References of "Taminiau, Bernard"
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See detailShort communication: Evaluation of the microbiota of kefir samples using metagenetic analysis targeting the 16S and 26S ribosomal DNA fragments
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Leclercq, Mathilde et al

in Journal of Dairy Science (in press)

Milk kefir is produced by fermenting milk in the presence of kefir grains. This beverage has several benefits for human health. The aim of this experiment was to analyze 5 kefir grains (and their products ... [more ▼]

Milk kefir is produced by fermenting milk in the presence of kefir grains. This beverage has several benefits for human health. The aim of this experiment was to analyze 5 kefir grains (and their products) using a targeted metagenetic approach. Of the 5 kefir grains analyzed, 1 was purchased in a supermarket, 2 were provided by the Ministry of Agriculture (Namur, Belgium), and 2 were provided by individuals. The metagenetic approach targeted the V1-V3 fragment of the 16S ribosomal (r)DNA for the grains and the resulting beverages at 2 levels of grain incorporation (5 and 10%) to identify the bacterial species population. In contrast, the 26S rDNA pyrosequencing was performed only on kefir grains with the aim of assessing the yeast populations. In parallel, pH measurements were performed on the kefir obtained from the kefir grains using 2 incorporation rates. Regarding the bacterial population, 16S pyrosequencing revealed the presence of 20 main bacterial species, with a dominance of the following: Lactobacillus kefiranofaciens, Lactococcus lactis ssp. cremoris, Gluconobacter frateurii, Lactobacillus kefiri, Acetobacter orientalis, and Acetobacter lovaniensis. An important difference was noticed between the kefir samples: kefir grain purchased from a supermarket (sample E) harbored a much higher proportion of several operational taxonomic units of Lactococcus lactis and Leuconostoc mesenteroides. This sample of grain was macroscopically different from the others in terms of size, apparent cohesion of the grains, structure, and texture, probably associated with a lower level of Lactobacillus kefiranofaciens. The kefir (at an incorporation rate of 5%) produced from this sample of grain was characterized by a lower pH value (4.5) than the others. The other 4 samples of kefir (5%) had pH values above 5. Comparing the kefir grain and the kefir, an increase in the population of Gluconobacter in grain sample B was observed. This was also the case for Acetobacter orientalis in sample D. In relation to 26S pyrosequencing, our study revealed the presence of 3 main yeast species: Naumovozymaspp., Kluyveromyces marxianus, and Kazachastania khefir. For Naumovozyma, further studies are needed to assess the isolation of new species. In conclusion, this study has proved that it is possible to establish the patterns of bacterial and yeast composition of kefir and kefir grain. This was only achieved with the use of high-throughput sequencing techniques. [less ▲]

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See detailAssociation of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Poster (2015, April 01)

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI ... [more ▼]

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, elderly care home residents are considered particularly vulnerable to CDI. The main objective of this study was to evaluate and follow the prevalence of C. difficile in a Belgian nursing home. During a 4-month period, stool samples from a group of 23 elderly care home residents were collected weekly. A C. difficile microbiological detection scheme was performed along with an overall microbial biodiversity study of the faeces content by Targeted Metagenomic analysis. Culture of samples was performed in a selective medium cycloserine cefoxitin fructose cholate. An identification of the isolated colonies was done by PCR detection of tpi, tcdA, tcdB and cdtA genes. Toxic activity was confirmed by a cytotoxic immunoassay. Further characterization was performed by PCR ribotyping. The Metagenomic analysis was targeted on the v1-v3 hyper-variable region of 16S rDNA. The taxonomical assignment of the populations was performed with MOTHUR and Blast algorithms. Seven out of 23 (30.4%) residents were (at least one week) positive for C. difficile. The most common PCR-ribotype identified was 027. Targeted Metagenomic analyses reveals that each resident has his own bacterial imprint, which is stable during the entire study. Residents’ positives for C. difficile by classical microbiology showed an important proportion of C. difficile sequences. However, Metagenomics analysis can’t substitute targeted protocols. It was not used as a diagnostic tool to detect C. difficile but rather to determine the identification and correlations of the major bacterial populations that are present in the gut microbiota. In conclusion, this unique association of classical microbiology protocol with pyrosequencing allowed to follow C. difficile in patients and to identify several other bacterial populations whose abundance is correlated with C. difficile. [less ▲]

