16S-23S rDNA intergenic spacer region polymorphism of Lactococcus garvieae, Lactococcus raffinolactis and Lactococcus lactis as revealed by PCR and nucleotide sequence analysis

Development of a quantitative polymerase chain reaction assay for detection of the aetiological agents of piscine lactococcosis

Piscine lactococcosis is an emergent bacterial disease that is associated with high economic losses in many farmed and wild aquatic species worldwide. Early and accurate detection of the causative agent of piscine lactococcosis is essential for management of the disease in fish farms. In this study, a TaqMan quantitative polymerase chain reaction (qPCR) targeting the 16S-23S rRNA internal transcribed spacer region was developed and validated. Validation of the qPCR was performed with DNA of previously typed L. petauri and L. garvieae recovered from different aquatic hosts from distinct geographical locations, closely related bacterial species and common pathogens in trout aquaculture. Further diagnostic sensitivity and specificity was investigated by screening of fish, water and faecal samples. The developed qPCR assay showed high specificity, sensitivity and accuracy in detection of L. petauri and L. garvieae with lack of signals from non-target pathogens, and in screening of rainbow trout (Oncorhynchus mykiss) posterior kidney and environmental samples. The detection limit of the qPCR was four amplicon copies. Moreover, the sensitivity of the qPCR assay was not affected by presence of non-target DNA from either fish or environmental samples. The robustness, specificity and sensitivity of the developed qPCR will facilitate fast and accurate diagnosis of piscine lactococcosis to establish appropriate control measures in fish farms and aquaria.

Analysis of Streptococcal Infection and Correlation with Climatic Factors in Cultured Tilapia Oreochromis spp. in Taiwan

Tilapia (Oreochromis spp.), a prominent warm water food fish, is one of the major fish species grown in the aquaculture industry in south-east Asia. Tilapia can tolerate adverse water quality and other stressors, like diverse salinity and fluctuation of pH value, better than most other commercial aquaculture species. Environmental fluctuations are one of the main factors that affect the outbreak of infectious diseases in cultured tilapia. Cultured tilapia in Taiwan appears to be more susceptible to infections caused by Streptococci during the summer season. The present study emphasizes the Streptococcus spp. infection in tilapia in Taiwan and is the first study on the analysis of the potential impact of climate change on streptococcal infection in cultured tilapia in Asia. The data collected from the treatment and diagnosis system (TDS) of the aquatic animal diseases database from 2006 to 2015 were used to analyze the endemic streptococcal infection and the effect of climatic factors. Based on the results, the factor, average atmospheric pressure, is negatively correlated to streptococcal infection, while the other three, including average temperature, ultraviolet (UV) index, and rainfall, are positively correlated to streptococcal infection. A multivariate logistic regression model with these four factors was also built. When the average temperature is above 27.0 °C, the average atmospheric pressure is lower than 1005.1 hPa, or the UV index is above 7.2, the percentage of cumulated positive farms from all submitted tilapia cases was more than 50%. In addition, within 3 days of rain, rainfall is relevant to the occurrence of Streptococcus in tilapia. Using TDS to alert the occurrence of streptococcal infection in tilapia can be a very useful tool for veterinary aquatic animal inspection stations, and reducing economic losses and labour costs in aquatic agriculture.

Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses

Background

Lactococcus members belonging to lactic acid bacteria are widely used as starter bacteria in the production of fermented dairy products. From kimchi, a Korean food made of fermented vegetables, Lactococcus raffinolactis WiKim0068 was isolated and its genome was analyzed.

Results

The complete genome of the strain WiKim0068 consists of one chromosome and two plasmids that comprises 2,292,235 bp, with a G + C content of 39.7 mol%. Analysis of orthoANI values among Lactococcus genome sequences showed that the strain WiKim0068 has > 67% sequence similarity to other species and subspecies. In addition, it displayed no antibiotic resistance and can metabolize nicotinate and nicotinamide (vitamin B3).

Conclusion

These results augments our understanding of the genus Lactococcus and suggest that this new strain has potential industrial applications.

