References of "Taminiau, Bernard"
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See detailImpact of agricultural practices on soil microbial communities in Belgium
Degrune, Florine ULg; Taminiau, Bernard ULg; Dufrêne, Marc ULg et al

Poster (2013, December 11)

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on ... [more ▼]

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on finding ways to reduce the use of chemicals, and investigating microbial life may lead to solutions. We know that bacteria and fungi are deeply involved in nutrient cycles. Recently the emergence of massive parallel sequencing has enabled us to realize that microbial diversity is huger than we expected. With such a tool it should be possible to study how soil management practices affect the microbial diversity of agricultural soils. A few such studies have been conducted, most of them focusing on bacteria. For Belgium in particular, there is a lack of data on this topic. Here the aim was to see how residue management and tillage practices affect communities of both bacteria and fungi in Belgian agricultural soils. For this we used 454 pyrosequencing of 16S bacterial and 28S fungal rRNA genes. Soil samples came from an experiment in which faba beans were grown with four soil management practices (tillage and no tillage, with and without crop residues), each repeated four times in a Latin square. Several chemical and physical characteristics were measured on each sample. The results show that fungi and bacteria are both impacted by Tillage practices. The main soil drivers are Magnesium and Phosphorus for Fungi communities, and Phosphorus and Potassium for bacteria communities. Finally, the fungi variance observed between plots is explained at 38% by Tillage, Magnesium and phosphorus. And the bacteria variance is explained at 28% by Tillage, Phosphorus and Potassium. [less ▲]

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See detailEvaluation of the bacterial diversity and its evolution during storage of fresh beef from British and Belgian origins under different atmosphere and temperature conditions
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Taminiau, Bernard ULg et al

Conference (2013, December 10)

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature, by using a metagenomic ... [more ▼]

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature, by using a metagenomic approach. Metagenomic analyzes revealed that the origin, atmosphere and temperature conditions influenced the selection of the predominant flora. Vacuum-packaged British samples presented higher concentrations of Lactobacillus algidus at the begging of the experiment than Belgian samples. Furthermore, the development of Lactobacillus algidus was favored in British and Belgian samples preserved under vacuum at −1 °C, while a predominance of Lactococcus piscium was observed for samples stored at +4 °C. These microorganisms have already been isolated from beef, but taking into account that the knowledge about these two species is currently limited, it is still not possible to state if the conservability of the tested samples was influenced by the presence of these bacteria. Moreover, storage under modified atmosphere favored the development of Leuconostoc gasicomitatum in both British and Belgian samples. This specie is often associated with spoilage of cold-stored modified-atmosphere-packaged (MAP) nutrient-rich foods. This result can partially explain the short shelf-life of the samples once they are stored under this condition. Metagenomics showed to be a useful tool to study the microbial population of a complex matrix since some of the identified genera could not have grown or have grown slowly in culture media commonly used. In addition, it helped to clarify the evolution of the bacterial ecosystem associated to meat during its storage. [less ▲]

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See detailClostridium difficile: an emerging zoonotic pathogen ?
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Conference (2013, November 21)

Clostridium difficile is an anaerobic, spore-forming bacterium that remains the main cause of nosocomial diarrhoea in humans after use of antibiotics. C. difficile has also been described in other ... [more ▼]

Clostridium difficile is an anaerobic, spore-forming bacterium that remains the main cause of nosocomial diarrhoea in humans after use of antibiotics. C. difficile has also been described in other environments outside of hospitals, such as soil, river and seawater samples (Pasquale et al., 2011) and in animals, in which it can also cause enteric disease (Songer and Anderson, 2006). The possibility of transmission of C. difficile pathogenic isolates between animals, environments and humans has been suggested (Janezic et al., 2012). In recent years, the interest in C. difficile in food and in food animals has increased, leading to studying animals as a possible reservoir and a potential risk for food borne infections linked to C. difficile. Studies in various countries have determined differences in the prevalence of C. difficile in animals just before slaughter (Houser et al., 2012; Rodriguez et al., 2012) as well as in retail meat (Houser et al., 2012). In addition, many types, including PCR-ribotype 078, are present in humans, animals and meat (Janezic et al.; Weese et al., 2009). The objective of this study was to evaluate the presence of C. difficile at the slaughterhouse and in retail meat. Intestinal and carcass samples were collected from pigs and cattle at a single slaughterhouse. Raw meat (beef and pork) was obtained from the retail trade. C. difficile was isolated in 1% and 9.9% of the pig and cattle intestinal contents and in 7.9% and 7% of cattle and pig carcass samples respectively. From retail meat, C. difficile was recovered from 2.3% of the beef samples and from 4.7% of the pork samples. A total of 21 different PCR-ribotypes were identified with a large percentage of types 078 and 014. This study confirms that animals are carriers of C. difficile at slaughter, and that carcass contamination occurs inside the slaughterhouse. Furthermore the results obtained also reveal the presence of toxigenic C. difficile in retail meat in Belgium with a predominance of isolates correlated with the PCR-ribotypes involved in human C. difficile infections. [less ▲]