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See detailSoil microbial community composition changes according to the tillage practice and plant development stage
Degrune, Florine ULg; Dufrêne, Marc ULg; Taminiau, Bernard ULg et al

Poster (2015, April)

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are ... [more ▼]

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these effects in relation to changes induced by agriculture (conventional and reduced tillage) and plant stage (germination and flowering) in soil conditions. Here, instead of examining this impact at a high taxonomic level such as phylum and/or class, thus missing potentially relevant information from lower levels, we propose an original method: exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. Results show that some microbial communities were impacted only by the tillage practice , while others were impacted only by the stage of plant. Changes in microbial community composition could be due to the soil conditions induced by the soil practice and the stage of plant. [less ▲]

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See detailA novel sub-phylum method discriminates better the impact of crop management on soil microbial community
Degrune, Florine ULg; Dufrêne, Marc ULg; Colinet, Gilles ULg et al

in Agronomy for Sustainable Development (2015)

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but ... [more ▼]

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13% of the variation, and fungal community composition, accounting for 18% of the variation. Whereas phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition, and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities. [less ▲]

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See detailClostridium difficile from food and surface samples in a Belgian nursing home: An unlikely source of contamination
Rodriguez Diaz, Cristina ULg; Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg et al

in Anaerobe (2015), 32

This study investigates the contamination of foods and surfaces with Clostridium difficile in a single nursing home. C. difficile PCR-ribotype 078 was found in one food sample and in none of the tested ... [more ▼]

This study investigates the contamination of foods and surfaces with Clostridium difficile in a single nursing home. C. difficile PCR-ribotype 078 was found in one food sample and in none of the tested surfaces. These results indicate that food and surfaces are an unlikely source of C. difficile infection in this setting. [less ▲]

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See detailMetagenomic analysis of the bacterial microbiota linked to the traditional Algerian date product "Btana"
Abekhti, Abdelkader; Taminiau, Bernard ULg; Kihal, Mabrouk et al

in Annals of Microbiology (2015)

In this study, using high throughput pyrosequencing, we highlighted the bacterial diversity of the traditional Algerian date product "Btana" that is produced in southern Algeria using both direct (DBM ... [more ▼]

In this study, using high throughput pyrosequencing, we highlighted the bacterial diversity of the traditional Algerian date product "Btana" that is produced in southern Algeria using both direct (DBM) and indirect (UBM) methods. Metagenomic analysis yielded a total of 103,379 reads, with a 606 total operational taxonomic units (OTUs) detected. Firmicutes represented 84.79 % of the total pyrosequencing reads. Phylogenetic analysis revealed that the Bacillales represented 90.20 % ± 15.12 % of the total reads. Among the phylotypes detected, Bacillus was the dominant genus (39.53 %). While Bacillus megaterium was shared among all of the samples, its distribution varied widely. Non-metric multidimensional scaling (nMDS) analysis showed that UBM samples clustered together, and three main OTUs were found in these UBM samples: Paenibacillus polymyxa, Paenibacillus xylanexedens, and Planomicrobium JN082684. Correlation analysis showed no association between parametersof the samples (age, pH, water activity) and the specific microbiota. [less ▲]

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See detailThermophilic and cellulolytic consortium isolated from composting plants improves anaerobic digestion of cellulosic biomass: toward a microbial resource management approach
Kinet, Romain ULg; Destain, Jacqueline ULg; Hiligsmann, Serge ULg et al

in Bioresource Technology (2015)

A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas ... [more ▼]