Species-Specific Identification of Streptococcus based on DNA Marker in 16S-23S rDNA Internal Transcribed Spacer

Streptococcus is closely correspondent to human. The accurate species-specific identification method of Streptococcus is important for the bacteria clinical diagnosis, molecular epidemiological analysis, and microecological study. In the last decades, DNA markers are widely utilized for identification of prokaryotic species. However, 16S rDNA, the most popular bacterial DNA marker, cannot properly distinguish closely related Streptococcus species. In present study, we employed 16S-23S rRNA gene internal transcribed spacer (ITS) sequence to explore the species-specific DNA marker. We predicted the secondary structure of Streptococcus ITS sequence transcribed products. Then we identified that the specific and consensus sequences in the primary structure can be found occupying an individual subunit in the secondary structure, which explained the foundation of the mosaic-like structure of ITS. We evaluated the specificity of ITS in Streptococcus, and found that the specificity can be detected by a further analysis of a BLAST result. Then, we developed an identification procedure based on the ITS sequence. We verified the procedure by 500 ITS sequence. The accuracy rate of this procedure was 100% for Streptococcus at genus level, and 99.3% at species level. It suggested that ITS can be utilized to accurately identify Streptococcus at the species level. This work suggests that further exploration of ITS could be applied in other bacterial genera for identification and classification, which may be a useful topic for future microbiology studies.

Determination of Probiotic Abilities and Lactic Acid Content of Pediococcus acidilactici

Background:

Probiotics are living microorganisms that have a healthy influence on a host.

Objective:

The aim of this study was to isolate a probiotic Pediococcus acidilactici strain from newborn faeces and develop and optimize a selective high-performance liquid chromatography method for the determination and validation of its lactic acid content and also evaluate some probiotic characteristics.

Methods:

Isolated strains were identified by the API 50 CH system and 16S rDNA gene sequence analysis and tested for antibiotic susceptibility, bile salt tolerance, low pH resistance, proteolytic, haemolytic activity, as well as the production of bacteriocin, hydrogen peroxide, and lactic acid. Antimicrobial activity of selected strain against standard test microorganisms was determined by the spot lawn method and the quantitation of lactic acid was carried out by high-performance liquid chromatography on a Rezex ROA organic acid (300x7.8 mm) analytical column.

Results:

P. acidilactici M7 strain was evaluated as a potential probiotic due to its ability to survive at low pH values or in the presence of pepsin, pancreatin, and bile salts. The lactic acid amount of strain was found in the range between 5.59-5.94 mg mL-1 by HPLC. M7 strain was also found to be resistant to vancomycin, had no bacteriocin, and hydrogen peroxide production and was able to inhibit the growth of P. aeruginosa and E. faecalis by its lactic acid content.

Conclusion:

This study explains a simple, selective, and fully validated procedure for the determination of lactic acid from probiotic bacteria.

Prevalence and Antibiotic Resistance of Listeria monocytogenes Isolated from Ready-to-Eat Foods in Turkey

The aim of the present study was the determination of the prevalence and antibiotic resistance of L. monocytogenes in ready-to-eat (RTE) foods in Ankara, Turkey. In order to detect and isolate L. monocytogenes from 201 RTE food samples, the EN ISO 11290:1 method was used. All isolates were identified using the polymerase chain reaction. The strains were also confirmed by the detection of the hemolysin gene (hlyA). The overall prevalence of L. monocytogenes was 8.5% among the food samples. Seventeen L. monocytogenes strains were examined by the disk diffusion assay for their resistance to 23 antibiotics. All strains were susceptible to erythromycin, clarithromycin, streptomycin, gentamicin, vancomycin, imipenem, trimethoprim, and chloramphenicol, while all strains were resistant to nalidixic acid, ampicillin, penicillin G, linezolid, and clindamycin. The higher resistance was found against oxacillin (94.1%), kanamycin (76.5%), levofloxacin (70.6%), and teicoplanin (64.7%), followed by amoxicillin/clavulanic acid (53.0%), rifampicin (47.1%), and ciprofloxacin (35.3%). A lower incidence of resistance was observed against tetracycline (5.9%), meropenem (5.9%), and trimethoprim/sulfamethoxazole (17.7%). All isolates were multidrug resistant showing resistance to at least three antibiotic classes. High L. monocytogenes prevalence among analyzed RTE foods represents a high risk for public health. Our findings show a high prevalence of L. monocytogenes in RTE foods in Turkey. More effective control strategies for L. monocytogenes are needed to reduce both prevalence and resistance of L. monocytogenes in Turkish RTE foods.

