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See detailOptimization of DNA extraction from the Algerian traditional date’s product “Btana”
Abekhti, Abdel; Dgeghati, S.; Taminiau, Bernard ULiege et al

in Applied Biology in Saharan Areas (2017), 1(1), 23-32

Btana is traditional preservation method that can sustain date’s supply during many years in comparaison to the commercial storage methods. However no scientific informations are available about ... [more ▼]

Btana is traditional preservation method that can sustain date’s supply during many years in comparaison to the commercial storage methods. However no scientific informations are available about biological factors that contribute to the successful of this method. Bacterial communities are a major key in preservation of many foods. Culture independent techniques are the most powerful tools to enhance bacterial diversity studies, but their efficiencies start with DNA extraction step. Therefore we have studied 3 protocols of DNA extraction from 11 Btana samples to evaluate their yield in total microbial DNA recovery. Protocols were based on a commercial kit DNeasy (QIAGEN, Germany) and two modified CTAB extraction methods (combined CTAB-DNeasy protocol, modified CTAB protocol) using polyvinyl pyrrolidone (PVP) and treatment with high salt solution (5M NaCl). Protocols were compared for quantity of DNA extracted using NanoDrop® ND-1000 Spectrophotometer and quality of DNA by 260/280 nm absorption ratio. The total extracted DNA was cheeked by PCR amplification of the 16S rRNA and visualized by electrophoresis on agarose gel (0.8%). Results showed that CTAB modified method provide the best DNA yield; however purification with NucleoSpin® Kit (Clontech, UK) was mostly needed for amplifying the DNA template. DNeasy kit protocol gave an amplified high quality DNA, but poor yields were obtained from date samples [less ▲]

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See detailDetection, isolation and characterization of Fusobacterium gastrosuis sp. nov. colonizing the stomach of pigs
De Witte, C.; Flahou, B.; Ducatelle, R. et al

in Systematic & Applied Microbiology (2017), 40(1), 42-50

Nine strains of a novel Fusobacterium sp. were isolated from the stomach of 6-8 months old and adult pigs. The isolates were obligately anaerobic, although they endured 2 hours exposure to air ... [more ▼]

Nine strains of a novel Fusobacterium sp. were isolated from the stomach of 6-8 months old and adult pigs. The isolates were obligately anaerobic, although they endured 2 hours exposure to air. Phylogenetic analysis based on 16S rRNA and gyrase B genes demonstrated that the isolates showed high sequence similarity with Fusobacterium mortiferum, Fusobacterium ulcerans, Fusobacterium varium, Fusobacterium russii and Fusobacterium necrogenes, but formed a distinct lineage in the genus Fusobacterium. Comparative analysis of the genome of the type strain of this novel Fusobacterium sp. confirmed that it is different from other recognized Fusobacterium spp. DNA-DNA hybridization, fingerprinting and genomic %GC determination further supported the conclusion that the isolates belong to a new, distinct species. The isolates were also distinguishable from these and other Fusobacterium spp. by phenotypical characterization. The strains produced indole and exhibited proline arylamidase and glutamic acid decarboxylase activity. They did not hydrolyse esculin, did not exhibit pyroglutamic acid arylamidase, valine arylamidase, α-galactosidase, β-galactosidase, β-galactosidase-6-phosphate or α-glucosidase activity nor produced acid from cellobiose, glucose, lactose, mannitol, mannose, maltose, raffinose, saccharose, salicin or trehalose. The major fatty acids were C16 : 0 and C18 : 1ω9c. The name Fusobacterium gastrosuis sp. nov. is proposed for the novel isolates with the type strain CDW1(T) (= DSM 101753(T) = LMG 29236(T)). We also demonstrated that Clostridium rectum and Fusobacterium mortiferum represent the same species, with nomenclatural priority for the latter. [less ▲]

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See detailLooking for phosphate-accumulating bacteria in activated sludge processes : a multidisciplinary approach
Tarayre, Cédric ULiege; Charlier, Raphaëlle; Delepierre, Anissa ULiege et al

in Environmental Science and Pollution Research (2017)

Over the past decades, an increasing need in renewable resources has progressively appeared. This trend concerns not only fossil fuels but also mineral resources. Wastewater and sewage sludge contain ... [more ▼]