A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas production, was observed for the cultures inoculated with the exogenous consortium. Metagenomics analyses pointed out a weak richness (related to the number of OTUs) of the exogenous consortium induced by the selective pressure (cellulose as sole carbon source) met during the initial isolation steps. Main microbial strains determined were strictly anaerobic and belong to the Clostridia class. During cellulose anaerobic degradation, pH drop induced a strong modification of the microbial population. Despite the fact that richness and evenness were very weak, the exogenous consortium was able to adapt and to maintain the cellulolytic degradation potential. This important result point out the fact that simplified microbial communities could be used in order to increase the robustness of mixed cultures involved in environmental biotechnology. [less ▲]

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See detailDetecting microbial patterns in relation to soil agricultural practices and the plant development stage
Degrune, Florine ULg; Dufrêne, Marc ULg; Taminiau, Bernard ULg et al

Poster (2014, December 02)

Agricultural practices have a strong impact on soil bacteria and fungi. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these ... [more ▼]

Agricultural practices have a strong impact on soil bacteria and fungi. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these effects in relation to changes induced by agriculture and plant stage in soil conditions. Some bacteria are influenced only by the plant stage, which induces changes in soil humidity, pH, nitrates, and carbon. We would thus expect these bacteria to be highly sensitive to these parameters. Other bacteria are affected only by the tillage practice applied. Further study is needed to identify the soil parameters responsible for this effect. The plant stage also has a great impact on fungal community composition. [less ▲]

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See detailPredictive microbiology combined with metagenomic analysis targeted on the 16S rDNA : A new approach for food quality
Delhalle, Laurent ULg; Ellouze, Mariem; Taminiau, Bernard ULg et al

Poster (2014, September 01)

The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods may not be relevant to understand the modifications of the microbial ecology in food products ... [more ▼]

The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods may not be relevant to understand the modifications of the microbial ecology in food products. Metagenomic analysis targeted on 16S ribosomal DNA can elucidate microbial community structures at a muche higher resolution than was previously possible. Combined with predictive microbiological models, a new approach was investigated to take into account bacterial populations dynamics in perishable foods under different environmental conditions. White pudding samples, a typical Belgian pork meat product, were packed under food wrap (atmospheric air condition). Durability studies were conducted at 4°C, 12°C and a dynamic temperature profile according to the NF V01-003 standards (4°C (1/3 of the shelf life) - 8°C (2/3 of the shelf life)) during 15 days. The effect of organic acids was also investigated using a lactic acid (1.8% w/w) treatment. At each day of the trials, classical microbiological (total flora) and 16S rDNA metagenomic analysis were carried out on all these samples. For the metagenomic analysis, a sequencing library was generated, targeting the V1-V3 region of the 16S rDNA. The two major bacterial populations were thus identified (Psychrobacter sp and Brochotrix thermosphacta) and predictive microbiology models used to assess the growth parameters. Cardinal parameters for temperature were collected on the two main bacterial species. The model was validated using the data obtained at a dynamic temperature profile. The results of the simulations for Psychrobacter sp and Brochotrix thermosphacta show a good compliance between predicted and observed data. Compared to culture based methods on selective media and previous independent culture techniques, metagenomic analysis combined with predictive microbiology gives more valuable information, and could be considered as a technological breakthrough to control the quality or for accurately determining shelf life. [less ▲]

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See detailMultilocus sequence typing analysis and antibiotic resistance of Clostridium difficile strains isolated from retail meat and humans in Belgium
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

in Food Microbiology (2014), 42

Clostridium difficile has been isolated from food animals and meat, specially ground pork and ground beef. The recovered isolates were closely related to C. difficile human strains, indicating that ... [more ▼]

Clostridium difficile has been isolated from food animals and meat, specially ground pork and ground beef. The recovered isolates were closely related to C. difficile human strains, indicating that animals and food are possible transmission routes of human C. difficile infection. The main objective of this study was to characterize C. difficile isolates from retail meat and to compare with human isolates recovered from hospital patients in Belgium. Raw meat (beef and pork) was obtained from the retail trade. C. difficile was recovered from 2.3% of the beef samples and from 4.7% of the pork samples. A total of 4 different PCR-ribotypes were identified with a large percentage of types 078 and 014. Resistance to moxifloxacin and erythromycin was detected. The multi-locus sequence typing (MLST) analysis showed that meat and human isolates cluster in the same lineage. This study reveals the presence of toxigenic C. difficile in retail meat in Belgium with predominance PCR-ribotypes 078 and 014, which are among the four most prevalent ribotypes of C. difficile isolated from humans in Europe. [less ▲]