Vibrio alginolyticus 16S-23S intergenic spacer region analysis, and PCR assay for identification of coral pathogenic strain XSBZ03

Porites andrewsi white syndrome (PAWS), caused by Vibrio alginolyticus strains XSBZ03 and XSBZ14, poses a serious threat to corals in the South China Sea. To obtain a specific target against which to develop a rapid PCR detection method for the coral pathogenic strain XSBZ03, the 16S-23S rRNA gene intergenic spacer (IGS) region of 4 strains of V. alginolyticus, including the XSBZ03 and XSBZ14 strains, was amplified, sequenced and analyzed. Six types of IGS were found: IGS0, IGSG, IGSIA, IGSAG, IGSGLV, and IGSGLAV. IGS0, IGSG, IGSIA, IGSAG and IGSGLV appeared to be the most prevalent forms in the 4 strains and the percentage identity range within each type was 91.4-100%, 89.3-98.5%, 83.0-99.8%, 91.5-95.6%, and 88.7-99.3%, respectively. IGSGLAV was found only in the HN08155 strain, a causative agent of fish disease. IGSGLAV, IGSGLV and IGSAG are reported here for the first time in V. alginolyticus. An IGS sequence specific to the XSBZ03 strain was identified following alignment of the homologous IGSs, and used to design strain-specific primers for its rapid identification by PCR. The results from PCR analysis suggest that the method is a rapid, practical, and reliable tool for the identification of the XSBZ03 strain in samples of isolated bacteria, as well as seawater and coral samples spiked with the bacterial strain. This is the first report of a rapid diagnostic assay for a causative agent of PAWS, based on PCR detection of a coral pathogen at the strain level. After applying this assay in coral transplantation, the survival rates of transplanted corals were significantly increased. This diagnostic assay should aid with both the elucidation of the cause of the disease, and transplantation of PAWS-free P. andrewsi in the South China Sea.

Antimicrobial Resistance of Enterococcus Species Isolated from Chicken in Turkey

The aim of the present work was to provide information about Enterococcus strains isolated from pre-packaged chicken samples in Ankara (Turkey), focusing on their prevalence, phenotypic and genotypic characteristics, and antibiotic resistance. We report the first study on the occurrence of antibiotic resistant enterococci in pre-packaged chicken samples in Ankara. A total of 97 suspicious enterococcal isolates were identified from 122 chicken samples. All isolates were identified to species level by phenotypic and molecular methods. In the 16S rDNA sequence analysis, Enterococcus faecium (61.85%) and Enterococcus faecalis (38.15%) were found to be the most frequently detected Enterococcus spp. Of the 97 isolates tested for hemolytic activity, 12.37% enterococcal strains were β-hemolytic. β-Hemolysin was most prevalent among E. faecium (58.33%) compared to E. faecalis (41.66%). Disk diffusion method was used for determining of antibiotic resistance. The analysis of the antimicrobial resistance of the 97 Enterococcus isolates revealed that the resistance to kanamycin (98.96%), rifampicin (80.41%) and ampicillin (60.82%) was most frequent. Furthermore, resistance to erythromycin (38.14%) and ciprofloxacin (34.02%) was also observed. The frequencies of resistance to tetracycline (9.27%), penicillin G (8.24%), and chloramphenicol (3.09%), gentamicin (2.06%) and streptomycin (1.03%) were low. None of the isolates was resistant to vancomycin. Multi-drug resistance was found in 97.93% of Enterococcus strains. E. faecium strains showed a more resistant phenotype than E. faecalis strains according to the antibiotic resistance levels. The results of this study indicated that chicken meat is a potential reservoir for the transmission of antibiotic resistance from animals to humans.

Lactococcus garvieae: an emerging bacterial pathogen of fish

Lactococcus garvieae is the causative agent of lactococcosis, a hyperacute, haemorrhagic septicaemia of fish. This bacterium is also considered an emerging zoonotic pathogen, as reports of human infection are increasing. Significant economic loss in aquaculture is suffered as a result of lactococcosis, as numerous freshwater and marine species of commercial interest are affected. Development of antibiotic resistance in L. garvieae to several chemotherapeutic agents complicates and restricts treatment options. Effective, sustainable treatment and prevention options are thus needed, but progress is impeded by the lack of knowledge concerning several aspects of the disease and the pathogen. This review aims to present the latest research on L. garvieae, with specific focus on pathogenesis, virulence factors, risks associated with chemotherapeutic administration and possible control options.

