References of "Nezer, Carine"
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See detailAssessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Hupperts, Caroline et al

in International Journal of Food Microbiology (2017), 247

The aim of this study was to investigate the influence of the slaughter technique (Halal vs. Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological ... [more ▼]

The aim of this study was to investigate the influence of the slaughter technique (Halal vs. Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one “legal” zone of 1,600 cm2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200 cm2). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87 log CFU/100 cm2 and 0.49 and 1.94 log CFU/100 cm2, for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the “legal” swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the “legal” swabbing zone in “Halal” samples, while Brevibacterium and Corynebacterium were encountered more in “Halal” samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups. [less ▲]

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See detailHigh-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

in Archives of Virology (2017), 16(4), 1019-1023

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in ... [more ▼]

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in genomic regions encompassing partial coding sequences for non-structural (NS) 1-2, NS5, NS6, NS7 proteins within open reading frame (ORF) 1. In a region encoding a portion of the major capsid protein (VP1) within ORF2 (also including the ORF4 region) and a portion of the minor structural protein (VP2), the mutation rates were estimated to be at least one order of magnitude higher. The VP2 coding region was found to have the highest mutation rate. [less ▲]

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See detailEffects of protein source and cooking procedure on intestinal microbiota and on fermentation end-products in rats
POELAERT, Christine ULg; Despret, Xavier; Portetelle, Daniel ULg et al

Poster (2016, June)

Animal and plant proteins are major proteins sources in the human diet. After their enzymatic degradation in the upper gastro-intestinal tract, the undigested fraction of these proteins is available for ... [more ▼]

Animal and plant proteins are major proteins sources in the human diet. After their enzymatic degradation in the upper gastro-intestinal tract, the undigested fraction of these proteins is available for fermentation by the microbiota of the large intestine leading to the production of short-chain fatty acids (SCFA), branched-chain fatty acids (BCFA), ammonia, biogenic amines, sulphur metabolites, phenols and indoles. As some of these compounds have genotoxic and cytotoxic effects, protein fermentation is considered as detrimental to the host’s epithelial health. BCFA are usually used as a marker of intestinal protein fermentation. We studied in vivo the impact of proteins from animal and plant origin, raw or after a cooking procedure, on the composition of gut microbiota and on fermentation end-products. Weanling rats were used as models of the human gut microbiota. Eight experimental diets were formulated with beef meat (Longissimus dorsi), chicken meat (Pectoralis major), white pea beans (Phaseolus vulgaris), soybeans (Glycine max), used raw and cooked, as sole source of protein in the diet. One casein diet was used as control. All diets, formulated to contain 15% of raw protein, were given to seven rats for four weeks. After euthanasia, caecal contents were collected. Pyrosequencing analyses (Roche 454 GS Junior Genome Sequencer) were performed to study the microbial composition. SCFA and BCFA were measured using HPLC (Waters 2690). Microbial composition in the caecum is associated to the type of dietary protein and to the cooking procedure applied. The proportion of BCFA in the caecal content is mainly affected by the type of protein. So BCFA represent respectively 04-06% and 35-44% of total SCFA with diets based on plant and on animal proteins. In conclusion, both the type of protein and the cooking procedure could impact the gut microbiota in terms of composition and of fermentative capacity. [less ▲]

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See detailNo favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium)
Degrune, Florine ULg; Theodorakopoulos, Nicolas ULg; Dufrêne, Marc ULg et al

in Agriculture, Ecosystems & Environment (2016), 224

Among the soil management practices used to promote sustainable agriculture, reduced tillage and retention of residues from the previous crop are reported to enhance significantly both soil fertility and ... [more ▼]

Among the soil management practices used to promote sustainable agriculture, reduced tillage and retention of residues from the previous crop are reported to enhance significantly both soil fertility and crop productivity. Here, high-throughput sequencing (454 technology) was used to see how the tillage regime (conventional vs. reduced tillage) and the fate of crop residues (retention or removal) affect microbial communities at two sampling depths (top soil: 0–5 cm and deeper soil: 15–20 cm) in a fertile silty loam soil in Belgium. All combinations of these three factors were studied. After 6 years of conversion from conventional to reduced tillage, depth emerged as the main factor responsible for variation in microbial diversity, tillage regime ranked second, and finally, crop residue fate had no influence on microbial diversity. For both bacteria and fungi, the diversity appeared higher in the top soil than in the deeper soil, and surprisingly, higher under conventional than under reduced tillage. These differences are explained by changes in community composition due to taxon loss rather than taxon replacement. The specific local set of environmental conditions (a loess-derived soil and an oceanic temperate climate) may explain these results. These observations raise the question: does impoverishment in indicator taxa influence soil processes, and thus crop production? To answer this question, we discuss how the presence of certain indicator taxa liable to play an ecological role might relate to crop productivity. [less ▲]

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See detailExploring the bacterial diversity of Belgian steak tartare using metagenetics and qPCR analysis
Delhalle, Laurent ULg; Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg et al

in Journal of Food Protection (2016), 79(2), 220-229

Steak tartare is a popular meat dish in Belgium. It is prepared with raw ground minced beef and eaten with sauce, vegetables, and spiced. Since it contains raw meat, steak tartare is highly prone to ... [more ▼]