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See detailAntimicrobial and molecular analysis of Salmonella serovar Livingstone strains isolated from humans in Tunisia and Belgium
Guedda, Intissar; Taminiau, Bernard ULg; Ferjani, Asma et al

in Journal of Infection in Developing Countries [=JIDC] (2014), 8

Introduction: Salmonella Livingstone is one of the most common serotypes responsible for nosocomial outbreaks in Tunisia. In this study, 42 isolates of Salmonella Livingstone were analyzed. Most of these ... [more ▼]

Introduction: Salmonella Livingstone is one of the most common serotypes responsible for nosocomial outbreaks in Tunisia. In this study, 42 isolates of Salmonella Livingstone were analyzed. Most of these were isolated from humans (31 strains from Tunisia and 9 strains from Belgium) and 2 isolates came from food products (beef and pork). Methodology: All strains were characterized by antibiogram, multilocus sequence typing (MLST), and virulotyping. This last technique was carried out by simple PCR of five chromosomal genes (agfA, hin/H2, iroB, phoP/Q, and slyA) and two plasmid genes (spvA and spvC). Results: All Tunisian strains were resistant to amoxicillin, amoxicillin-clavulanic acid, ticarcillin, cefalotin, gentamicin, and kanamycin. They were also resistant to third-generation cephalosporin antibiotics (cefotaxim and ceftazidim). Belgian isolates were susceptible to all antibiotics tested. Further to MLST analyses, Tunisian strains belonged to the same sequence type, ST543. For Belgian isolates, eight strains had a ST543 profile, two strains had a ST638 profile, and one strain had a ST457 profile. Analyses of the virulence gene contents showed that strains isolated in different years and from different origins had the same virulence profile. These carried all five chromosomal genes and lacked plasmid-located virulence genes spvA and spvC. Conclusions: A combination of different typing methods showed that the majority of Belgian strains and all Tunisian strains were closely related; they belonged to the same sequence type (ST543) and had the same virulence profile, but different antibiotic resistance profiles depended on the country of origin. [less ▲]

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See detailHigh throughput sequencing analysis reveals genetic variability and selection pressure in different murine norovirus genomic regions during in vitro replication
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Poster (2014, July)

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most ... [more ▼]

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most important etiological cause of both epidemic and sporadic gastroenteritis cases worldwide. Four open reading frames are described into its genome: ORF1 codes the non-structural (NS) proteins, including the viral RNA dependent RNA polymerase (RdRp); ORF2 codes the single capsid protein (VP1), wherein two domains are present: a relatively conserved domain (“shell”) and a more variable domain (“protruding”); ORF3 codes a minor structural protein; and ORF4, currently only found in viruses genetically related to MuNoV codes a virulence factor. In this study, we demonstrated by high throughput sequencing that, during serial passages of MuNoV in cell culture, the substitution rates, estimated by Bayesian inferences, did not significantly differ across the five targeted genomic regions except one. These rates were similar in four genomic regions encompassing partial non-structural 1-2 protein (NS1-2)-, NS5-, NS6-, NS7 (RdRp)- and VP1-coding sequences (coding the conserved part of the protein also including the ORF4 region). In the partial minor structural protein-coding region, this substitution rate was however estimated to be at least one log higher when expressed as substitution/site/day. The precise localisation of the detected nucleotide point mutations (substitution, deletion and insertion) were reported as well as the quantitative increase or decrease of the sequences harbouring them along ten cell culture passages. The non-silent amino acid mutations were also depicted in 3D models for four out of the five studied regions. These results have important implications for different norovirus research fields, especially in terms of diagnosis, classification methodology and genetic evolution. [less ▲]

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See detailComparison and molecular characterization of animal and human Clostridium difficile strains
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg et al

Poster (2014, May 07)