Effect of diet supplementation with Ascophyllum nodosum on cow milk composition and microbiota

Iodine deficiency remains a major public health concern in many countries, including some European regions. This study aimed at understanding the effect of a supplement of marine alga Ascophyllum nodosum as a iodine fortifier in the cow diet, on the compositional and microbiological quality of milk. The results obtained in this work indicated that the dietary inclusion of A. nodosum exerted significant effects on cow milk composition. In particular, it increased iodine content and reduced the quantity of free amino acids without modifying the free fatty acid content. From a microbiological point of view, statistically significant differences were found in presumptive mesophilic lactobacilli, mesophilic lactococci, and Pseudomonas spp. counts. Based on a culture-independent method, milk obtained after dietary inclusion of A. nodosum harbored the highest number of Firmicutes (e.g., Lactococcus lactis) and the lowest number of Proteobacteria (e.g., Pseudomonas). In addition to changes in bacterial population, diet supplementation with A. nodosum changed the catabolic profiles of the milk community, according to Biolog Ecoplate (Biolog Inc., Hayward, CA) results. The results of this study suggest that the dietary inclusion of the marine alga A. nodosum led to an improvement of the iodine content in milk, and to a modification of its microbiota with a positive effect on milk hygiene and transformation.

Identification of Lactobacillus strains of goose origin using MALDI-TOF mass spectrometry and 16S-23S rDNA intergenic spacer PCR analysis

The objective of our study was to identify Lactobacillus sp. strains of goose origin using MALDI-TOF mass spectrometry, ITS-PCR and ITS-PCR/RFLP. All three techniques proved to be valuable tools for identification of avian lactobacilli and produced comparable classification results. Lactobacillus strains were isolated from 100% of geese aged 3 weeks to 4 years, but from only 25% of chicks aged 1-10 days. Among the 104 strains isolated, we distinguished 14 Lactobacillus species. The dominant species was Lactobacillus salivarius (35.6%), followed by Lactobacillus johnsonii (18.3%), Lactobacillus ingluviei (11.5%) and Lactobacillus agilis (7.7%). The intact-cell MALDI-TOF mass spectrometry enabled rapid species identification of the lactobacilli with minimal pretreatment. However, it produced more than one identification result for 11.5% examined strains (mainly of the species L. johnsonii). ITS-PCR distinguished 12 genotypes among the isolates, but was not able to differentiate closely related strains, i.e. between Lactobacillus amylovorus and Lactobacillus kitasatonis and between Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus zeae. These species were differentiated by ITS-PCR/RFLP using the restriction enzymes TaqI and MseI. The results obtained indicate that ITS-PCR and ITS-PCR/RFLP assays could be used not only for interspecific, but also for intraspecific, typing.

Rapid Species Identification and Partial Strain Differentiation ofClostridium butyricumby PCR Using 16S-23S rDNA Intergenic Spacer Regions

Some Clostridium butyricum strains have been used as probiotics for both humans and animals. Strain-specific identification is necessary for the manufacturing process of probiotics. The aim of this study was to determine whether there are sufficient genetic variations in 16S-23S intergenic spacer regions (ISRs) to discriminate C. butyricum at the biovar level. We amplified ISRs from five reference strains, a probiotic strain (MIYAIRI 588) and 22 isolates, and we classified them into four groups on the basis of amplification patterns (type A through D). However, amplification of ISRs is not sufficient for discriminating strains. Moreover, we compared genetic structures of these ISRs. Sequence analysis revealed that the size variations of ISRs were generated by the insertion of tRNA genes and unique sequences into the internal portion, while the external portions were highly conserved. On the basis of the highly conserved nucleotide sequences within the ISRs, we developed a PCR primer set specific to C. butyricum. In addition, the PCR primer designed from the unique inserted sequence in type B strain was useful to differentiate probiotic strains at the biovar level.

Cloning and recombinant expression of a cellulase from the cellulolytic strain Streptomyces sp. G12 isolated from compost

BACKGROUND

The use of lignocellulosic materials for second generation ethanol production would give several advantages such as minimizing the conflict between land use for food and fuel production, providing less expensive raw materials than conventional agricultural feedstock, allowing lower greenhouse gas emissions than those of first generation ethanol. However, cellulosic biofuels are not produced at a competitive level yet, mainly because of the high production costs of the cellulolytic enzymes. Therefore, this study was aimed at discovering new cellulolytic microorganisms and enzymes.

