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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)

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See detailChallenge testing with Brochothrix thermosphacta on minced pork meat shows interest to couple metagenetics to metabolomics to study food spoilage
Baré, Ghislain ULg; Cauchie, Emilie ULg; Leenders, Justine ULg et al

Poster (2016, July)

The spoilage of perishable foods is mainly caused by bacterial activity. The risk of unwanted bacterial growth is particularly high in the minced pork meat. In this work, the natural microbial ... [more ▼]

The spoilage of perishable foods is mainly caused by bacterial activity. The risk of unwanted bacterial growth is particularly high in the minced pork meat. In this work, the natural microbial contaminants of the minced pork meat were followed by 16S ribosomal DNA deep sequencing (metagenetics) during aging tests at different temperatures. Brochothrix thermosphacta MM008 strain was selected as one of the main contaminants responsible for the spoilage of the meat. Minced pork meat previously sterilized by gamma irradiation was inoculated with B. thermosphacta MM008 for challenge tests measuring growth and then incubated at different temperatures. Minced meat samples were taken and analyzed by H-NMR 1D at time 0 and at final time (from 14 to 19 days, depending on the incubation temperature). Orthogonal partial least square discriminant analysis (OPLS-DA) showed that samples, regardless of the incubation temperature, could be splitted into 3 groups according to their spectral profile: 1) samples taken at time 0, 2) samples inoculated with B. thermosphacta and taken at final time, 3) samples uninoculated, taken at final time. From the analysis of the metabolomics data, higher concentrations of glycerol, glucose, taurine, lactate, carnitine, betaine and glycine were identified in the samples of uninoculated minced pork meat and an increased production of creatine, acetate and acetone was found in the samples of minced pork meat inoculated with B. thermosphacta MM008. These observations showed that -omics technologies (metagenetics and metabolomics) could be used conclusively to study microbial spoilage of minced pork meat. [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 detailLaboratory identification of anaerobic bacteria isolated on Clostridium difficile selective medium
Rodriguez Diaz, Cristina ULg; Warszawski, Nathalie; Korsak Koulagenko, Nicolas ULg et al

in Acta Microbiologica et Immunologica Hungarica (2016)

Despite increasing interest in the bacterium, the methodology for Clostridium difficile recovery has not yet been standardised. Cycloserine cefoxitin fructose taurocholate (CCFT) has historically been the ... [more ▼]

Despite increasing interest in the bacterium, the methodology for Clostridium difficile recovery has not yet been standardised. Cycloserine cefoxitin fructose taurocholate (CCFT) has historically been the most used medium for C. difficile isolation from human, animal, environmental and food samples, and presumptive identification is usually based on colony morphologies. However, CCFT is not totally selective. This study describes the recovery of 24 bacteria species belonging to 10 different genera other than C. difficile, present in the environment and foods of a retirement establishment that were not inhibited in the C. difficile selective medium. These findings provide insight for further environmental and food studies as well as for isolation of C. difficile on supplemented CCFT. [less ▲]

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See detailAssociation of Targeted metagenomic analysis and classical microbiology for Clostridium difficile detection and microbial ecosystem mapping of surfaces hands and foodstuffs in a meat processing plant
Rodriguez Diaz, Cristina ULg; Oukbir, Meriem; Taminiau, Bernard ULg et al

Poster (2016, May 11)

INTRODUCTION Zoonoses are infectious that can be transmitted between animals and humans through direct contact, close proximity or the environment. Since domestic and food animals frequently test positive ... [more ▼]

INTRODUCTION Zoonoses are infectious that can be transmitted between animals and humans through direct contact, close proximity or the environment. Since domestic and food animals frequently test positive for the bacterium, it seems plausible that C. difficile could be zoonotic. PURPOSE This study aimed to determine the prevalence and the epidemiology of C. difficile in cattle farms and the possible spread of the bacterium among animals and farmers. METHODS A total of 176 faecal samples of cattle were collected from 5 different Belgian farms. A stool sample of each farmer was also requested. Detection of C. difficile was performed by classical culture on C. difficile selective medium (cycloserine cefoxitin fructose cholate). Isolates were characterised by PCR-ribotyping and Genotype Cdiff test (Hain Lifescience), which allows the detection of all toxin genes, mutations in gyrA gene and the deletion in the regulator gene tcdC. RESULTS C. difficile was detected in 14/178 (7.9%) animal samples. Isolates were grouped into five different types, including PCR-ribotype 015. All of them were identified as toxigenic. In contrast, none of the 5 farmers studied were positive for the bacterium. SIGNIFICANCE Results obtained indicate that PCR-ribotypes commonly isolated from hospitalised patients are also present in cattle, indicating an animal reservoir. However, a zoonotic transmission could be not demonstrated in the farms studied. [less ▲]