The main objective of this study was to characterize and compare animal and human C. difficile strains with respect to the PCR-ribotype and the antibiotic resistance. Multilocus sequence typing analysis ... [more ▼]

The main objective of this study was to characterize and compare animal and human C. difficile strains with respect to the PCR-ribotype and the antibiotic resistance. Multilocus sequence typing analysis (MLST) was performed in order to study clonal relationships of the isolates. [less ▲]

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See detailStudy of the microbial flora of steak tartare by metagenomic approach
Korsak Koulagenko, Nicolas ULg; Delhalle, Laurent ULg; Nezer, Carine et al

Poster (2014, May 06)

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See detailL'analyse par séquençage à haut débit révèle la variabilité génétique et la pression de sélection dans différentes régions génomiques du norovirus murin durant sa réplication in vitro
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Conference (2014, March)

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes ... [more ▼]

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes étiologiques les plus importantes dans les cas de gastroentérite épidémique ou sporadique dans le monde entier. Quatre cadres de lecture ouverts (ORF) sont décrits au sein de son génome : l’ORF1 code les protéine non structurales (NS), dont l’ARN polymérase ARN dépendante virale (RdRp) ; l’ORF2 code l’unique protéine de capside (VP1), dans laquelle sont décrites deux régions : une relativement conservée (domaine « shell ») et une autre beaucoup plus variable (domaine « protruding ») ; l’ORF3 code une protéine structurale mineure ; et l’ORF4, actuellement uniquement décrit chez les virus génétiquement apparentés au MuNoV, code un facteur de virulence. Dans cette étude, nous démontrons par séquençage à haut débit que, durant des passages successifs du MuNoV en culture cellulaire, les taux de substitution, estimés par inférences Bayésiennes, n’ont pas significativement différé au travers des cinq régions génomiques ciblées à l’exception d’une région bien précise. Ces taux étaient similaires pour quatre régions englobant des séquences partielles codant les protéines non structurales NS1-2, NS5, NS6 et NS7 (RdRp) et VP1 dans sa région conservée (incluant également l’ORF4). Dans la région codant partiellement la protéine structurale mineure, ce taux de substitution, exprimé en substitution/site/jour, a été cependant estimé être plus élevée d’au moins une unité logarithmique. La localisation précise des mutations ponctuelles détectées (substitution, délétion et insertion) est rapportée ainsi que l’augmentation ou la diminution quantitative du nombre des séquences qui les présentaient au cours de dix passages successifs en culture cellulaire. Les localisations des mutations non silencieuses ont aussi été représentées dans une modélisation tridimensionnelle de quatre des cinq régions étudiées. Ces résultats ont d’importantes implications pour différents champs de recherche sur les norovirus, spécialement en termes de diagnostic, de méthodologie de classification et d’évolution génétique. [less ▲]

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See detailGenome encyclopaedia of type strains of the genus Bifidobacterium
Milani, Christian; Lugli, Gabriele; Duranti, Sabrina et al

in Applied and Environmental Microbiology (2014)

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See detailClostridium difficile infection in elderly nursing home residents.
Rodriguez Diaz, Cristina ULg; Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg et al

in Anaerobe (2014), 30

Age-related changes in intestinal flora and host defences, the receipt of antibiotic treatment, and the presence of underlying diseases are some of the most common risk factors associated with Clostridium ... [more ▼]

Age-related changes in intestinal flora and host defences, the receipt of antibiotic treatment, and the presence of underlying diseases are some of the most common risk factors associated with Clostridium difficile infection. Therefore, retirement care facilities for elderly people have been pinpointed as frequent sources of contamination. There is only limited data regarding the presence and epidemiology of C. difficile in nursing homes, and this gap in the current literature emphasises the need to gain a better understanding of the situation in order to prevent the emergence of new outbreaks among this population group. [less ▲]

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See detailInvestigation of the evolutionary development of the genus bifidobacterium by comparative genomics
Lugli, Gabriele; Milani, Christian; Turroni, Francesca et al

in Applied and Environmental Microbiology (2014)

