Comparison of the use of rRNA probes and conventional methods in identifying strains of Lactobacillus sake and L. curvatus isolated from meat

Use of PCR primers and probes based on the 23S rRNA and internal transcription spacer (ITS) gene sequence for the detection and enumerization of Lactobacillus acidophilus and Lactobacillus plantarum in feed supplements

Novel polymerase chain reaction (PCR) primers designed from the 16S-23S internal transcription spacer (ITS) rRNA and 23S rRNA genes, respectively, were used for the specific detection of Lactobacillus acidophilus and Lactobacillus plantarum. Molecular weights of the PCR products were 221 and 599 bp, respectively. Strains of L. acidophilus and L. plantarum obtained from the culture center, dairy products, infant stool and other samples, could be identified with these PCR primers. DNAs from other lactic acid bacteria (LAB) species including strains of Lactobacillus pentosus which was closely related to L. plantarum, and bacteria species other than LAB, would not generate the false positive results. When this PCR primer set was used for the detection of L. acidophilus and L. plantarum in feed supplement or feed starter samples, reliable results were obtained. Furthermore, when these L. acidophilus or L. plantarum specific primers were used as DNA probes for the colony hybridization of L. acidophilus and L. plantarum, the viable cells of these LAB species in culture and feed supplements or starter products could be identified and enumerized. The method described here thus offers a rapid and economic way to inspect and assure the quality of the feed supplements or fermentation starters.

Identification of lactic acid bacteria involved in the spoilage of pasteurized "foie gras" products

The spoiling microflora of a re-packaged French "foie gras" product was studied. A total of 54 isolates, originating from two different factories, were identified using phenotypical and molecular methods (partial 16S rDNA sequencing). Weissella viridescens was the main species detected in the products from factory 1 (64% of the isolates). These products had a low lactic acid concentration and were considered as non-spoiled. The microflora of factory 2 was dominated mainly by the genus Lactobacillus (95% of the isolates), and the high lactic acid concentration of these products was linked with a strong spoilage. Among the 30 Lactobacillus strains, three species were predominant: Lactobacillus sakei (nine isolates), Lactobacillus coryniformis (eight isolates) and Lactobacillus paraplantarum (five isolates). Challenge tests were performed to confirm the involvement of the Lactobacillus strains in the spoilage of the product. Sterile "foie gras" samples were inoculated with 14 LAB strains from the collection. The most acidifying strains belonged to the species L. sakei, Lactobacillus plantarum and L. paraplantarum. This confirmed the role of the strains from the Lactobacillus genus as the main spoilers of "foie gras" products and will be useful to design new quality protocols and extend the shelf-life of these products.

Selection criteria for lactic acid bacteria to be used as functional starter cultures in dry sausage production: An update

Lactic acid bacteria (LAB) have long been used as starter cultures in the production of fermented dry sausages and other meat-derived commodities. These cultures are generally designed to meet food safety, shelf-life, technological effectiveness and economic feasibility criteria. Besides all these traditional properties, novel starter cultures should take into account the risks posed by the formation of biogenic amines in food, and the development and spreading of bacterial resistance to antibiotics. Further, 'functional starters' could protect consumers from harmful bacteria either by a rapid acidification or by the production of antimicrobials (bacteriocins). Specially-selected cultures may also provide probiotic benefits, and, if properly modified, they may even be endorsed with nutraceutical traits. The present review discusses the technological and new selection criteria that should be taken into account when selecting LAB starter cultures for the production of fermented dry sausages.

Use of molecular tools to characterize Lactobacillus spp. isolated from Greek traditional fermented sausages

In this study, our purpose was to molecular characterize Lactobacillus strains isolated from naturally fermented sausages, produced in three different processing plants in continental Greece, in order to investigate the differences of strains coming from different producing areas. Three-hundred and thirty eight strains were isolated throughout the fermentation periods on MRS. They were identified by species-specific PCR and sequencing of partial 16S rRNA gene. The results obtained highlighted that the main populations involved in the fermentations studied belonged to the species Lactobacillus sakei, Lactobacillus plantarum and Lactobacillus curvatus. However, for each of the fermentations, the percentage of isolation for the three main species was different. Molecular characterization of these strains was performed by RAPD-PCR with primer M13 and cluster analysis was applied to define relations and degrees of similarities between strains. This analysis led to the understanding that some strains were plant-specific, whereas others shared a degree of homology independently of the provenience. This evidence is highlighting the capability of the strains to adapt to specific production condition, becoming the main responsible for the transformations, thereby influencing the final characteristics of the sausages.

Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR

A quick and simple method for quantitative detection of Lactobacillus sakei in fermented sausages was successfully developed. It is based on Chelex-100-based DNA purification and real-time PCR enumeration using a TaqMan fluorescence probe. Primers and probes were designed in the L. sakei 16S-23S rRNA intergenic transcribed spacer region, and the assay was evaluated using L. sakei genomic DNA and an artificially inoculated sausage model. The detection limit of this technique was approximately 3 cells per reaction mixture using both purified DNA and the inoculated sausage model. The quantification limit was established at 30 cells per reaction mixture in both models. The assay was then applied to enumerate L. sakei in real samples, and the results were compared to the MRS agar count method followed by confirmation of the percentage of L. sakei colonies. The results obtained by real-time PCR were not statistically significantly different than those obtained by plate count on MRS agar (P > 0.05), showing a satisfactory agreement between both methods. Therefore, the real-time PCR assay developed can be considered a promising rapid alternative method for the quantification of L. sakei and evaluation of the implantation of starter strains of L. sakei in fermented sausages.

New developments in the study of the microbiota of naturally fermented sausages as determined by molecular methods: A review

The microflora of different types of fermented sausages has been defined by isolation and biochemical identification of the microorganisms commonly found in these products. It is generally agreed that the main microbial groups involved in such products are lactic acid bacteria and coagulase-negative cocci. In addition, and depending on the product, other groups may play a role, such as yeasts and enterococci. Since it appears that the types of microbial groups, or even the specific strains of a given microbial group, that dominate the fermentation, significantly affect the organoleptic profile of the final product, there is an increasing interest in the description of the microbiota that are found in different fermented sausages. More recently, new tools, based on molecular methods, allowing fast and unequivocal identification of strains, isolated from fermented sausages, became available. These methods have been successfully applied and, in general, biochemical and molecular identification compared well. However, new information comes to light when molecular methods are applied to DNA and/or RNA extracted directly from sausages. This approach eliminates problems related to traditional isolation. This review deals with the recent findings and results of the application of molecular methods, in a culture-dependent and culture-independent manner, on the study of the microflora of fermented sausages.

Safety properties and molecular strain typing of lactic acid bacteria from slightly fermented sausages

AIM

To evaluate the biodiversity of lactobacilli from slightly fermented sausages (chorizo, fuet and salchichon) by molecular typing, while considering their safety aspects.

METHODS AND RESULTS

Species-specific PCR, plasmid profiling and randomly amplified polymorphic DNA (RAPD)-PCR were used to characterize 250 lactic acid bacteria (LAB) isolated from 21 low acid Spanish fermented sausages. Lactobacillus sakei was the predominant species (74%) followed by Lactobacillus curvatus (21.2%) and Leuconostoc mesenteroides (4.8%). By plasmid profiling and RAPD-PCR 144 different strains could be differentiated, 112 belonging to Lact. sakei, 23 to Lact. curvatus and 9 to Leuc. mesenteroides. Ion-pair high performance liquid chromatography was used to detect biogenic amine production. Tyramine and phenylethylamine were produced by 14.4 and 12.4% of the isolates, respectively, all belonging to the species Lact. curvatus. The production of tyramine was stronger than that of phenylethylamine. Partial sequencing of the tyrosine decarboxylase gene from Lact. curvatus was achieved. A specific PCR assay to detect the Lact. curvatus tyramine-producers was designed. The disc diffusion test was used to detect antibiotic resistance among the isolates. Most isolates displayed resistance to vancomycin and gentamicin. Only four strains were resistant to most of the antibiotics tested. None of the isolates were resistant to erythromycin.

CONCLUSIONS

Lactobacillus sakei would be the species of choice for further use as starter culture in fermented sausage production. Strain typing and characterization of biogenic amine production together with antibiotic susceptibility testing for the selection of starter cultures could help to increase the quality and safety of the products.

SIGNIFICANCE AND IMPACT OF THE STUDY

Species-specific PCR, RAPD and plasmid profiling proved to be efficient at typing LAB at species and strain level. Information on biogenic amine production and transferable antibiotic resistance is important in order to avoid selection of strains with undesirable properties as starter cultures.

