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

Evaluation of genetic polymorphism among Lactobacillus rhamnosus non-starter Parmigiano Reggiano cheese strains

Parmigiano Reggiano (PR) is an Italian cooked, long-ripened cheese made with unheated cow's milk and natural whey starter. The microflora is involved in the manufacturing of this cheese, arising from the natural whey starter, the raw milk and the environment. Molecular studies have shown that mesophilic non-starter lactic acid bacteria (NSLAB) are the dominant microflora present during the ripening of PR. In this study, a characterisation of Lactobacillus rhamnosus isolated from a single PR manufacturing and ripening process is reported, using a combination of genotypic fingerprinting techniques (RAPD-PCR and REP-PCR). The intraspecies heterogeneity evidenced for 66 strains is correlated to their abilities to adapt to specific environmental and technological conditions. The detection of biotypes that correlate with specific moments in cheese ripening or differential development throughout this process suggests that these strains may have specific roles closely linked to their peculiar technological properties.

Synthesis of isoflavone aglycones and equol in soy milks fermented by food-related lactic acid bacteria and their effect on human intestinal Caco-2 cells

One hundred and three strains of lactic acid bacteria, isolated from various food ecosystems, were assayed for β-glucosidase activity toward p-nitrophenyl-β-D-glucopyranoside substrate. Lactobacillus plantarum DPPMA24W and DPPMASL33, Lactobacillus fermentum DPPMA114, and Lactobacillus rhamnosus DPPMAAZ1 showed the highest activities and were selected as the mixed starter to ferment various soy milk preparations, which mainly differed for chemical composition, protein dispersibility index, and size dimension. The soy milk made with organically farmed soybeans (OFS) was selected as the best preparation. All selected strains grew well in OFS soy milk, reaching almost the same values of cell density (ca. 8.5 log cfu/mL). After 96 h of fermentation with the selected mixed starter, OFS soy milk contained 57.0 μM daidzein, 140.3 μM genistein, 20.4 μM glycitein, and 37.3 μM equol. Fermented and nonfermented OFS soy milks were used for the in vitro assays on intestinal human Caco-2/TC7 cells. Fermented OFS soy milk markedly inhibited the inflammatory status of Caco-2/TC7 cells as induced by treatment with interferon-γ (IFN-γ) (1000 U/mL) and lipopolysaccharide (LPS) (100 ng/mL), maintained the integrity of the tight junctions, even if subjected to negative stimulation by IFN-γ, and markedly inhibited the synthesis of IL-8, after treatment with interleukin-1β (2 ng/mL). As shown by using chemical standards, these effects were due to the concomitant activities of isoflavone aglycones and, especially, equol, which were synthesized in the fermented OFS soy milk preparation.

Evaluation of virulence factor profiling in the characterization of veterinary Escherichia coli isolates

Escherichia coli has been used as an indicator organism for fecal contamination of water and other environments and is often a commensal organism in healthy animals, yet a number of strains can cause disease in young or immunocompromised animals. In this study, 281 E. coli isolates from bovine, porcine, chicken, canine, equine, feline, and other veterinary sources were analyzed by BOXA1R PCR and by virulence factor profiling of 35 factors to determine whether they had utility in identifying the animal source of the isolates. The results of BOXA1R PCR analysis demonstrated a high degree of diversity; less than half of the isolates fell into one of 27 clusters with at least three isolates (based on 90% similarity). Nearly 60% of these clusters contained isolates from more than one animal source. Conversely, the results of virulence factor profiling demonstrated clustering by animal source. Three clusters, named Bovine, Chicken, and Porcine, based on discriminant components analysis, were represented by 90% or more of the respective isolates. A fourth group, termed Companion, was the most diverse, containing at least 84% of isolates from canine, feline, equine, and other animal sources. Based on these results, it appears that virulence factor profiling may have utility, helping identify the likely animal host species sources of certain E. coli isolates.

Characterisation of Lactobacillus helveticus strains producing antihypertensive peptides by RAPD and inverse-PCR of IS elements

Lactobacillus helveticus is used for the manufacture of cheeses and milk-based products. Although it is not considered a probiotic microorganism, some strains demonstrated beneficial effects through the production of antihypertensive peptides from the hydrolysis of casein during milk fermentation. Strain-specificity of bioactive peptide production by L. helveticus makes the availability of reliable typing methods essential for both legal and good manufacturing processes. Accordingly, RAPD and inverse-PCR of five insertion sequence elements were comparatively evaluated for the molecular characterisation of four L. helveticus dairy cultures producing antihypertensive peptides and fourteen reference strains. Calculation of discriminatory indices and cluster analysis of the DNA fingerprints confirmed the suitability of both approaches for acceptable strain differentiation. Although RAPD was more discriminating, for a few test strains a neat discrimination was only achieved through multiplex inverse-PCR, thus suggesting the suitability of a combined analytical approach for a finer strain discrimination.