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See detailASSOCIATION OF CLASSICAL MICROBIOLOGY AND TARGETED METAGENOMIC ANALYSIS TO EVALUATE THE PRESENCE OF CLOSTRIDIUM DIFFICILE IN A BELGIAN NURSING HOME
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg et al

Conference (2013, October 22)

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. Surfaces and diary meals were also sampled in order to determinate the possible role of environmental and food contamination in the acquisition of CDI. 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. C. difficile was not detected in any of the tested meals or surfaces samples. For the stools samples, 6 of the 23 controlled residents were identified as C. difficile carriers. The isolates belonged to 4 different PCR ribotypes, including types 020 and 027. 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 detailBacterial diversity and its evolution during storage of fresh beef from different origins under different atmosphere and temperature conditions
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Taminiau, Bernard ULg et al

Poster (2013, October 11)

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature. Two batches of three vacuum ... [more ▼]

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature. Two batches of three vacuum packed striploins from United Kingdom and Belgium were obtained from a food wholesaler located in the Walloon Region. Fifteen days after slaughter, the striploins were sliced and individually kept under vacuum for 30 days: i) at −1 °C; ii) at +4 °C and iii) at −1 °C for 15 days and then at +4 °C for 15 days. The bacterial diversity was evaluated by metagenomic approach 15, 30 and 45 days after slaughter. Furthermore, each 15 days part of the vacuum packed striploin slices were repacked under modified atmosphere (70 % O2/30 % CO2), stored at +4 °C for 2 days and at +8 °C for 5 days, and then analyzed. Metagenomic analysis revealed a selection of the initial flora depending on atmosphere and temperature conditions. The development of Lactobacillus algidus was favored in samples preserved under vacuum at −1 °C, while a predominance of Lactococcus piscium was observed for samples stored at +4 °C. Moreover, storage under modified atmosphere favored the development of Leuconostoc gasicomitatum. These microorganisms have already been isolated from beef, but no study has evaluated their role in food conservation. The next step of this study will be to isolate and characterize strains of Lactobacillus algidus from meat and to assess their bioprotective potential. [less ▲]

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See detailPresence of Clostridium difficile in pigs and cattle intestinal contents and carcass contamination at the slaughterhouse in Belgium.
Rodriguez Diaz, Cristina ULg; Avesani, V.; Van Broeck, J. et al

in International Journal of Food Microbiology (2013), 166(2), 256-262

The objective of this study was to evaluate the presence of Clostridium difficile in intestinal and carcass samples collected from pigs and cattle at a single slaughterhouse. C. difficile was isolated in ... [more ▼]

The objective of this study was to evaluate the presence of Clostridium difficile in intestinal and carcass samples collected from pigs and cattle at a single slaughterhouse. C. difficile was isolated in 1% and 9.9% of the pig and cattle intestinal contents and in 7.9% and 7% of cattle and pig carcass samples respectively. A total of 19 different PCR-ribotypes were identified, among them types 078 and 014. Seven of 19 ribotypes correlated with the PCR-ribotypes involved in human C. difficile infections in Belgium. This study confirms that animals are carriers of C. difficile at slaughter and ribotypes are identical than those in humans, and that carcass contamination occurs inside the slaughterhouse. [less ▲]

