subspecies populations. The low infra-species sequence polymorphism detected in the variable region of the 16S rRNA gene did not enable to group the strains with the same sensitivity reached by PCR-RFLP of protein-coding genes. PCR-RFLP of protein-coding genes applied to L. delbrueckii seems a promising tool to evaluate microbial diversity within bacterial subpopulations. Differences among bacterial subpopulations based upon molecular heterogeneity in protein-coding genes would enable to better understand the role of strains from different ecological niches.

Selection and identification of a Listeria monocytogenes target strain for pulsed electric field process optimization

Nine Listeria monocytogenes strains were treated individually with a continuous pulsed electric field (PEF) apparatus, and their sensitivities to the treatment were compared at 25 kV/cm. When cell suspensions of these strains in 0.1% NaCl (pH 7.0) were treated at 23 degrees C for 144 micro s, inactivation ranged from 0.7 to 3.7 log(10) CFU/ml. Inactivation by 72- micro s PEF treatments at 37 degrees C ranged from 0.3 to 2.5 log(10) CFU/ml. L. monocytogenes OSY-8578 was substantially more resistant than other strains when cells were PEF treated in 0.1% NaCl, whereas Scott A was one of the most sensitive strains. The superiority of OSY-8578's resistance to that of Scott A was confirmed in 50% diluted acid whey (pH 4.2). Changes in sensitivity to PEF during phases of growth were minimal in OSY-8578 and substantial in Scott A. Use of L. monocytogenes OSY-8578, therefore, is recommended in studies to optimize PEF processes that target L. monocytogenes. The nine L. monocytogenes strains were genotyped with pulsed-field gel electrophoresis (PFGE) and arbitrarily primed PCR (AP-PCR) techniques. These strains were better differentiated with PFGE than with AP-PCR. The target strain (OSY-8578) was characterized by both molecular typing techniques, but resistance to PEF, in general, was not associated with a particular genotype group.

Genotypic and phenotypic heterogeneity of Streptococcus thermophilus strains isolated from dairy products

AIMS

Forty strains of Streptococcus thermophilus isolated from dairy products were identified and typed by a polyphasic approach which included phenotypic and genotypic criteria.

METHODS AND RESULTS

Strains were identified by sugar fermentation pattern and species-specific PCR. Phenotypic diversity was evaluated by a chemometric model taking into account some biochemical characteristics (e.g. acidifying and peptidase activities) of technological interest. Genotypic diversity was evidenced by PCR fingerprinting. The overall phenotypic and genotypic information was elaborated on a multivariate statistical basis by principal components analysis and cluster analysis, respectively. When acidifying and peptidase activities were considered, PCA indicated that most of the strains isolated from Pecorino Toscano cheese were separable from the others. Similarly, most of the starter culture strains tended to separate from the cheese isolates.

CONCLUSIONS

A wide strain heterogeneity among Strep. thermophilus strains isolated from dairy products was observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

A computerized analysis of genotypic and phenotypic information could be applied successfully to differentiate and characterize reliably and rapidly isolates occurring in different dairy products and to comprehend the technological role of specific Strep. thermophilus strains in dairy technology.