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See detailDaily intake and bacteriological quality of meat consumed in the households of Kigali, Rwanda
Niyonzima, Eugene ULg; Ongol, Martin Patrick; Brostaux, Yves ULg et al

in Food Control (2016), 69

Meat is consumed worldwide as a source of animal proteins, but it is recognized as one of the most important vehicles for food borne infections in humans. This study was conducted to determine the daily ... [more ▼]

Meat is consumed worldwide as a source of animal proteins, but it is recognized as one of the most important vehicles for food borne infections in humans. This study was conducted to determine the daily intake; the levels of hygiene indicator bacteria, namely the total mesophilic bacteria (TMC) and Escherichia coli counts (ECC); and the prevalence of Salmonella in meat consumed within the households of Kigali (Rwanda). The survey on meat consumption was carried out in 400 households by using a questionnaire, whereas the bacteriological analyses of meat samples were performed by using conventional culture methods. The results from the survey indicated that beef was the type of meat mostly consumed in Kigali city households, and the daily meat intake significantly varied with the social category of the household. No significant difference was observed between daily meat intakes in different age classes of household members. In the samples where microorganisms were detected, the average levels of TMCs and ECCs in raw meat were found to be 5.4 and 1.6 log cfu/g, respectively, whereas in cooked meat they were significantly reduced to 3.1 and 1.1 log cfu/g, respectively. The prevalence of Salmonella was reduced from 21.4% in raw meat to 3.4% in ready-to-eat cooked meat. Salmonella was not detected in cooked meat consumed in high-income households. The results from this study highlight the need for hygiene improvements in meat shops as well as in the households of Kigali, particularly those with low and medium incomes. [less ▲]

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See detailOral administration of a Spirulina extract protects old mice against hepatic “ammaging”
Neyrinck, A.; Taminiau, Bernard ULg; Daube, Georges ULg et al

in Nutrition Clinique et Metabolisme (2016), 30(1), 64

Background & aims: Ageing predisposes to hepatic dysfunction and inflammation that can evolve to non-alcoholic fatty liver disease. Spirulina, a cyanobacterium used as a food additive or food supplement ... [more ▼]

Background & aims: Ageing predisposes to hepatic dysfunction and inflammation that can evolve to non-alcoholic fatty liver disease. Spirulina, a cyanobacterium used as a food additive or food supplement, has been shown to impact immune functions and to improve non-alcoholic steatohepatitis in obese mice. The aim of the present study was to test the potential hepatoprotective effects of Spirulina extract supplementation in aged mice and to determine whether these effects can be related to a modulation of the gut microbiota. Methods: Old mice of 24 months were fed a control diet supplemented with or without 5% Spirulina extract (Biores, Liège, Belgium) and were compared to young mice of 3 months during 6 weeks. Results: Combination of pyrosequencing and qPCR analyses of the 16S rRNA gene revealed a decrease in total bacteria and -among specific changes of gut microbiota composition,- an increase in Allobaculum, Blautia, Roseburia, and Lactobacillus populations by Spirulina treatment. Interestingly, parameters related to the innate immunity, especially T Regulatory cells (FoxP3), CD11b-dendritic cells, cytokines (IL6, IFN MCP-1) and antimicrobial peptides (Pla2g2, Reg3) were upregulated in the small intestine of Spirulina-treated mice. Aged mice exhibited inflammation and oxidative stress in the liver tissue as compared to young mice. The supplementation with Spirulina extract reduced several hepatic inflammatory and oxidative stress markers in old mice. Conclusions: Our study shows for the first time that the oral administration of a Spirulina is able to modulate the gut microbiota, to activate immune system in the gut, thereby improving hepatic inflammation in aged mice. Those data allow to envisagesuggest a new therapeutic tools in the management of immune and metabolic alterations in ageing, based on gut microbes-host interactions. [less ▲]

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See detailIdentification of Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli in diarrhoeic calves and comparative genomics of O5 bovine and human STEC
Fakih, Ibrahim; Thiry, Damien ULg; Duprez, Jean-Noël ULg et al

in Veterinary Microbiology (2016)

Escherichia coli producing Shiga toxins (Stx) and the attaching-effacing (AE) lesion (AE-STEC) are responsible for (bloody) diarrhoea in humans and calves while the enteropathogenic E. coli (EPEC ... [more ▼]