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See detailIdentification and typing of Salmonella serotypes isolated from guinea fowl (Numida meleagris) farms in Benin during four laying seasons (2007-2010)
Boko, C; Kpodekon, T; Duprez, Jean-Noël ULg et al

in Avian Pathology : Journal of the W.V.P.A (2013), 42

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See detailClostridium difficile in young farm animals and slaughter animals in Belgium
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Vandebroek, Johan et al

in Anaerobe (2012), 18(6), 621-625

Faecal carriage of Clostridium difficile in healthy animals has been reported recently, especially in piglets and calves. However there is limited data about carriage in animals just prior to slaughter in ... [more ▼]

Faecal carriage of Clostridium difficile in healthy animals has been reported recently, especially in piglets and calves. However there is limited data about carriage in animals just prior to slaughter in Europe. The main objective of this study was to determine the presence of C. difficile in pigs and cattle at the slaughterhouse. C. difficile was isolated in 6.9% of the cattle at the slaughterhouse. None of the pig slaughter samples were positive for C. difficile after an enrichment time of 72 h. For complementary data, a short study was conducted in piglets and calves at farms. C. difficile was more prevalent in piglets (78.3%) than in calves (22.2%) on the farms. Regarding the piglet samples, 27.8% of the positive samples were detected without enrichment of stools. The PCR ribotype 078 was predominant in farm animals. Samples isolated from slaughter cattle presented the widest range in PCR-ribotype variety, and the most prevalent PCR ribotype was 118a UCL. The results of this study confirm that C. difficile is present in slaughter animals in Belgium with a large percentage of toxigenic strains also commonly found in humans. [less ▲]

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See detailLa diversité bactérienne et son évolution pendant la conservation de viandes bovines fraîches de différentes origines conditionnées sous vide
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Taminiau, Bernard ULg et al

Poster (2012, December)

Le but de cette étude à été d'évaluer la diversité bactérienne et son évolution pendant la conservation de viandes bovine fraîches sous vide, en fonction de leur origine et du respect ou non d’une ... [more ▼]

Le but de cette étude à été d'évaluer la diversité bactérienne et son évolution pendant la conservation de viandes bovine fraîches sous vide, en fonction de leur origine et du respect ou non d’une température proche du point de congélation. Les dénombrements réalisés ont mis en évidence que les viandes d’origines britannique et belge testées présentent un écosystème microbien différent. Les analyses par approche métagénomique permettront d’éclaircir ces différences, surtout en ce qui concerne la présence de bactéries pouvant jouer un rôle "bioprotecteur" permettant d’améliorer la conservabilité des viandes. [less ▲]

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See detailValidation de la qualité de la viande hachée de porc par une approche métagénomique ciblée
Taminiau, Bernard ULg; Nezer, Carine; Adolphe, Ysabelle ULg et al

Conference (2012, November 13)

Food products represent great biotopes for bacteria. The optimization of foodstuffs conservation pass by a better understanding of those biotopes and their spoilage. The current techniques of new ... [more ▼]

Food products represent great biotopes for bacteria. The optimization of foodstuffs conservation pass by a better understanding of those biotopes and their spoilage. The current techniques of new generation sequencing give a new dimension to the microbial ecology, through the metagenomic analysis of individuals' large number, within a mixed microbial population. Our aim is to demonstrate that this methodology can be successfully applied to the validation of the quality of foodstuffs during storage. This study was carried out on pork minced meat with shelf-life tests in various conditions of preservation (temperature and packaging). The analysis was performed in parallel with standardized microbiological methods and with massive sequencing of two hypervariables regions of the rDNA 16S. The results show an excellent correlation between the two approaches and underline the tremendous utility of metagenomic analysis for in-depth characterization of the potential altering bacteria in fresh meat. [less ▲]

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See detailViandes bovines à longue durée de conservation conditionnées sous vide : isolement et caractérisation de souches de Carnobacterium
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Baptista Rodrigues, Ana Lucia ULg et al

Poster (2012, November 13)

The lactic acid bacteria Carnobacterium divergens and Carnobacterium maltaromaticum are often associated to meat and meat products and may be used as a protective culture, improving the microbial ... [more ▼]

