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See detailIdentification of bacterial strains isolated from the traditional date product "Btana" produced in south regions of Algeria
Abekhti, Abdelkader; Taminiau, Bernard ULg; Kihal, Mabrouk et al

in Folia Microbiologica (in press)

Eleven samples of the traditional date product " Btana" prepared by direct (DBM) and indirect method (UBM) were analysed to characterize their bacterial diversity. A total of 42 representative isolates ... [more ▼]

Eleven samples of the traditional date product " Btana" prepared by direct (DBM) and indirect method (UBM) were analysed to characterize their bacterial diversity. A total of 42 representative isolates have been chosen for molecular identification. 16S rRNA gene sequencing revealed the presence of 20 species within 30.9% belonged to the genus Bacillus, 28.6% of the Staphylococcus, and Enterococcus genus. Within the minority represented species, two isolates were identified as Paenibacillus (isolated from UBM exclusively), Streptococci salivarius, Lactobacillus sakei and Klebsiella pneumoniae. Preliminary results indicate that IBM is more selective for spore former bacilli contrary to DBM that show more diversity in the bacterial flora with a prevalence of Enterococcus. API ZYM test showed that the bacilli species have a weak hydrolase activity. [less ▲]

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See detailImpact of 3’-­‐sialyllactose and Bifidobacterium crudilactis on infant feces microbial composition and virulence modulation of Escherichia coli O157:H7, using the SHIME® gastrointes6nal model
Bondue, Pauline ULg; Lebrun, Sarah ULg; Crevecoeur, Sébastien ULg et al

Poster (2017, June)

Bifidobacterium crudilactis, a bacterial species from bovine origin, growths on bovine milk oligosaccharides (BMO). Cell free spent media (CFSM) from B. crudilactis and 3’-sialyllactose (3’SL), a major ... [more ▼]

Bifidobacterium crudilactis, a bacterial species from bovine origin, growths on bovine milk oligosaccharides (BMO). Cell free spent media (CFSM) from B. crudilactis and 3’-sialyllactose (3’SL), a major BMO, modulated Escherichia coli O157:H7 virulence gene expressiona. In this study, the SHIME® gastrointestinal model was inoculated with 4 different treatments: 3’SL (ttm1), B. crudilactis (ttm2), 3’SL and B. crudilactis (ttm3) and CFSM from 3’SL and B. crudilactis culture (ttm4). In each section of the colon, samples were collected and analysed for short chain fatty acid (SCFA) concentration using HPLC, microbial populations using 16S rDNA metagenetic analysis and correlated with E. coli O157:H7 virulence gene expression. The results showed that SCFA levels were stable during the experiments. Metagenetic analysis showed a microbial diversity in transverse (TC) and descending colon (DC) close to feces, dominated by Bacteroides, Prevotella and Fusobacterium, while the ascending colon (AC) showed a different microbial diversity dominated by Veillonella. Ttm4 and ttm2 induced mainly a down-regulation of virulence genes: fliC in DC with ttm4, and luxS, stx1, qseA in AC, DC or TC with ttm2. Ttm1 also showed a down-regulation of fliC in DC, similar to the one observed with ttm4, but this was associated with an up-regulation of fliC and stx1 in AC or TC. Finally, ttm3 showed slight upregulation of ler, fliC and qseA in AC. These results show that ttm4 and ttm2 might have a positive effect against virulence expression of E. coli O157:H7. However, this trend has to be validated with the further replicates on the SHIME® system. [less ▲]

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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 detailUse of a metagenetic approach to monitor the bacterial microbiota of “Tomme d’Orchies” cheese during the ripening process
Ceugniez, Alexandre; Taminiau, Bernard ULg; Coucheney, Françoise et al

in International Journal of Food Microbiology (2017), 247

The study of microbial ecosystems in artisanal foodstuffs is important to complete in order to unveil its diversity. The number of studies performed on dairy products has increased during the last decade ... [more ▼]

The study of microbial ecosystems in artisanal foodstuffs is important to complete in order to unveil its diversity. The number of studies performed on dairy products has increased during the last decade, particularly those performed on milk and cheese derivative products. In this work, we investigated the bacterial content of "Tomme d'Orchies" cheese, an artisanal pressed and uncooked French cheese. To this end, a metagenetic analysis, using Illumina technology, was utilized on samples taken from the surface and core of the cheese at 0, 1, 3, 14 and 21 days of ripening process. In addition to the classical microbiota found in cheese, various strains likely from environmental origin were identified. A large difference between the surface and the core content was observed within samples withdrawn during the ripening process. The main species encountered in the core of the cheese were Lactococcus spp. and Streptococcus spp., with an inversion of this ratio during the ripening process. Less than 2.5% of the whole population was composed of strains issued from environmental origin, as Lactobacillales, Corynebacterium and Brevibacterium. In the core, about 85% of the microbiota was attributed to the starters used for the cheese making. In turn, the microbiota of the surface contained less than 30% of these starters and interestingly displayed more diversity. The predominant genus was Corynebacterium sp., likely originating from the environment. The less abundant microbiota of the surface was composed of Bifidobacteria, Brevibacterium and Micrococcales. To summarize, the “Tomme d’Orchies” cheese displayed a high diversity of bacterial species, especially on the surface, and this diversity is assumed to arise from the production environment and subsequent ripening process. [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 ULg; Charlier, Raphaëlle; Delepierre, Anissa ULg 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 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 ULg 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 ULg 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 ULg 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 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 detailUse of the potential probiotic strain Lactobacillus salivarius SMXD51 to control Campylobacter jejuni in broilers.
Saint-Cyr, Manuel Jimmy; Haddad, Nabila; Taminiau, Bernard ULg 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 detailComparative analysis of the respiratory microbiota of healthy dogs and dogs with canine idiopathic pulmonary fibrosis
Roels, Elodie ULg; Taminiau, Bernard ULg; Darnis, Elodie ULg 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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See detailMetagenetics and predictive microbiology: a new tool to understand the kinetics of microbial subpopulations in Belgian white pudding
Cauchie, Emilie ULg; Gand, Mathieu; Kergourlay, Gilles et al

Poster (2016, July 18)

Detailed reference viewed: 39 (15 ULg)