Over the past decades, an increasing need in renewable resources has progressively appeared. This trend concerns not only fossil fuels but also mineral resources. Wastewater and sewage sludge contain significant concentrations in phosphate and can be considered as a fertilizer source of the utmost importance. In wastewater treatment plants, the biological uptake of phosphate is performed by a specific microbiota: the phosphate-accumulating organisms. These microorganisms are recovered in sewage sludge. Here, we aimed to investigate the occurrence of phosphate accumulators in four wastewater treatment plants. A 16S metagenetic analysis identified the main bacterial phyla extracted from the aerobic treatment: α-Proteobacteria, β-Proteobacteria, and Sphingobacteria. An enrichment stage was performed to stimulate the specific growth of phosphate-accumulating bacteria in an acetate medium. An analysis of metabolic activities of sulfur and phosphorus highlighted strong modifications related to phosphorus and much less distinguishable effects with sulfur. A solid acetate medium containing 5-Br-4-Cl-3-indolyl phosphate was used to select potential phosphate-accumulating bacteria from the enriched consortia. The positive strains have been found to belong in the genera Acinetobacter, Corynebacterium, and Pseudomonas. Finally, electron microscopy was applied to the strains and allowed to confirm the presence of polyphosphate granules. Some of these bacteria contained granules the size of which exceeded 100 nm. [less ▲]

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See detailMoku Virus in Invasive Asian Hornets, Belgium, 2016.
Garigliany, Mutien-Marie ULiege; Taminiau, Bernard ULiege; El Agrebi, Noémie ULiege et al

in Emerging Infectious Diseases (2017), 23(12), 2109-2112

We report the detection of Moku virus in invasive Asian hornets (Vespa velutina nigrithorax) in Belgium. This constitutes an unexpected report of this iflavirus outside Hawaii, USA, where it was recently ... [more ▼]

We report the detection of Moku virus in invasive Asian hornets (Vespa velutina nigrithorax) in Belgium. This constitutes an unexpected report of this iflavirus outside Hawaii, USA, where it was recently described in social wasps. Although virulence of Moku virus is unknown, its potential spread raises concern for European honeybee populations. [less ▲]

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See detailAnti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese named "Tomme d'Orchies"
Ceugniez, Alexandre; Coucheney, Françoise; Jacques, Philippe et al

in Research in Microbiology (2017)

Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 were recently isolated from a traditional French cheese, Tomme d'Orchies, and characterized here for their advantages using a different ... [more ▼]

Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 were recently isolated from a traditional French cheese, Tomme d'Orchies, and characterized here for their advantages using a different application perspective. First, we established their anti-Salmonella activity and downregulation of the virulence sopD gene of Salmonella enterica subsp. enterica serovar Typhimurium, mainly in the presence of K. marxianus S-2-05. In addition to their antagonism, these non-Saccharomyces yeasts were able to survive under conditions mimicking the gastrointestinal environment and to form biofilms on an abiotic device such as polystyrene. These strains also displayed highly hydrophilic cell wall surfaces properties and capacity for adhesion to intestinal Caco-2 cells, thus enhancing their potential as probiotic strains. [less ▲]

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See detailTemporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes
Degrune, Florine; Theodorakopoulos, Nicolas; Colinet, Gilles ULiege et al

in Frontiers in Microbiology (2017)

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See detailRhubarb extract prevents hepatic inflammation induced by acute alcohol intake, an effect related to the modulation of the gut microbiota.
Neyrinck, Audrey M.; Etxeberria, Usune; Taminiau, Bernard ULiege et al

in Molecular Nutrition & Food Research (2017), 61(1), 1500899

SCOPE: Binge consumption of alcohol is an alarming global health problem. Acute ethanol intoxication is characterized by inflammation and oxidative stress, which could be promoted by gut barrier function ... [more ▼]

SCOPE: Binge consumption of alcohol is an alarming global health problem. Acute ethanol intoxication is characterized by inflammation and oxidative stress, which could be promoted by gut barrier function alterations. In this study, we have tested the hypothesis of the hepatoprotective effect of rhubarb extract in a mouse model of binge drinking and we explored the contribution of the gut microbiota in the related- metabolic effects. METHODS AND RESULTS: Mice were fed a control diet supplemented with or without 0.3% rhubarb extract for 17 days and were necropsied 6 hours after an alcohol challenge. Supplementation with rhubarb extract changed the microbial ecosystem (assessed by 16S rDNA pyrosequencing) in favor of Akkermansia muciniphila and Parabacteroides goldsteinii. Furthermore, it improved alcohol-induced hepatic injury, down-regulated key markers of both inflammatory and oxidative stresses in the liver tissue, without affecting significantly steatosis. In the gut, rhubarb supplementation increased crypt depth, tissue weight, the expression of antimicrobial peptides. CONCLUSIONS: These findings suggest that some bacterial genders involved in gut barrier function, are promoted by phytochemicals present in rhubarb extract, and could therefore be involved in the modulation of the susceptibility to hepatic diseases linked to acute alcohol consumption. This article is protected by copyright. All rights reserved. [less ▲]