The lactic acid bacteria Carnobacterium divergens and Carnobacterium maltaromaticum are often associated to meat and meat products and may be used as a protective culture, improving the microbial stability and the safety of these products. In this context, the aim of this study was to isolate and characterize Carnobacterium from long shelf-life vacuum-packed beef. LAB counts after culture at +22°C remained below 2.0 log UFC/cm², even at the end of shelf life. On the other hand, the ecosystem evaluation performed by metagenomics revealed the predominance of Carnobacterium and Lactobacillus on the samples. After spreading of a peptone water suspension obtained from the samples on PCA, pure isolates were collected and identified by API 50 CHL galleries. Seventy-eight % of isolates were C. maltaromaticum, 3 % C. divergens and 19 % could not be identified. The next step of this work will consist in performing a genotypic and functional characterization of these Carnobacterium isolates. [less ▲]

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See detailStudy of the microbial flora of freshwater and seawater fish filets in different packaging conditions by metagenomic analysis targeted on the 16S ribosomal DNA
Delhalle, Laurent ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Conference (2012, October 19)

Metagenomics has appeared as a powerful tool to study bacterial composition of various environmental samples. This work describes the application of this technique to study the bacterial population of two ... [more ▼]

Metagenomics has appeared as a powerful tool to study bacterial composition of various environmental samples. This work describes the application of this technique to study the bacterial population of two fresh fish filets. The two fish species are from freshwater (pangasius) and seawater (haddock), respectively. Samples where directly analyzed the day of receipt. Others samples were analyzed at the end their shelf life after storage at 4°C (1/3 of their shelf life) and 8°C (2/3 of their shelf life). For these samples, packagings were made in plastic wrap for atmospheric air condition and in trays under modified atmosphere. Classical microbiological and 16S rDNA metagenomic analysis were carried out on all these samples. The composition and evolution of microbial populations of fish filet stored under different packaging conditions and temperatures of storage were investigated with identification of bacteria species. A total of 40 different species were identified for both fish types. Gram-negative bacteria are always predominated among the initial flora and at the end of the shelf life in all the trials. At the beginning of storage, the predominant Gram-negative microflora consisted of Moraxellaceae (Acinetobacter spp, Psychrobacter spp.), Pseudomonadaceae (Pseudomonas spp), and Shewanella spp and the Gram-positive flora was identified as Lactobacillaceae (Carnobacterium spp), Brochothrix thermosphacta and Planococcus donghaensis (only for pangasius). For the pangasius, Planococcus donghaensis is only present before the fish is packed and its dominant presence could provide an indication of the freshness of the fish. The metagenomic analysis is a useful tool to identify and to measure the relative proportions of bacterial species in fish filet samples. [less ▲]

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See detailMetagenomic analysis as a tool to better characterize the bacterial content of food and food preparations.
Taminiau, Bernard ULg; Delhalle, Laurent ULg; Nezer, Carine et al

Conference (2012, September 04)

Metagenomic analysis is a new culture-independent approach for assigning a taxonomic, genic or functional identity to bacterial DNA fragments of unknown origin. Its power and utility is increasingly ... [more ▼]

Metagenomic analysis is a new culture-independent approach for assigning a taxonomic, genic or functional identity to bacterial DNA fragments of unknown origin. Its power and utility is increasingly rising thanks to the next generation sequencing techniques. It is now mature and cheap enough to be transposed to more applied fields like the food microbiology. We demonstrated in several studies the extraordinary potential of the targeted metagenomic analysis to different problematics related to food products. First, this approach is highly useful for the validation of the shelf life of food products. We analyzed standardized pork minced meat and meat product samples packaged either under modified atmosphere (MAP - 30% CO2, 70% O2) or under permeable atmosphere packaging, stored at different temperature (4°C, 4-8°C and 12°C) until the end of shelf-life. The metagenomic analysis allowed to identify species of all the sub-dominant bacterial populations. This approach showed why MAP can improve meat quality by favoring certain species rather than others. As a second example, we sought to identify the potential spoiling bacteria in several food products like raw fish, rind cheese or vacuum packed beef meats in order to illustrate the usefulness of metagenomics for the quality control of food preparations. Samples from various food matrices were screened to identify the bacterial contaminants. We combined the bioinformatics analysis with a classical approach to generate effective quantitative data for the various bacterial populations detected. This analysis characterizes the samples both on the identity of the potential spoiling bacteria present and on the quantification level of the contaminants. Finally, the metagenomic analysis reveals the presence of numerous uncultured and uncharacterized bacteria. The use of a carefully designed analysis pipeline has been used to ensure to label the bacterial population with a precise taxonomic identity and to determine whether the targeted population corresponds to a known species or not. This way, even if the nearest known homologous sequence is an environmental sample, its relatedness to known species can be deduced. This represents a new tool to trace yet uncharacterized food spoiling bacteria. [less ▲]