RESULTS

Different bacteria isolated from raw composting materials obtained from vegetable processing industry wastes were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. Four strains belonging to the actinomycetes group were selected on the basis of their phenotypic traits and cellulolytic activity on solid medium containing carboxymethylcellulose. The strain showing the highest cellulolytic activity was identified by 16S rRNA sequencing as belonging to Streptomyces genus and it was designated as Streptomyces sp. strain G12. Investigating the enzymes responsible for cellulase activity produced by Streptomyces G12 by proteomic analyses, two endoglucanases were identified. Gene coding for one of these enzymes, named CelStrep, was cloned and sequenced. Molecular analysis showed that the celstrep gene has an open reading frame encoding a protein of 379 amino acid residues, including a signal peptide of 37 amino acid residues. Comparison of deduced aminoacidic sequence to the other cellulases indicated that the enzyme CelStrep can be classified as a family 12 glycoside hydrolase. Heterologous recombinant expression of CelStrep was carried out in Escherichia coli, and the active recombinant enzyme was purified from culture supernatant and characterized. It catalyzes the hydrolysis of carboxymethylcellulose following a Michaelis-Menten kinetics with a KM of 9.13 mg/ml and a vmax of 3469 μM min-1. The enzyme exhibits a half life of around 24 h and 96 h at 60°C and 50°C, respectively and shows a retention of around 80% of activity after 96 h at 40°C.

CONCLUSIONS

In this manuscript, we describe the isolation of a new cellulolytic strain, Streptomyces sp. G12, from industrial waste based compost, the identification of the enzymes putatively responsible for its cellulolytic activity, the cloning and the recombinant expression of the gene coding for the Streptomyces sp. G12 cellulase CelStrep, that was characterized showing to exhibit a relevant thermoresistance increasing its potential for cellulose conversion.

Industrial waste based compost as a source of novel cellulolytic strains and enzymes

Ninety bacteria isolated from raw composting materials were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. The bacteria producing the highest cellulolytic activity levels were identified by 16S rRNA sequencing as Bacillus licheniformis strain 1, Bacillus subtilis subsp. subtilis strain B7B, Bacillus subtilis subsp. spizizenii strain 6, and Bacillus amyloliquefaciens strain B31C. Cellulase activity production by the most productive strain B. amyloliquefaciens B31C was optimized in liquid culture varying the carbon source. Comparison of growth curves of B. amyloliquefaciens B31C at temperatures from 28 to 47 °C indicated its thermotolerant nature. Moreover, analysis of time courses of cellulase activity production in this thermal range showed that increase of temperature from 28 to 37 °C causes an increase of cellulase activity levels. Investigating the enzymes responsible for cellulase activity produced by B. amyloliquefaciens B31C by proteomic analyses, an endoglucanase was identified. It was shown that the purified enzyme catalyzes carboxymethylcellulose's hydrolysis following Michaelis-Menten kinetics with a K(M) of 9.95 mg ml(-1) and a v(max) of 284 μM min(-1) . It shows a retention of 90% of its activity for at least 144 h of incubation at 40 °C and exhibits a range of optimum temperatures from 50 to 70 °C.

Development of a novel PCR assay based on the 16S-23S rRNA internal transcribed spacer region for the detection of Lactococcus garvieae

Lactococcus garvieae is recognized as an emerging pathogen in fish. Several PCR-based methods have been developed for the detection and identification of L. garvieae; however, the sensitivity of these methods is still in question regarding the discrimination of this organism from other closely related species. Two primers, ITSLg30F and ITSLg319R, were designed from the sequence in the 16S-23S internal transcribed spacer (ITS) region and used for the specific detection of L. garvieae. L. garvieae strains including fish isolates were positive by this method. In contrast, previously developed PCR methods showed false-positive results with non-L. garvieae species. Our results indicate that a PCR method using the newly designed ITS primer set provides a sensitive and efficient tool for the detection of L. garvieae in fish and aquaculture environments.

Novel multiplex polymerase chain reaction primer set for identification of Lactococcus species

AIMS

The gram-positive bacterial genus Lactococcus has been taxonomically classified into seven species (Lactococcus lactis, Lactococcus garvieae, Lactococcus piscium, Lactococcus plantarum, Lactococcus raffinolactis, Lactococcus chungangensis and Lactococcus fujiensis). This study aimed to develop a novel multiplex polymerase chain reaction (PCR) primer set for the identification of the seven lactococcal species, as well as to differentiate the two industrially important dairy subspecies, L. lactis subsp. lactis and L. lactis subsp. cremoris.

METHODS AND RESULTS

A multiplex PCR primer set was designed based on the nucleotide sequences of the 16S rRNA gene of the seven lactococcal species. The specificity of the established one-step multiplex PCR scheme was verified using more than 200 bacterial strains, in which a complete sequence match was confirmed by partial sequencing of their 16S rRNA gene.

CONCLUSIONS

The one-step multiplex PCR enables the identification and speciation of bacterial strains belonging to the genus Lactococcus and the differentiation of strains of L. lactis subsp. lactis and L. lactis subsp. cremoris.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides an efficient method for identification of lactococcal strains of industrial importance.