Species and strain identification of lactic acid bacteria using FTIR spectroscopy and artificial neural networks

Lactic acid bacteria (LAB) are a heterogeneous group of micro-organisms with high relevance for fermented food and beverages as well as human and animal health. Identification of LAB is complicated by species richness, a high degree of heterogeneity between species and the presence of very closely related species at the same time. In the present study we developed identification systems based on FTIR spectra and artificial neural networks (ANNs) for species identification of 92 LAB species out of nine genera and strain identification of probiotic and environmental Enterococcus faecium strains used as additives for animal feed. The reference databases established in this work permit reliable identification of LAB with accuracies of 93.2% at species and 97.1% at strain level for Ec. faecium, demonstrating the excellent suitability of FTIR spectroscopy as a technique applicable for simultaneous species and strain identification.

Comparative evaluation of automated ribotyping and RAPD-PCR for typing of Lactobacillus spp. occurring in dental caries

A group of 67 Lactobacillus spp. strains containing Lactobacillus casei/paracasei, Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus rhamnosus and Lactobacillus salivarius species isolated from early childhood caries and identified to the species level in a previous study (Svec et al., Folia Microbiol 54:53-58, 2009) was characterized by automated ribotyping performed by the RiboPrinter microbial characterization system and by randomly amplified polymorphic DNA fingerprinting (RAPD-PCR) with M13 primer to evaluate these techniques for characterization of lactobacilli associated with dental caries. Ribotyping revealed 55 riboprints among the analysed group. The automatic identification process performed by the RiboPrinter system identified 18 strains to the species level, however cluster analysis divided obtained ribotype patterns into individual clusters mostly corresponding to the species assignment of particular strains. RAPD-PCR fingerprints revealed by the individual Lactobacillus spp. showed higher variability than the ribotype patterns and the fingerprint profiles generated by the analysed species were distributed among one to four clusters. In conclusion, ribotyping is shown to be more convenient for the identification purposes while RAPD-PCR fingerprinting results indicate this method is a better tool for typing of Lactobacillus spp. strains occurring in dental caries.

Intra- and interspecies conjugal transfer of Tn916-like elements from Lactococcus lactis in vitro and in vivo

Tetracycline-resistant Lactococcus lactis strains originally isolated from Polish raw milk were analyzed for the ability to transfer their antibiotic resistance genes in vitro, using filter mating experiments, and in vivo, using germfree rats. Four of six analyzed L. lactis isolates were able to transfer tetracycline resistance determinants in vitro to L. lactis Bu2-60, at frequencies ranging from 10(-5) to 10(-7) transconjugants per recipient. Three of these four strains could also transfer resistance in vitro to Enterococcus faecalis JH2-2, whereas no transfer to Bacillus subtilis YBE01, Pseudomonas putida KT2442, Agrobacterium tumefaciens UBAPF2, or Escherichia coli JE2571 was observed. Rats were initially inoculated with the recipient E. faecalis strain JH2-2, and after a week, the L. lactis IBB477 and IBB487 donor strains were introduced. The first transconjugants were detected in fecal samples 3 days after introduction of the donors. A subtherapeutic concentration of tetracycline did not have any significant effect on the number of transconjugants, but transconjugants were observed earlier in animals dosed with this antibiotic. Molecular analysis of in vivo transconjugants containing the tet(M) gene showed that this gene was identical to tet(M) localized on the conjugative transposon Tn916. Primer-specific PCR confirmed that the Tn916 transposon was complete in all analyzed transconjugants and donors. This is the first study showing in vivo transfer of a Tn916-like antibiotic resistance transposon from L. lactis to E. faecalis. These data suggest that in certain cases food lactococci might be involved in the spread of antibiotic resistance genes to other lactic acid bacteria.

Application of AFLP fingerprint analysis for studying the biodiversity of Streptococcus thermophilus

Streptococcus thermophilus is a lactic acid bacteria (LAB) widely used in milk fermentation processes as a starter culture. In this work the genetic diversity of S. thermophilus isolates from different sources was analyzed using Amplified Fragment Length Polymorphism fingerprinting (AFLP). Since this is the first report that indicates the application of AFLP in order to study genotypic polymorphism in S. thermophilus species, an optimization of experimental conditions was carried out to decide the optimal AFLP analysis protocol. Furthermore the fingerprinting resolutions of AFLP and RAPD (Random Amplified Polymorphic DNA) were evaluated and compared. The overall data suggest that genotypic characterization performed by AFLP provide a better view of microbial diversity of S. thermophilus, indicating that RAPD is less discriminating than AFLP. The successful use of AFLP analysis in the characterization of S. thermophilus strains reported in this study suggests the potential uses for this technique to define the whole-genome diversity of each specific strain, as an alternative to the fingerprinting methods used till now.