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See detailComparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.
Iskandar, Christelle F.; Borges, Frederic; Taminiau, Bernard ULiege et al

in Frontiers in Microbiology (2017), 8

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and ... [more ▼]

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium. [less ▲]

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See detailUnraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods.
Coton, Monika; Pawtowski, Audrey; Taminiau, Bernard ULiege et al

in FEMS Microbiology Ecology (2017), 93(5),

Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites ... [more ▼]

Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization. [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 ULiege; Taminiau, Bernard ULiege; 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 detailUse of the potential probiotic strain Lactobacillus salivarius SMXD51 to control Campylobacter jejuni in broilers.
Saint-Cyr, Manuel Jimmy; Haddad, Nabila; Taminiau, Bernard ULiege et al

in International Journal of Food Microbiology (2017)

Campylobacteriosis is the most frequently reported zoonotic disease in humans in the EU since 2005. As chicken meat is the main source of contamination, reducing the level of Campylobacter in broiler ... [more ▼]

Campylobacteriosis is the most frequently reported zoonotic disease in humans in the EU since 2005. As chicken meat is the main source of contamination, reducing the level of Campylobacter in broiler chicken will lower the risk to consumers. The aim of this project was to evaluate the ability of Lactobacillus salivarius SMXD51 to control Campylobacter jejuni in broilers and to investigate the mechanisms that could be involved. Thirty broilers artificially contaminated with C. jejuni were treated by oral gavage with MRS broth or a bacterial suspension (107CFU) of Lb. salivarius SMXD51 (SMXD51) in MRS broth. At 14 and 35days of age, Campylobacter and Lb. salivarius loads were assessed in cecal contents. The impact of the treatment on the avian gut microbiota at day 35 was also evaluated. At day 14, the comparison between the control and treated groups showed a significant reduction (P<0.05) of 0.82 log. After 35days, a significant reduction (P<0.001) of 2.81 log in Campylobacter loads was observed and 73% of chickens treated with the culture exhibited Campylobacter loads below 7log10CFU/g. Taxonomic analysis revealed that SMXD51 treatment induced significant changes (P<0.05) in a limited number of bacterial genera of the avian gut microbiota and partially limited the impact of Campylobacter on Anaerotruncus sp. decrease and Subdoligranulum sp. increase. Thus, SMXD51 exhibits an anti-Campylobacter activity in vivo and can partially prevent the impact of Campylobacter on the avian gut microbiota. [less ▲]

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See detailChemical composition and antimicrobial activity of essential oils of Ocimum basilicum, Ocimum canum and Ocimum gratissimum in function of harvesting time
Mith, Hasika; Yayi-Ladékan, Eléonore; Dosso Sika Kpoviessi, Salomé et al

in Journal of Essential Oil-Bearing Plants [=JEOBP] (2016), 19(6), 1413-1425

The chemical composition of essential oils obtained by hydrodistillation from aerial parts of Ocimum basilicum, Ocimum canum and Ocimum gratissimum from Benin as affected by harvesting time, were analyzed ... [more ▼]

The chemical composition of essential oils obtained by hydrodistillation from aerial parts of Ocimum basilicum, Ocimum canum and Ocimum gratissimum from Benin as affected by harvesting time, were analyzed by GC-FID (Gas chromatography-Flame ionization detector) and GC-MS (Gas chromatography-Mass spectrometry). Based on the composition analysis, major components were as follows: estragol (43.0-44.7%) and linalool (24.6 29.8%) in O. basilicum oils; carvacrol (12.0-30.8%) and p-cymene (19.5-26.2%) in O. canum oils; thymol (28.3-37.7%) and γ-terpinene (12.5-19.3 %) in O. gratissimum oils. Disc diffusion and broth microdilution assays were used to evaluate the antibacterial activity of essential oils and their main components against two foodborne bacteria, Listeria monocytogenes and Salmonella enterica serotype Typhimurium. The tested oils and their components exhibited notable antimicrobial activities against L. monocytogenes and S. Typhimurium. The O. canum and O. gratissimum oils collected at 7h and 19h showed significant higher activities against L. monocytogenes and S. Typhimurium (MICs and MBCs 0.34 - 2.5 μL/mL) (p < 0.05), whereas O. basilicum showed lower activity (MICs and MBCs 2.0 - 8.0 μL/mL) at any daytime of harvest, the weakest being at 19h (MIC and MBC 12.0 - 32.0 μL/mL). The daytime of harvest can influence the composition of oils and their activities on bacteria. [less ▲]