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.

National survey outcomes on commercial probiotic food supplements in Italy

To assess whether the probiotic food supplements, produced and distributed on the Italian market during 2005-2006, complied with the Italian Guidelines on Prebiotics and Probiotics, 72 samples from 29 processing plants were analyzed. The survey included 41 samples from processing plants and 31 samples of the same brand from retailers collected at timed intervals (3, 8 and 13 months). A polyphasic approach based on a suitable analytical collection method (genotypic identification of total bacteria - differential presumptive enumeration - genotypic identification of viable bacteria) was adopted to identify and quantify the microorganisms labelled and recovered from the probiotic supplements examined. Most supplements analyzed (87%) did not conform to the Italian guidelines and the differences were both quantitative and qualitative (number determination, purity, types and viability of microorganisms). Even though most labelled supplements (25 samples) indicated the presence of Bifidobacterium bifidum, this organism was only detected sporadically and always as dead cells. Unexpected results were obtained during our survey due to the absence of viability of Bacillus coagulans spores in some labelled supplements. Besides this, some of these supplements also contained other spore-forming species, identified as B. cereus that are toxin producing. We have also documented a widespread use of misclassified microbial species or species with fictitious names. The main factors involved in the absence of compliance were examined and the poor quality control applied by manufacturers was emphasized.

Polyphasic taxonomic studies of lactic acid bacteria associated with Tunisian fermented meat based on the heterogeneity of the 16S-23S rRNA gene intergenic spacer region

The objective of this work was to investigate the structure and diversity of lactic acid bacteria (LAB) communities in traditionally fermented meat collected from different areas of Tunisia. A polyphasic study, which involves phenotypic tests and ribosomal DNA-based techniques, was used to identify Gram-positive and catalase-negative isolates. PCR amplification of the 16S-23S rDNA ISR of 102 isolates and other reference LAB strains gave (1) one type of rrn operon (M-ISR) for lactococci, (2) two types of rrn operon (S-ISR and M-ISR) for enterococci, (3) two types of rrn operon (S-ISR and L-ISR) for Lactobacilli, and (4) three PCR amplicons (S-ISR, M-ISR, and L-ISR) obtained for Pediococcus spp. and Weissella genus. The clustering and comparison of ISR-RFLP profiles given by the isolates with those given by reference LAB strains, allowed their identification as Lactococcus lactis, Enterococcus faecium, Enterococcus faecalis, Enterococcus sanguinicola, Enterococcus hawaiiensis, Lactobacillus sakei, Lactobacillus curvatus, Lactobacillus plantarum, Lactobacillus alimentarius, Pediococcus pentosaceus, and Weissella confusa. Combined 16S-23S rDNA ISR and RFLP patterns can be considered as a good potential target for a rapid and reliable differentiation between isolates of LAB and provided further information on the organization of their rrn operons.

Investigating the relationship between raw milk bacterial composition, as described by intergenic transcribed spacer-PCR fingerprinting, and pasture altitude

AIMS

To assess the bacterial biodiversity level in bovine raw milk used to produce Fontina, a Protected Designation of Origin cheese manufactured at high-altitude pastures and in valleys of Valle d'Aosta region (North-western Italian Alps) without any starters. To study the relation between microbial composition and pasture altitude, in order to distinguish high-altitude milk against valley and lowland milk.

METHODS AND RESULTS

The microflora from milks sampled at different alpine pasture, valley and lowland farms were fingerprinted by PCR of the 16S-23S intergenic transcribed spacers (ITS-PCR). The resulting band patterns were analysed by generalized multivariate statistical techniques to handle discrete (band presence-absence) and continuous (altitude) information. The fingerprints featured numerous bands and marked variability indicating complex, differentiated bacterial communities. Alpine pasture milks were distinguished from lowland ones by cluster analysis, while this technique less clearly discriminated alpine pasture and valley samples. Generalized principal component analysis and clustering-after-ordination enabled a more effective distinction of alpine pasture, valley and lowland samples.

CONCLUSIONS

Alpine raw milks for Fontina production contain highly diverse bacterial communities, the composition of which is related to the altitude of the pasture where milk was produced.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research may provide analytical support to the important issue represented by the authentication of the geographical origin of alpine milk productions.

Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

AIMS

The design and evaluation of an oligonucleotide microarray in order to detect and identify viable bacterial species that play a significant role in beer spoilage. These belong to the species of the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus.