Spelt and emmer flours: characterization of the lactic acid bacteria microbiota and selection of mixed starters for bread making

AIMS

This study aimed at characterizing the lactic acid bacteria microbiota and selecting mixed endogenous starters to be used for sourdough fermentation of spelt or emmer flours.

METHODS AND RESULTS

Identification of lactic acid bacteria was carried out by partial sequencing of the 16S rRNA, recA, 16S/23S rRNA spacer region and pheS genes. Spelt flour showed the largest biodiversity, while Lactobacillus plantarum dominated in emmer flour. Isolates were subjected to RAPD-PCR analysis and screened based on the kinetics of growth and acidification, quotient of fermentation and liberation of free amino acids (FAA) during sourdough fermentation. After selection, mixed starters were used according to a two-step fermentation process. Wheat flour was fermented by the same starters. Spelt and emmer sourdoughs had slightly higher pH than wheat sourdoughs but titratable acidity, concentration of FAA and phytase activity were higher. Specific volume and crumb grain of emmer and, especially, spelt breads approached those of wheat breads. Sensory analysis confirmed the suitability of spelt and emmer for bread making.

CONCLUSIONS

The sourdough biotechnology was indispensable to completely exploit the potential of spelt and emmer flours.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results filled up the lack of knowledge on the lactic acid bacteria microbiota and technological performances of spelt and emmer flours.

Dynamics of whole and lysed bacterial cells during Parmigiano-Reggiano cheese production and ripening

Microbial succession during Parmigiano-Reggiano cheesemaking was monitored by length heterogeneity PCR (LH-PCR), considering the intact and lysed cells at different stages of cheese production and ripening. When starter species underwent autolysis, species coming from milk were able to grow. For the first time, the LH-PCR technique was applied to study a fermented food.

Selection and use of autochthonous mixed starter for lactic acid fermentation of carrots, French beans or marrows

Strains of Leuconostoc mesenteroides, Lactobacillus plantarum, Weissella soli/Weissella koreensis, Enterococcus faecalis, Pediococcus pentosaceus and Lactobacillus fermentum were identified from raw carrots, French beans and marrows by partial 16S rRNA gene sequence. L. plantarum M1, Leuc. mesenteroides C1 and P. pentosaceus F4 were selected based on the rates of growth and acidification in vegetable juice media, and used as the autochthonous mixed starter for the fermentation of carrots, French beans or marrows. An allochthonous starter, consisting of the same species, was also used for fermentation. A two-step fermentation process (1 day at 25 degrees C and 7 days at 15 degrees C) in brine (1% w/v) followed by storage at room temperature in olive oil until 40 days was set up. Unstarted vegetables subjected to the same treatments were used as the controls. Cell numbers of lactic acid bacteria in the started vegetables were ca. 10,000 (autochthonous starter) and 1000 (allochthonous starter) times higher than unstarted samples throughout the process. When fermented with the autochthonous starter, carrots, French beans or marrows were characterized by the rapid decrease of pH (<4.5), marked consumption of fermentable carbohydrates, and inhibition of Enterobacteriaceae and yeasts. Fermentation with the allochthonous starter did not acidify and inhibit bacteria and yeasts so rapidly. After 40 days, carrots, French beans and marrows fermented with the autochthonous starter had significantly (P<0.05) higher total concentration of vitamin C (ascorbate+dehydroascorbate) with respect to those fermented with the allochthonous starter and, especially unstarted vegetables. The same was found for the indexes of color. Firmness of both started vegetables was higher than unstarted vegetables. Sensory analysis differentiated started vegetables. Carrots and French beans fermented with the autochthonous starter were, especially, appreciated for fragrance. Appearance was the sensory attribute that mainly distinguished marrows fermented with the autochthonous starter.