Sakacin P non-producing Lactobacillus sakei strains contain homologues of the sakacin P gene cluster

Some strains of Lactobacillus sakei are known to produce the bacteriocin sakacin P, encoded by the spp gene cluster. In strains unable to produce sakacin P, spp homologues were observed. The analysis of 15 strains not producing sakacin P revealed that all contained a region corresponding to a part of sppKR encoding the regulatory elements for sakacin P production. In some strains homologues of sppE and sppT, responsible for sakacin P transport, and the sakacin P structural gene sppA and its immunity gene spiA, were also present. The sequence of the chromosomal spp-related gene cluster was determined in two non-producing strains: L. sakei Lb790 and L. sakei 23K. The L. sakei Lb790 spp gene cluster encompasses genes homologous to sppK, sppR, sppT and sppE. In L. sakei 23K, only sppK and sppR homologues were present. The sppK homologues appeared non-functional as they contained mutations and/or an insertion element. In addition to the spp homologues, several small putative genes were found in the gene clusters of the two strains. Some were similar in both strains, and their organization suggests a mosaic structure resulting from successive rearrangements. Transcriptional analysis showed that the genes of the L. sakei Lb790 spp cluster were expressed when genes encoding an operative sakacin P regulatory system were introduced in this strain, thus complementing the inactive sppK gene. Expression experiments also suggested that some of the spp homologues maintained their function in non-producing strains.

Monitoring the bacterial population dynamics during fermentation of artisanal Argentinean sausages

The dynamics of the microbial community responsible for the artisanal fermentation of dry sausage produced in Argentina was investigated by using classical and molecular approaches. The combined use of RAPD analysis with primers M13, XD9, RAPD1 and RAPD2 and 16S rDNA sequencing were applied to the identification and intraspecific differentiation of 100 strains of lactobacilli and Micrococcaceae. DGGE analysis was used to monitor the dynamic changes in population after total microbial DNA was directly extracted from sausages and subjected to PCR using V3f (GC), Bact-0124f-GC and Univ-0515r primers. The sequence analysis of 16S rDNA of the dominant species was also carried out. Lactobacillus sakei and Lactobacillus plantarum were the dominant lactic acid organisms during the fermentation while Staphylococcus saprophyticus represented the dominant species of Micrococcaceae. It was demonstrated that the ripening process of Argentinean artisanal fermented sausage is driven by a limited number of Lactobacillus and Staphylococcus strains selected from environmental microbiota by the ability to best compete under the prevailing conditions of the ecological niche. The identification of dominant communities present in this artisanal fermented sausage can help in the selection of starter cultures consisting in well adapted strains to the particular production technology.

FT-IR spectroscopy for identification of closely related lactobacilli

Fourier Transform Infrared (FT-IR) spectroscopy was used to analyse 56 strains from four closely related species of Lactobacillus, L. sakei, L. plantarum, L. curvatus and L. paracasei. Hierarchical Cluster Analysis (HCA) was used to study the clusters in the data, but in the dendrogram, the spectra were not differentiated into four separate clusters corresponding to species. When the data were analysed with Partial Least Squares Regression (PLSR), the strains were differentiated into four clusters according to species. It was also possible to recognise strains that were incorrectly identified by conventional methods prior to the FT-IR analysis. PLSR was used to identify strains from three of the species, and the results were compared to two other multivariate methods, Soft Independent Modelling of Class Analogy (SIMCA) and K-Nearest Neighbour (KNN). The three methods gave equally good identification results. The results show that FT-IR spectroscopy in combination with PLSR, or other multivariate methods, is well suited for identification of Lactobacillus at the species level, even in quite large data sets.

Evaluation of the robustness of FT-IR spectra of lactobacilli towards changes in the bacterial growth conditions

In order to use Fourier Transform Infrared (FT-IR) spectroscopy for identification of microorganisms on a routine basis, it is important that the spectra are robust against small, uncontrollable variations in the bacterial growth conditions. In this study, the effect of small variations in growth temperature, growth time, growth medium and atmospheric conditions on the separation of Lactobacillus based on their FT-IR spectra was investigated. The resulting spectra were shown to be robust against the variations in the cultivation conditions, and the separation of both strains and species was unaffected. Larger variations in the growth medium influenced only the separation of strains. FT-IR spectroscopy for identification of lactobacilli therefore seems to be robust against small variations in the cultivation conditions.