METHODS AND RESULTS

Oligonucleotide probes specific to beer spoilage bacteria were designed. In order to detect viable bacteria, the probes were designed to target the intergenic spacer regions (ISR) between 16S and 23S rRNA. Prior to hybridization the ISR were amplified by combining reverse transcriptase and polymerase chain reactions using a designed consenus primer. The developed oligonucleotide microarrays allows the detection of viable beer spoilage bacteria.

CONCLUSIONS

This method allows the detection and discrimination of single bacterial species in a sample containing complex microbial community. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non growing bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage micro-organisms within a mixed population.

Genetic traceability of the geographical origin of typical Italian water buffalo Mozzarella cheese: a preliminary approach

AIMS

To distinguish Italian Protected Designation of Origin (PDO) water buffalo Mozzarella from different producers on a molecular basis in relation to the place of manufacturing within the production district, and to develop a tool for genetic traceability of typical dairy products.

METHODS AND RESULTS

Microbial DNA was isolated from Mozzarella's governing liquid to amplify the whole microflora's ribosomal 16S-23S internal transcribed spacers (ITS)-PCR fingerprinting by means of an original primer pair. Phylogenetic distance analyses were performed on the obtained electrophoretic band patterns by maximum parsimony and neighbour-joining tree construction algorithms for discrete binary data, using a conventional bootstrap resampling test. The observed band profiles showed high repeatability and specificity, allowing unambiguous distinction of each sample; phylogenetic analyses yielded the same tree topology with good strength of nodal support. Moreover, a relationship between the genetic distances among samples and the actual geographical ones separating the respective producing dairies was observed.

CONCLUSIONS

The genetic diversity of PDO water buffalo Mozzarella's microflora, observed by ITS-PCR fingerprinting, can be exploited to discriminate cheeses from differently located dairies.

SIGNIFICANCE AND IMPACT OF THE STUDY

Given the increasing importance of food traceability for safety, quality and typicalness issues, the ITS-PCR fingerprinting protocol described here may represent a suitable tool for tracing the geographical origin of Italian Mozzarella.

Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.

Use of unsupervised and supervised artificial neural networks for the identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins

Conventional multivariate statistical techniques (hierarchical cluster analysis, linear discriminant analysis) and unsupervised (Kohonen Self Organizing Map) and supervised (Bayesian network) artificial neural networks were compared for as tools for the classification and identification of 352 SDS-PAGE patterns of whole cell proteins of lactic acid bacteria belonging to 22 species of the genera Lactobacillus, Leuconostoc, Enterococcus, Lactococcus and Streptococcus including 47 reference strains. Electrophoretic data were pre-treated using the logistic weighting function described by Piraino et al. [Piraino, P., Ricciardi, A., Lanorte, M. T., Malkhazova, I., Parente, E., 2002. A new procedure for data reduction in electrophoretic fingerprints of whole-cell proteins. Biotechnol. Lett. 24, 1477-1482]. Hierarchical cluster analysis provided a satisfactory classification of the patterns but was unable to discriminate some species (Leuconostoc, Lb. sakei/Lb. curvatus, Lb. acidophilus/Lb. helveticus, Lb. plantarum/Lb. paraplantarum, Lc. lactis/Lc. raffinolactis). A 7x7 Kohonen self-organizing map (KSOM), trained with the patterns of the reference strains, provided a satisfactory classification of the patterns and was able to discriminate more species than hierarchical cluster analysis. The map was used in predictive mode to identify unknown strains and provided results which in 85.5% of cases matched the classification obtained by hierarchical cluster analysis. Two supervised tools, linear discriminant analysis and a 23:5:2 Bayesian network were proven to be highly effective in the discrimination of SDS-PAGE patterns of Lc. lactis from those of other species. We conclude that data reduction by logistic weighting coupled to traditional multivariate statistical analysis or artificial neural networks provide an effective tool for the classification and identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins.

Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP–16S rDNA analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae

Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component analysis which indicated the differences among strains and allowed them to be divided into seven different groups.

Development of a strain-specific assay for detection of viable Lactobacillus sp. HOFG1 after application to cattle feed

A strain-specific assay was developed for the detection of viable Lactobacillus on cattle feed. The DNA sequences of the 16S rRNA gene and four different 16S/23S rRNA intergenic spacer regions (ISR) from Lactobacillus sp. HOFG1 were determined. Based on these sequences, a strain-specific primer was designed for the amplification of one of the ISRs. When combined with a Lactobacillus group primer, the polymerase chain reaction (PCR) assay detected only Lactobacillus sp. HOFG1 and not other closely related L. animalis or L. murinus strains. The feed assay uses a combination of enrichment culturing and PCR to detect and enumerate viable Lactobacillus sp. HOFG1 after its application onto cattle feed. The high degree of primer specificity and use of selective culturing allows for the detection of viable Lactobacillus which is useful in tracking bacteria applied to complex feed mixtures that contain a high background of endogenous bacteria.