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See detailPsychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014
Pothakos, Vasileios; Taminiau, Bernard ULg; Huys, Geert et al

in International Journal of Food Microbiology (2014), 191

Between 2010 and 2014 several spoilage cases in Belgium occurring in retail foodstuffs prior to the end of shelf-life have been reported to our laboratory. Overall, seven cases involved strictly ... [more ▼]

Between 2010 and 2014 several spoilage cases in Belgium occurring in retail foodstuffs prior to the end of shelf-life have been reported to our laboratory. Overall, seven cases involved strictly psychrotrophic lactic acid bacteria (LAB) contamination in packaged and chilled-stored food products. The products derived either fromrecalls of entire production batches or as specimens of sporadic spoilage manifestations. Some of these samples were returned to the manufacturing companies by consumers who observed the alterations after purchasing the products. The products covered a wide range of foodstuffs (i.e. meat, dairy, vegetable, egg products and composite food) and denoted different spoilage defects. However, the microbiota determined by means of 16S rRNA gene high throughput sequencing analysis underpin few LAB genera (i.e. Leuconostoc, Lactobacillus, Weissella and Lactococcus), which are frequently encountered nowadays as specific spoilage organisms (SSO) albeit overlooked by mesophilic enumeration methods due to their strictly psychrotrophic character. The present study confirms the spreading of psychrotrophic LAB in Belgian food processing environments leading to unexpected spoilage, corroborating their spoilage dynamics and prevalence in all kinds of packaged and refrigerated foodstuffs in Northern Europe. [less ▲]

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See detailValidation of real-time PCR for detection of six major pathogens in seafood products
Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg; Lemaire et al

in Food Control (2014), 44

Seafood can pose a public health concern to consumers. It is often consumed rawand may be contaminated with several foodborne pathogens. In order to guarantee the safety of seafood, real-time polymerase ... [more ▼]

Seafood can pose a public health concern to consumers. It is often consumed rawand may be contaminated with several foodborne pathogens. In order to guarantee the safety of seafood, real-time polymerase chain reaction (PCR) protocols may be used as these enable results to be provided within 24 h. The first goal of our work was to develop real-time PCR protocols enabling the detection of six foodborne pathogens that may be present in seafood products (Campylobacter jejuni, Campylobacter coli, enterohemorrhagic Escherichia coli, Salmonella spp., Vibrio parahaemolyticus, and Vibrio vulnificus). The corresponding gene targets were: 50S/VS1, rfbE, ttr, tlh, and vvp. A multiplex PCR was also developed to detect the virulence genes of V. parahaemolyticus: tdh and trh. A total of 420 bacterial strains belonging to four different genera/strains were used in this study. Sensitivity and specificity were always 100%, except in the case of Salmonella spp., where three strains were not detected by our PCR protocols. The second objective of our work was to assess the detection limit of our real-time PCR protocols on artificially contaminated seafood products (raw shrimps, cooked shrimps, and raw mussels), purchased in public stores. Six different levels of contamination were assayed in four replicates for each matrix. The real-time PCR protocols enabled a better level of detection than the ISO methods, except for Salmonella in raw shrimps and for V. vulnificus in shrimps (raw and cooked). The estimated level of detection was between 1 and 47 cfu/25 g sample for the ISO norms and between 1 and 315 cfu/25 g sample for the realtime PCR protocols tailored in our work. The real-time PCRs developed in our work allowed for good selectivity, sensitivity, and specificity. The sensitivity on seafood products was estimated at a level of 100%, except for Salmonella (97%). In the spiking assays, the levels of detection were lower with the real-time PCR protocol than those obtained with the ISO method. This was not the case for V. vulnificus in raw and cooked shrimps and for Salmonella in raw shrimps. These real-time PCR protocols appear to be good alternative methods for surveillance of seafood products to ensure the absence of foodborne pathogens. One additional conclusion is that laboratories have to use enrichment media that are compatible with those recommended by ISO standards. This may facilitate the isolation of the pathogen if the real-time PCR protocol gives a suspect positive signal during the first step of the seafood analysis. [less ▲]

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