Microbial quality and direct PCR identification of lactic acid bacteria and nonpathogenic Staphylococci from artisanal low-acid sausages

Detection of six species of lactic acid bacteria and six species of gram-positive catalase-positive cocci from low-acid fermented sausages (fuets and chorizos) was assessed by species-specific PCR. Without enrichment, Lactobacillus sakei and Lactobacillus curvatus were detected in 11.8% of the samples, and Lactobacillus plantarum and Staphylococcus xylosus were detected in 17.6%. Enriched samples allowed the detection of L. sakei and S. xylosus in all of the samples (100%) and of Enterococcus faecium in 11.8% of the sausages. The percentages of L. curvatus, L. plantarum, Staphylococcus carnosus, and Staphylococcus epidermidis varied depending on the sausage type. L. curvatus was detected in 80% of fuets and in 57% of chorizos. L. plantarum was found in 50% of fuets and 100% of chorizos. S. epidermidis was detected in only 11.8% of fuets, and S. carnosus was detected in only 5.9% of chorizos. Lactococcus lactis, Staphylococcus warneri, and Staphylococcus simulans were not detected in any sausage type. From a microbiological point of view, 70.6% of the samples could be considered of high quality, as they had low counts of Enterobacteriaceae and did not contain any of the food-borne pathogens assayed.

Disinfectant and antibiotic resistance of lactic acid bacteria isolated from the food industry

Quaternary ammonium compounds (QACs) are widely used as disinfectant in medical and food environments. There is a growing concern about the increasing incidence of disinfectant-resistant microorganisms from food. Disinfectant-resistant lactic acid bacteria (LAB) may survive disinfection and cause spoilage problems. Moreover, resistant LAB may potentially act as a reservoir for resistance genes. A total number of 320 LAB from food industry and meat were screened for resistance to the QAC benzalkonium chloride (BC). Out of 320 strains, five strains (1.5%) were considered to be resistant and 56 (17.5%) were tolerant to BC. The resistant strains were isolated from food processing equipment after disinfection. The resistant, tolerant, and some sensitive control bacteria were examined for susceptibility to 18 different antibiotics, disinfectants, and dyes using disc agar diffusion test and microdilution method. Little systematic cross-resistance between BC and any of the antimicrobial agents tested were detected except for gentamycin and chlorhexidine. A BC-tolerant strain was much easier to adapt to higher levels of BC as compared to a BC-sensitive strain. No known gram-positive QAC resistance genes (qacA/B, qacC, qacG, and qacH) were detected in the BC-resistant strains. Identification to species level of the BC-resistant isolates was carried out by comparative analysis of 16S-rDNA sequencing. In conclusion, resistance to BC is not frequent in LAB isolated from food and food environments. Resistance may occur after exposure to BC. The BC resistant isolates showed no cross-resistance with other antimicrobial compounds, except for gentamycin and chlorhexidine. Nevertheless, BC-resistant LAB may be isolated after disinfection and may contribute to the dissemination of resistance.

RAPD-PCR characterization of lactobacilli isolated from artisanal meat plants and traditional fermented sausages of Veneto region (Italy)

AIMS

The study was carried out to evaluate the use of randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) as a method for the identification of lactobacilli isolated from meat products.

METHODS AND RESULTS

RAPD-PCR with primers M13 and D8635 was applied to the identification and intraspecific differentiation of 53 lactobacilli isolates originating from traditional fermented sausages and artisanal meat plants of the Veneto region (Italy). Most of the isolates were assigned to the species Lactobacillus sakei and Lact. curvatus; differentiation of groups of strains within the species was also possible.

CONCLUSION

RAPD-PCR could be applied to the identification of lactobacilli species most commonly found in meat products.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method, which is easy and rapid to perform, could be useful for the study of the lactobacilli populations present in fermented sausages, and could help in the selection of candidate strains to use as starter cultures in meat fermentation.

Phenotypic diversity of lactic acid bacteria isolated from fermented sausages produced in Basilicata (Southern Italy)

AIMS

to evaluate the evolution of lactic acid bacteria (LAB) populations in traditional fermented sausages (salsiccia and soppressata) produced in artisanal and industrial plants in Basilicata (Southern Italy).