Diversity and dynamics of communities of coagulase-negative staphylococci in traditional fermented sausages

AIMS

Evaluation of composition and evolution of the coagulase-negative staphylococci (CNS) communities in two traditionally fermented sausages (salsiccia and soppressata lucana) produced in Basilicata, southern Italy.

METHODS AND RESULTS

A culture-dependent approach based on isolation on selective media and identification with phenotypic and molecular methods was used. Phenotypic data of 471 strains were analysed by multivariate statistical methods by using 28 strains from culture collections and 48 strains identified by molecular methods (such as 16S rDNA sequencing, species-specific PCR assays, intergenic spacer region-PCR and PCR-denaturing gradient gel electrophoresis) as a reference. The CNS microflora of the sausages was found to be dominated by different biotypes of Staphylococcus xylosus (51.2%), followed by S. pulvereri/vitulus, S. equorum and S. saprophyticus (13.4, 10.2 and 10%, respectively). Other species (S. succinus, S. pasteuri, S. epidermidis, S. warneri and Macrococcus caseolyticus) were also present at lower levels. Identification of 25% of the isolates was impossible.

CONCLUSIONS

The composition of CNS communities varied significantly with sausage type, plant and ripening time and clear differences were found among communities of salsiccia and soppressata at the end of ripening.

SIGNIFICANCE AND IMPACT OF THE STUDY

Phenotypic characterization, supported by molecular and statistical analyses, can be considered a useful approach for typing a large number of isolates and for monitoring the evolution of staphylococcal communities during sausage fermentation but does not always provide a satisfactory identification of the isolates.

Design and evaluation of specific PCR primers for rapid and reliable identification of Staphylococcus xylosus strains isolated from dry fermented sausages

Rapid and reliable identification of Staphylococcus xylosus was achieved by species-specific PCR assays. Two sets of primers, targeting on xylulokinase (xylB) and 60 kDa heat-shock protein (hsp60) genes of S. xylosus, respectively, were designed. Species-specificity of both sets of primers was evaluated by using 27 reference strains of the DSM collection, representing 23 different species of the Staphylococcus genus and 3 species of the Kocuria genus. Moreover, 90 wild strains isolated from different fermented dry sausages were included in the analysis. By using primers xylB-F and xylB-R the expected PCR fragment was obtained only when DNA from S. xylosus was used. By contrast, amplification performed by using primers xylHs-F and xylHs-R produced a single PCR fragment, of the expected length, when DNA from S. xylosus, S. haemolyticus, S. intermedius and S. kloosii were used as template. Nevertheless, AluI digestion of the xylHs-F/xylHs-R PCR fragment allowed a clear differentiation of these 4 species. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. xylosus strains.

Combining Denaturing Gradient Gel Electrophoresis of 16S rDNA V3 Region and 16S–23S rDNA Spacer Region Polymorphism Analyses for the Identification of Staphylococci from Italian Fermented Sausages

Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (PCR-DGGE) and 16S-23S rDNA intergenic spacer region polymorphism (ISR-PCR) analyses were tested as tool for differentiation of staphylococcal strains commonly isolated from fermented sausages. Variable V3 regions of 25 staphylococcal reference strains and 96 wild strains of species belonging to the genera Staphylococcus, Micrococcus and Kocuria were analyzed. PCR-DGGE profiles obtained were species-specific for S. sciuri, S. haemolyticus, S. hominis, S. auricularis, S. condimenti, S. kloosi, S. vitulus, S. succinus, S. pasteuri, S. capitis and S. (Macrococcus) caseolyticus. Moreover, 7 groups could be distinguished gathering the remaining species as result of the separation of the V3 rDNA amplicons in DGGE. Furthermore, the combination of the results obtained by PCR-DGGE and ISR-PCR analyses allowed a clear differentiation of all the staphylococcal species analysed, with exception of the pairs S. equorum-S. cohnii and S. carnosus-S. schleiferi. The suitability of both molecular techniques and of the combination their results for the identification of staphylococci was validated analysing partial nucleotide sequence of the 16S rDNA of a representative number of wild strains.