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See detailDevelopment of an analytical method for the simultaneous measurement of 10 biogenic amines in food
Douny, Caroline ULiege; Benmedjadi, Soumaya; Blaszczyk, Marie et al

Poster (2016, October 21)

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See detailMetabolites from media supplemented with 3’-sialyllactose and fermented by bifidobacteria have an antivirulent effect against intestinal pathogens
Bondue, Pauline ULiege; Daube, Georges ULiege; Delcenserie, Véronique ULiege

Poster (2016, October 21)

Complex oligosaccharides from human milk (HMO) promote growth of Bifidobacterium bifidum. Oligosaccharides from cow milk (BMO), similar to HMO, are mainly represented in colostrum by 3’-sialyllactose ... [more ▼]

Complex oligosaccharides from human milk (HMO) promote growth of Bifidobacterium bifidum. Oligosaccharides from cow milk (BMO), similar to HMO, are mainly represented in colostrum by 3’-sialyllactose (3’SL). Bifidobacterium crudilactis, a species from bovine origin and encoding for β galactosidases and α-glucosidases, could be able to metabolise them. Also, fermentation products could have antivirulent activity against intestinal pathogens. This study focused on capacity of bifidobacteria to metabolise 3’SL and on potential antivirulent effect of cell-free spent media (CFSM) against pathogenic bacteria. B. bifidum BBA1 and B. crudilactis FR/62/B/3 isolated respectively from breastfed children feces and cow raw milk cheese were grown on media supplemented with 3’SL as sole source of carbon. Next, CFSM effects were tested against virulence gene expression using ler and hilA promoter activity of luminescent constructs of Escherichia coli 0157:H7 ATCC 43888 and Salmonella Typhimurium SA 941256, respectively. The effect was confirmed on wild type strains of E. coli O157:H7 ATCC 43890 and S. Typhimurium ATCC 14028 using RT-qPCR. Both strains were able to grow in presence of 3’SL. CFSM resulted in under-expression of hilA and ler genes for the luminescent constructs and in under-expression of ler (ratios of -15.4 and -8.1) and qseA (ratios of -2.1 and -3.1) genes for the wild type strain of E. coli O157:H7. No effect was observed with S. Typhimurium. Little is known about CFSM metabolites and they have to be isolated and identified. The potential synbiotic effect between 3’SL and bifidobacteria will be tested using the Shime®, a human gastrointestinal model. [less ▲]

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See detailConsumption patterns, bacteriological quality and risk factors for Salmonella contamination in meat-based meals consumed outside the home in Kigali, Rwanda
Niyonzima, Eugène; Ongol, Martin Patrick; Brostaux, Yves ULiege et al

in Food Control (2016)

Meat-based meals are consumed as a source of animal proteins and constitute one of the leading vehicles for food borne infections in humans. The main objective of this study was to determine the ... [more ▼]

Meat-based meals are consumed as a source of animal proteins and constitute one of the leading vehicles for food borne infections in humans. The main objective of this study was to determine the consumption pattern and the bacteriological quality of meat-based meals consumed outside households in Kigali. A survey on meat consumption patterns was carried out in 400 households by using a questionnaire, whereas different meat-based meals were sampled from 150 snack bars and restaurants. Enumeration of hygiene indicator bacteria (total mesophilic bacteria and Escherichia coli) and the qualitative detection of Salmonella were carried out by using conventional culture methods. The results indicated that goat was the type of meat that was consumed the most outside the home in Kigali and the meat intake varied significantly (p ≤0.05) with the social category of the household. The average levels of total aerobic bacteria and E. coli in meat-based meals were found to be 4.7 and 1.4 log cfu/g, respectively, whereas Salmonella was detected in 11.7% of all meat-based meals. Eight factors mostly linked to the cooking treatments and hygienic handling practices for cooked meals were found to be significantly (p ≤ 0.05) associated with the risk of Salmonella occurrence in meat-based meals consumed outside the home in Kigali. The findings from this study strongly suggest the need for proper cooking and/or improvements in hygiene in the establishments selling ready-to-eat meat-based meals in Kigali, particularly those located in rural localities. [less ▲]

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See detailComparative analysis of the respiratory microbiota of healthy dogs and dogs with canine idiopathic pulmonary fibrosis
Roels, Elodie ULiege; Taminiau, Bernard ULiege; Darnis, Elodie ULiege et al

in Journal of Veterinary Internal Medicine (2016, September)

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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, P.A.; Burteau, S.; Detry, E. et al

Poster (2016, July 19)

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