METHODS AND RESULTS

Four hundred and fourteen lactic acid bacteria (LAB) cultures were isolated from samples of sausages at different stages of ripening. A phenotypic characterization of the isolates was carried out using a set of 28 tests, and 34 clusters were identified at the 80% similarity level using hierarchical cluster analysis. Of the isolates 50% were identified as Lactobacillus sakei (with several biotypes), 22% as Pediococcus spp. (mainly Ped. pentosaceus), 7% as Leuconostoc (Leuc. carnosum, Leuc. gelidum, Leuc. pseudomesenteroides), 6% as Lact. plantarum, 1% as Lact. curvatus. Other lactobacilli, including unidentified species, were present in lower numbers.

CONCLUSION

The phenotypic diversity and composition of the LAB flora varied as a function of the production plant, product type and ripening time. SIGNIFICANCE AND IMPACT OT THE STUDY: A new procedure based on bootstrapping and Multidimensional Scaling was successfully used to obtain a graphical representation of the evolution of the LAB populations.

The use of multiplex PCR reactions to characterize populations of lactic acid bacteria associated with meat spoilage

A rapid, systematic and reliable approach for identifying lactic acid bacteria associated with meat was developed, allowing for detection of Carnobacterium spp., Lactobacillus curvatus, Lact. sakei and Leuconostoc spp. Polymerase chain reaction primers specific for Carnobacterium and Leuconostoc were created from 16S rRNA oligonucleotide probes and used in combination with species-specific primers for the 16S/23S rRNA spacer region of Lact. curvatus and Lact. sakei in multiplex PCR reactions. The method was used successfully to characterize lactic acid bacteria isolated from a vacuum-packaged pork loin stored at 2 degrees C. Seventy isolates were selected for identification and 52 were determined to be Lact. sakei, while the remaining 18 isolates were identified as Leuconostoc spp.

High levels of background flora inhibits growth of Escherichia coli O157:H7 in ground beef

The influence of natural background flora under aerobic and anaerobic incubation on the growth of Escherichia coli O157:H7 in ground beef was investigated. The background flora from eight different commercial ground beef were added to ground beef spiked with E. coli O157:H7 and stored either aerobically or anaerobically at 12 degrees C. The results showed that the presence of a large number of background bacteria in the ground meat inhibited the growth of E. coli O157:H7 both aerobically and anaerobically. Inhibition was more pronounced under anaerobic conditions. The background floras consisted mainly of lactic acid bacteria of which approximately 80% were Lactobacillus sakei. These results show the importance of the natural background flora in meat for inhibition of growth of E. coli O157:H7.

Protective cultures inhibit growth of Listeria monocytogenes and Escherichia coli O157:H7 in cooked, sliced, vacuum- and gas-packaged meat

Contamination of cooked meat products with Listeria monocytogenes poses a constant threat to the meat industry. The aim of this study was therefore to investigate the use of indigenous lactic acid bacteria (LAB) as protective cultures in cooked meat products. Cooked, sliced, vacuum- or gas-packaged ham and servelat sausage from nine meat factories in Norway were inoculated with 10(3) cfu/g of a mixture of three rifampicin resistant (rif-mutant) strains of L. monocytogenes and stored at 8 degrees C for four weeks. Growth of L. monocytogenes and indigenous lactic acid flora was followed throughout the storage period. LAB were isolated from samples where L. monocytogenes failed to grow. Five different strains growing well at 3 degrees C. pH 6.2, with 3% NaCl, and producing moderate amounts of acid were selected for challenge experiments with the rif-resistant strains of L. monocytogenes. a nalidixic acid/streptomycin sulphate-resistant strain of Escherichia coli O157:H7 and a mixture of three rif-resistant strains of Yersinia enterocolitica O:3. All five LAB strains inhibited growth of both L. monocytogenes and E. coli O157:H7. No inhibition of Y. enterocolitica O:3 was observed. A professional taste panel evaluated cooked, sliced, vacuum-packaged ham inoculated with each of the five test strains after storage for 21 days at 8 degrees C. All samples had acceptable sensory properties. The five LAB strains hybridised to a 23S rRNA oligonucleotide probe specific for Lactobacillus sakei. These indigenous LAB may be used as protective cultures to inhibit growth of L. monocytogenes and E. coli O157:H7 in cooked meat products.