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See detailMolecular identification of the bacterial populations of steak tartare, a raw consumed meat preparation: a practical use of targeted metagenomic analysis
Taminiau, Bernard ULg; Delhalle, Laurent ULg; Nezer, Carine et al

Poster (2012, September 04)

Steak tartare is a popular meat dish in Belgium and other european countries. It is often consumed with french fries or as sandwich spread. This product, due to its raw nature, is highly sensitive to ... [more ▼]

Steak tartare is a popular meat dish in Belgium and other european countries. It is often consumed with french fries or as sandwich spread. This product, due to its raw nature, is highly sensitive to bacterial alteration. A better understanding of the bacterial content of this meat product will thus be insightful to master the alteration hazards. Throughout a targeted metagenomic analysis we characterized the bacterial populations of several steak tartare samples. These samples were bought and analyzed during the same day, from three different commercial sources: butchery, sandwich vendor and restaurant. A classic microbiological analysis was performed in parallel. The metagenomic analysis was targeted on two different hypervariable regions of the bacterial 16S rDNA, in order to compare the bacterial identification efficiency. A total of 60,500 sequences for 12 samples were submitted to a metagenomic analysis. The best hypervariable region enabled us to identify 356 different bacterial species. Lactobacillus algidus is the leading bacterial species, representing 52% of the total analyzed sequences, followed by an uncultured Pseudomonas sp. (8.43%) and Photobacterium phosphoreum (7.92%). The analysis of the results shows that remarkable differences appear between the three sources of steak tartare. First, the samples from the butchery are mainly composed of Lactobacillus populations and to a lesser extend of environmental contaminants like Xanthomonas campestris. On the opposite, the samples from the restaurant are contaminated with higher level of Leuconostocaceae like Leuconostoc carnosum or an uncultured Weissella sp., or with gamma-proteobacteria like Pseudomonas sp. or Psychrobacter sp. These last samples were characterized with some alteration (slime, off odor) that can thus be put in relation with the bacterial populations identified. Combining a broad-range sequencing effort to a rigorous computer analysis gives a powerful tool for the microbiology of food products. Its application can be virtually extended to every food product be readily transposed to the food industry. [less ▲]

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See detailThe extraordinary potential of metagenomic tools for food microbiology: an example with bacterial microbiota of raw and pasteurized milk cheeses
Delhalle, Laurent ULg; Nezer, Carine; Taminiau, Bernard ULg et al

Poster (2012, September 03)

Among the culture-independent techniques, ultra-sequencing has contributed to place metagenomic analysis as the best alternative to study complex microbiota. During the last three years, metagenomic ... [more ▼]

Among the culture-independent techniques, ultra-sequencing has contributed to place metagenomic analysis as the best alternative to study complex microbiota. During the last three years, metagenomic studies were used essentially for environmental samples but it could be used also to analyse bacterial populations of food samples. This work describes the application of this technique to study the bacterial population of different types of soft cheeses. Among these, three of them are a typical Belgian soft cheese with washed rind (two with raw milk and the third with pasteurized milk). The fourth is a French creamy soft cheese made with raw milk. Classical microbiological and 16S rDNA metagenomic analysis were carried out in the core and on the rind of the four cheeses, giving a total of 8 samples. In total, 48 genus and 163 species were identified for all samples. As expected Lactoccocus lactis and/or cremoris are the most representative species in the core of the four cheeses. On the rind of cheeses, the predominant bacterial species are Psychrobacter glacinola, Staphylococcus equorum, Corynebacterium casei and Marinilactibacillus psychrotolerans. Brevibacterium spp and Psychroflexus spp are important for the rind of washed rind cheeses. All these species are present in different proportions following the origin and the cheese making process and they are well known for their organoleptic properties on the rind of cheese. The two Belgian soft cheese made with raw milk are composed of many more different bacterial species. While the cheese made from pasteurized milk contains less species mainly composed by Lactococcus lactis (97,6%) in the core. An unexpected result is the low diversity of the a French creamy soft cheese made with raw milk with only two predominent species : Lactoccocus cremoris and Leuconostoc citreum are present in the core (94,9% and 4,9% , respectively) and on the rind (93,8% and 5% , respectively). Compared with the other cheeses made with raw milk, this result is surprising. The bacterial cheese microbiota plays a central role in cheese-making. The subtleties of cheese character, as well as their shelf-life, are largely determined by the evolution of their microbiota. [less ▲]