Phenotypic and genotypic heterogeneity of Enterococcus species isolated from food in Southern Brazil

Enterococcus is an important group of lactic acid bacteria (LAB), which inhabits the gastrointestinal tract of humans and animals. These microorganisms can also be found in large groups of foods where they can play a beneficial role during food maturation processes or, conversely, can be used as a food contamination indicator. These microorganisms have an additional importance in various aspects of clinical microbiology. The aim of this study was to investigate and determine the phenotypic and genetic diversity in 55 enterococci isolated from different food sources. Phenotypic characteristics based upon substrate hydrolysis differences were used to identify different Enterococcus species. Analysis of the resultant data divided these species into eight Enterococcus phenotype groups. E. faecalis was the food isolate species with the greatest phenotypic variability. Fifty-five previously isolated Enterococcus strains were re-confirmed as belonging to this genus by PCR techniques. Randomly amplified polymorphic DNA (RAPD-PCR) was used to study the genetic variability using M13 primers and the resultant DNA fragments produced a database of different fingerprints. After statistical analyses of the RAPD-PCR profiles, 42 patterns were obtained and 6 different Enterococcus RAPD clusters (ERC) were identified. Genetic diversity was highest in ERC I, which grouped together approximately 40% of the E. faecium and E. faecalis isolates obtained from dairy products. Samples isolated from meat and vegetables offered the greatest genotype variability. Results of the present study suggest the presence of both phenotypic and genotypic variability within enterococci strains isolated from diverse sources of food common to Southern Brazil.

Incidence of antibiotic resistance and virulence determinants among Enterococcus italicus isolates from dairy products

The main objective of this work was to investigate the biosafety of Enterococcus italicus, a recently described enterococcal species widely diffused in dairy products. For this purpose, the antibiotic susceptibility and the incidence of virulence factors among 30 E. italicus isolates originating mainly from different Italian cheeses were tested. Although not all 30 isolates showed unique genotypes, PCR fingerprinting evidenced a notable genotypic diversity among the E. italicus collection under study. All isolates were susceptible to vancomycin, gentamicin, erythromycin, ampicillin, chloramphenicol and bacitracin. Five isolates corresponding to three unique genotypes exhibited phenotypic resistance to tetracycline with MICs ranging from 64-256mug/ml. By PCR-based detection, the genetic basis of the Tet(R) phenotype in these strains was linked to the tet(S) gene whereas detection of tet(L) and tet(M) genes and the integrase element int of the Tn916/Tn1545 family of transposons were negative. Likewise, none of the strains appeared to contain any of the tested virulence genes gelE, asaI, cpd, agg, cylA, cylB, cylM, ace and hyl(Efm). The results of this study warrant further research into the environmental dissemination of Tet(R)E. italicus and into the potential transferability of its tet(S) genes.

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.

Nonstarter lactobacilli isolated from soft and semihard Argentinean cheeses: genetic characterization and resistance to biological barriers

Nonstarter lactic acid bacteria isolated from Argentinean cheeses were identified and characterized by focusing on their resistance to biological barriers, along with other physiological features of potential interest, in the search for future probiotic organisms. Lactobacilli were enumerated and isolated from semihard and soft cheeses made with multistrain Streptococcus thermophilus starters. Lactobacilli counts in 1-week-old cheeses were between 10(5) and 10(7) CFU/g and then reached 10(7) CFU/ g in all 1-month samples, while streptococci were always above 10(9) CFU/g. A total number of 22 lactobacilli isolates were retained, identified, and characterized by in vitro tests. Species identity was determined by carbohydrate metabolism and species-specific PCR assays. Genetic diversity was explored by random amplified polymorphic DNA (RAPD) PCR analysis. The Lactobacillus strains were assigned to the species L. casei, L. plantarum, L. rhamnosus, L. curvatus, L. fermentum, and L. perolens. All the strains studied tolerated 25 ppm of lysozyme, and most of them showed resistance to 0.3% bile. After incubation in gastric solution (pH 2.0), counts decreased by several log units, ranging from 3.2 to 7.0. The strains were able to grow in the presence of bile salts, but only three isolates were capable of deconjugation. The nonstarter lactobacilli that were assayed fermented the prebiotic substrates (especially lactulose and inulin). Some strains showed high cell hydrophobicity and beta-galactosidase activity, as well as inhibitory activity against pathogenic bacteria. It was concluded that most of the lactobacilli isolated in this study demonstrated resistance to biological barriers and physiological characteristics compatible with probiotic properties, which make them suitable for further research in in vivo studies aimed at identifying new probiotic organisms.

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.

Beneficial lactobacilli in food and feed: long-term use, biodiversity and proposals for specific and realistic safety assessments

Lactobacilli have played a crucial role in the production of fermented products for millennia. Their probiotic effects have recently been studied and used in new products. Isolated cases of lactobacillemia have been reported in at-risk populations, but lactobacilli present an essentially negligible biological risk. We analyzed the current European guidelines for safety assessment in food/feed and conclude that they are not relevant for the Lactobacillus genus. We propose new specific guidelines, beginning by granting a 'long-standing presumption of safety' status to Lactobacillus genus based on its long history of safe use. Then, based on the available body of knowledge and intended use, only such tests as are useful will be necessary before attributing 'qualified presumption of safety' status.