Cell surface characteristics of Lactobacillus casei subsp. casei, Lactobacillus paracasei subsp. paracasei, and Lactobacillus rhamnosus strains

Hydrophilic and electrostatic cell surface properties of eight Lactobacillus strains were characterized by using the microbial adhesion to solvents method and microelectrophoresis, respectively. All strains appeared relatively hydrophilic. The strong microbial adhesion to chloroform, an acidic solvent, in comparison with microbial adhesion to hexadecane, an apolar n-alkane, demonstrated the particularity of lactobacilli to have an important electron donor and basic character and consequently their potential ability to generate Lewis acid-base interactions with a support. Regardless of their electrophoretic mobility (EM), strains were in general slightly negatively charged at alkaline pH. A pH-dependent behavior concerning cell surface charges was observed. The EM decreased progressively with more acidic pHs for the L. casei subsp. casei and L. paracasei subsp. paracasei strains until the isoelectric point (IEP), i.e., the pH value for which the EM is zero. On the other hand, the EM for the L. rhamnosus strains was stable from pH 8 to pH 3 to 4, at which point there was a shift near the IEP. Both L. casei subsp. casei and L. paracasei subsp. paracasei strains were characterized by an IEP of around 4, whereas L. rhamnosus strains possessed a markedly lower IEP of 2. The present study showed that the cell surface physicochemical properties of lactobacilli seem to be, at least in part and under certain experimental conditions, particular to the bacterial species. Such differences detected between species are likely to be accompanied by some particular changes in cell wall chemical composition.

Selective detection, enumeration and identification of potentially probiotic Lactobacillus and Bifidobacterium species in mixed bacterial populations

Lactobacillus and Bifidobacterium species constitute a significant proportion of probiotic cultures used in developed countries in 'microbial adjunct nutrition'. A number of differential plating methodologies have been developed which seek to selectively detect and enumerate these bacterial groups in bioproducts. Differences in oxygen tolerance, nutritional requirements, antibiotic susceptibility, and colony morphology and colour constitute the bases of differentiation in these methods. The choice of methodology depends on the nature of the bioproduct to be examined (wet or dry) and the presence of other bacteria such as starter cultures. In addition, a number of nucleic acid methods have been developed in recent years which enable the specific detection of these bacterial groups at species, subspecies and strain level in mixed populations. The methods use synthetic 16S and 23S rRNA-targeted hybridisation probes, the specificity of which can be adjusted to fit any taxonomic ranking from genus to genotype, for detection, enumeration and identification in situ or after differential plating. The combined use of differential plating and molecular strain typing methodologies provides food and medical microbiologists with a powerful and targeted approach to the detection, enumeration and identification of these bacterial groups and their members in a wide range of food and biological materials. An overview of these methods is presented in this review.

Rapid GC analysis of cellular fatty acids for characterizing Lactobacillus sake and Lact. curvatus strains of meat origin

A rapid procedure based on the gas chromatographic analysis of cellular fatty acids was used to differentiate between strains of Lactobacillus sake and Lact. curvatus isolated from dry salami. All strains had very similar fatty acid profiles except four of them which lacked C19 cycl acid, but neither this feature nor other differences in single fatty acid contents could be successfully correlated with the biochemical discrimination of Lact. sake from Lact. curvatus. When, however, strains were compared on the basis of the total content of fatty acids with 18 carbon atoms divided by that with 16 carbon atoms, a very good correlation with strain characterization by classical methods was achieved. It was concluded that selected cellular fatty acids ratios might be useful for characterizing phylogenetically related strains of lactic acid bacteria.

DNA based typing, identification and detection systems for food spoilage microorganisms: development and implementation

The rapid identification of spoilage microorganisms is of eminent importance to the food industry. It provides the food industry with the opportunity to reduce economical losses by designing adequate intervention measures. The use of identification systems based on biochemical and physiological characteristics resulted often in disappointing identification results and misidentifications. This will inevitably lead to inappropriate strategies to prevent spoilage. This review discusses the potential of the DNA based identification technology including the polymerase chain reaction (PCR) for the identification and specific detection of microorganisms. Fingerprinting methods based on the DNA-probe technology enable a clear insight in the identity of microorganisms on different levels, varying from genus to strain level depending on the systems used. Discrimination between subspecies and strain level is shown to be helpful for investigating routes and sources of contamination. Differentiation at the species level is demonstrated to be essential in order to design a highly specific detection system enabling to signalize a microorganism that belongs to a particular species. Also indicated in this review is the necessity and the technical approach to detect microorganisms that display a particular undesirable trait.