Steak tartare is a popular meat dish in Belgium. It is prepared with raw ground minced beef and eaten with sauce, vegetables, and spiced. Since it contains raw meat, steak tartare is highly prone to bacterial spoilage. The objective of this study was to explore the bacterial flora diversity in steak tartare in Belgium according to the source and to determine which bacteria are able to grow during the shelf life. A total of 58 samples from butchers’ shops, restaurants, sandwich shops and supermarkets were collected. These samples were analyzed using 16S rDNA metagenetics, a classical microbiological technique, and quantitative real-time PCR (qPCR) targeting the Lactobacillus genus. Samples were analyzed at the beginning and at the end of their shelf life, except for those from restaurants and sandwich shops analyzed only at the purchase date. Metagenetic analysis identified up to 180 bacterial species and 90 genera in some samples. But only seven bacterial species were predominant in the samples, depending on the source: Brochothrix thermosphacta, Lactobacillus algidus, Lactococcus piscium, Leuconostoc gelidum, Photobacterium kishitani, Pseudomonas spp. and Xanthomonas oryzae. With this work, an alternative method is proposed to evaluate the total flora in food samples based on the number of reads from metagenetic analysis and the results of qPCR. The degree of underestimation of aerobic plate counts (APCs) at 30°C estimated with the classical microbiology method was demonstrated in comparison with the proposed culture independent method. Compared to culture-based methods, metagenetic analysis combined with qPCR targeting Lactobacillus provides valuable information for characterizing the bacterial flora of raw meat. [less ▲]

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See detailAdding mucins to an in vitro batch fermentation model of the large intestine induces changes in microbial population isolated from porcine feces depending on the substrate
Tran, Thi Hanh Tham ULg; Boudry, Christelle ULg; Everaert, Nadia ULg et al

in FEMS Microbiology Ecology (2016), 92(2), 13

Adding mucus to in vitro fermentation models of the large intestine showed that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosa layers to ... [more ▼]

Adding mucus to in vitro fermentation models of the large intestine showed that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosa layers to increase their activity. This study investigates whether this dependence on mucus is substrate-dependent and to which extend other genera are impacted by the presence of mucus. Inulin and cellulose were fermented in vitro by a fecal inoculum from pig in the presence or not of mucin-beads in order to compare fermentation patterns and bacterial communities. Mucins increased final gas production with inulin and shifted short-chain fatty acids molar ratios (P<0.001). QPCR analyses revealed that Lactobacillus spp. and Bifidobacterium spp. decreased with mucins, but Bacteroides spp. increased when inulin was fermented. A more in-depth community analysis indicated that the mucins increased Proteobacteria (0.55 vs. 0.25 %, P=0.013), Verrucomicrobia (5.25 vs. 0.03 %, P=0.032), Ruminococcaceae, Bacteroidaceae, and Akkermansia spp.. Proteobacteria (5.67 vs. 0.55 %, P<0.001) and Lachnospiraceae (33 vs. 10.4 %) were promoted in the mucuscompared to the broth, while Ruminococcaceae decreased. The introduction of mucins affected many microbial genera and fermentation patterns, but from PCA results, the impact of mucus was independent from the fermentation substrate. [less ▲]

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See detailIdentification and traceability of animal and human faecal contamination in bathing sites in Wallonia
Taminiau, Bernard ULg; Hanon, M.; Nezer, Carine et al

Poster (2015, October 16)

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See detailStudy of the microbial diversity of microbial ring trials by metagenomic analysis : Quantification of alive bacteria by exclusion of dead bacteria
Fall, Papa Abdoulaye; Burteau, Sophie; Detry, Émilie et al

Poster (2015, October 16)

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See detailMetagenomic analysis of samples
Daube, Georges ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Patent (2015)

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See detailMethod of testing for animal-derived ingredients in foods
Daube, Georges ULg; Burteau, Sophie; Nezer, Carine et al

Patent (2015)

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See detailÉtude de la diversité microbienne de poudre de lait dopée par analyse métagénomique: Quantification des bactéries vivantes par exclusion de bactéries mortes
Fall, Papa Abdoulaye; Burteau, Sophie; Detry, Émilie et al

Poster (2015, June 17)

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See detailUse of 16S rDNA Metagenetics and classical Microbiology to Assess the bacterial superficial Contamination Patterns in Bovines Classically Slaughtered or following the Halal Ritual
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Hupperts, Caroline et al

Poster (2015, June 17)

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining ... [more ▼]

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining the stunning and the sticking in one single step. The main difference lies in the fact that, in the halal protocol, a single cut with a sharp knife is practiced directly on live cattle, instead of two cutting steps with two different knives for the sticking in the classical slaughtering technique. The unique section in the halal technique results generally in the cross section of trachea and esophagus of cattle. The aim of this study was to seek if the two slaughtering techniques were similar regarding the superficial contamination of carcasses, swabbed between 2 and 4 hours after the killing step. For this purpose, classical microbiological tests (TVC and Enterobacteriaceae) and 16S rDNA metagenetic analysis were carried out from 20 cattle carcasses (swabbing of “legal” zone – 1.600 cm2 – and in the neck area – 200 cm2). The classical microbiological results revealed no significant differences between the two slaughtering practices. Statistical analysis of pyrosequencing data showed that differences in bacterial population abundance between slaughtering methods were mainly found in the “legal” swabbing zone compared to the neck area. Bacterial genera belonging to Actinobacteria (Brevibacterium, Corynebacterium) were more aundant in “Halal” samples whereas populations from the Proteobacteria (Caulobacteraceae, Comamonadaceae, Bradyrhizobiaceae) and Firmicutes (Lactobacillus) were more abundand in the “classical” group. The analysis of OTU abundance of bacteria from the digestive or respiratory tract revealed no differences beteween groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis to the genus level underlines differences between methods, the legal swabbing zone being still the best sampling zone compared to the neckline. The next step will be the identification of precise contamination origin of the differences found between slaughtering methods. [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 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 (2015), 98

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 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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