Escherichia coli producing Shiga toxins (Stx) and the attaching-effacing (AE) lesion (AE-STEC) are responsible for (bloody) diarrhoea in humans and calves while the enteropathogenic E. coli (EPEC) producing the AE lesion only cause non-bloody diarrhoea in all mammals. The purpose of this study was (i) to identify the pathotypes of enterohaemolysin-producing E. coli isolated between 2009 and 2013 on EHLY agar from less than 2 month-old diarrhoeic calves with a triplex PCR targeting the stx1, stx2, eae virulence genes; (ii) to serotype the positive isolates with PCR targeting the genes coding for ten most frequent and pathogenic human and calf STEC O serogroups; and (iii) to compare the MLSTypes and virulotypes of calf and human O5 AE-STEC after Whole Genome Sequencing using two server databases (www.genomicepidemiology.org). Of 233 isolates, 206 were triplex PCR-positive: 119 AE-STEC (58%), 78 EPEC (38%) and 9 STEC (4%); and the stx1+eae+ AE-STEC (49.5%) were the most frequent. Of them, 120 isolates (84% of AE-STEC, 23% of EPEC, 22% of STEC) tested positive with one O serogroup PCR: 57 for O26 (47.5%), 36 for O111 (30%), 10 for O103 (8%) and 8 for O5 (7%) serogroups. The analysis of the draft sequences of 15 O5 AE-STEC could not identify any difference correlated to the host. As a conclusion, (i) the AE-STEC associated with diarrhoea in young calves still belong to the same serogroups as previously (O5, O26, O111) but the O103 serogroup may be emerging, (ii) the O5 AE-STEC from calves and humans are genetically similar [less ▲]

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See detailOral administration of a spirulina extract protects old mice against hepatic "inflammaging"
Neyrinck, A.; Taminiau, Bernard ULg; Daube, Georges ULg et al

Poster (2016, February 18)

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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 detailFlow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation
Kinet, Romain ULg; Dzaomuho, Phidias; Baert, Jonathan ULg et al

in Bioresource Technology (2016)

Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is ... [more ▼]

Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The Flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses. [less ▲]

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See detailThe use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding
Cauchie, Emilie ULg; Gand, Mathieu; Kergourlay, Gilles ULg et al

in International Journal of Food Microbiology (2016)

In order to control food losses and wastage,monitoring the microbial diversity of food products, during processing and storage is important, as studies have highlighted the metabolic activities of ... [more ▼]

In order to control food losses and wastage,monitoring the microbial diversity of food products, during processing and storage is important, as studies have highlighted the metabolic activities of somemicroorganismswhich can lead to spoilage. Knowledge of this diversity can be greatly improved by using a metagenetic approach based on high throughput 16S rRNA gene sequencing, which enables a much higher resolution than culture-based methods. Moreover, the Jameson effect, a phenomenon described by Jameson in 1962, is often used to classify bacterial strains within an ecosystem. According to this, we have studied the bacterial microbiota of Belgian white pudding during storage at different temperatures using culture-dependent and independent methods. The product was inoculated with a mix of dominant strains previously isolated from this foodstuff at the end of its shelf life (Carnobacterium maltaromaticum, Lactobacillus fuchuensis, Lactobacillus graminis, Lactobacillus oligofermentans, Lactococcus lactis, Leuconostoc mesenteroides, Raoultella terrigena and Serratia sp.). Daily during 16 days, the absolute abundance of inoculated strain was monitored by combining total count on plate agar and metagenetic analysis. The resultswere confirmed by qPCR analysis. The growth of each specieswasmodelled for each temperature conditions, representative of good or bad storage practices. These data allowed the bacterial strains subdivision into three classes based on criteria of growth parameters for the studied temperature: the “dominant”, the “subdominant” and the “inhibited” bacterial species, according to their maximal concentration (Nmax, log CFU/g), growth rate (μmax, 1/h) and time to reach the stationary phase (TRSP, days). Thereby, depending on the storage conditions, these data have permitted to follow intrinsically the evolution of each strain on the bacterial ecosystemof Belgianwhite pudding. Interestingly, it has shown that the reliability of the Jameson effect can be discussed. For example, at 4 °C when Lactococcus lactis and Serratia sp. stopped growth at day 12, at the same time Carnobacterium maltaromaticum reached its maximal concentration and entered its stationary phase. In opposition to this, it can be noticed that in the same condition, the “sub-dominant” organisms continued their growth independently of the “dominant” species behaviour. In this case, the Jameson effect was not illustrated. This pattern is described for all storage conditions with the same strain classifications. These results highlighted the importance of combining metagenetic analysis and classical methods, with modelling, to offer a new tool for studying the evolution ofmicroorganisms present in perishable foodwithin different environmental conditions. [less ▲]

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See detailClostridium difficile in Food and Animals: A Comprehensive Review.
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Van Broeck, J. et al

in Advances in Experimental Medicine and Biology (2016)

Zoonoses are infections or diseases that can be transmitted between animals and humans through direct contact, close proximity or the environment. Clostridium difficile is ubiquitous in the environment ... [more ▼]

Zoonoses are infections or diseases that can be transmitted between animals and humans through direct contact, close proximity or the environment. Clostridium difficile is ubiquitous in the environment, and the bacterium is able to colonise the intestinal tract of both animals and humans. Since domestic and food animals frequently test positive for toxigenic C. difficile, even without showing any signs of disease, it seems plausible that C. difficile could be zoonotic. Therefore, animals could play an essential role as carriers of the bacterium. In addition, the presence of the spores in different meats, fish, fruits and vegetables suggests a risk of foodborne transmission. This review summarises the current available data on C. difficile in animals and foods, from when the bacterium was first described up to the present. [less ▲]

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