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See detailA new approach of food microbiology with the metagenomic tools: an application on fish
Delhalle, Laurent ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Poster (2012, September 03)

Metagenomics has appeared as a powerful tool to study bacterial composition of various environmental samples. Its interest has started to appear in food microbiology but only on the study of very ... [more ▼]

Metagenomics has appeared as a powerful tool to study bacterial composition of various environmental samples. Its interest has started to appear in food microbiology but only on the study of very particular bacterial populations of fermented food. This work describes the application of this technique to study the bacterial population of two fresh fish filets. The two fish species are from freshwater (pangasius) and seawater (haddock), respectively. Samples where directly analyzed the day of receipt. Others samples were analyzed at the end their shelf life after storage at 4°C (1/3 of their shelf life) and 8°C (2/3 of their shelf life). For these samples, packagings were made in plastic wrap for atmospheric air condition and in trays under modified atmosphere. Classical microbiological and 16S rDNA metagenomic analysis were carried out on all these samples. The composition and evolution of microbial populations of fish filet stored under different packaging conditions and temperatures of storage were investigated with identification of bacteria species. A total of 40 different species were identified for both fish types. Gram-negative bacteria are always predominated among the initial flora and at the end of the shelf life in all the trials. At the beginning of storage, the predominant Gram-negative microflora consisted of Moraxellaceae (Acinetobacter spp, Psychrobacter spp.), Pseudomonadaceae (Pseudomonas spp), and Shewanella spp and the Gram-positive flora was identified as Lactobacillaceae (Carnobacterium spp), Brochothrix thermosphacta and Planococcus donghaensis (only for pangasius). Regardless the packaging and the fish origin, significant variations of the initial flora were noted. The important growth of some Gram negative populations could indicate a risk of spoilage. Thus, the metagenomic approach could be used to adequately determine the duration of shelf-life. For the pangasius, Planococcus donghaensis is only present before the fish is packed and its dominant presence could provide an indication of the freshness of the fish. The metagenomic analysis is a useful tool to identify and to measure the relative proportions of bacterial species in fish filet samples. [less ▲]

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See detailThe Metagenomic in the Service of the Food Microbiology.
Taminiau, Bernard ULg; Nezer, Carine; Poullet, Jean-Baptiste et al

Poster (2012, July 23)

Introduction: Food products represent great biotopes for bacteria. The optimisation of foodstuffs conservation, mattering so economically as from the point of view of the public health, pass by a better ... [more ▼]

Introduction: Food products represent great biotopes for bacteria. The optimisation of foodstuffs conservation, mattering so economically as from the point of view of the public health, pass by a better understanding of those biotopes and their spoilage. Microbiologists had already tried to resolve this problem throughout several approaches. Studies based on classical microbiology cultures were completed by strategies centred on approaches independent from the microbiological culture. Purpose: The current techniques of new generation sequencing give a new dimension to the microbial ecology, through the metagenomic analysis of individuals' large number, within a mixed microbial population. Our aim is to demonstrate that this methodology can be successfully applied to the study of foodstuffs microbial flora, and can be adapted to the specific requirements of food microbiology. Methods: This study was carried out on pork's minced meat and white sausage, with shelf-life tests in various conditions of preservation (temperature and packaging). The rDNA 16S was extracted from the original products and samples in the best-before date and, after standardization, hypervariable regions V5 were sequenced. Results: A total about 130.000 sequences were obtained and a metagenomic analysis succeeded in the taxonomic classification to the genus level for 80 % of this population. The subsequent analysis of microbial populations shows that the majority microbial populations at the expiration date are the same ones which are generally observed during microbiological analysis of these meat products. However, the population subdominants and especially several populations of not cultivable germs were able to be identified. These groups of bacteria, more difficult to obtain by the other methods, must be studied because they participate in the spoilage process of food products. Significance: The sensibility of this technology makes possible the analysis of foodstuffs presenting a very low microbial rate and, thus, allows the identification of the microbial contaminants before they grow the levels detected by cultural methods. [less ▲]

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