References of "Taminiau, Bernard"
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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 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 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)

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 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 (2016)

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 detailClostridium difficile in foods and animals: A comprehensive review
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Van Broeck, Johan et al

in Advances in Experimental Medicine and Biology (2016), 27

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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 (2016)

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 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 detailExistence of two groups of Staphylococcus aureus strains isolated from bovine mastitis based on biofilm formation, intracellular survival, capsular profile and agr-typing.
Bardiau, Marjorie ULg; Caplin, Jonathan; Detilleux, Johann ULg et al

in Veterinary microbiology (2016), 185

Staphylococcus (S.) aureus is recognised worldwide as an important pathogen causing contagious acute and chronic bovine mastitis. Chronic mastitis account for a significant part of all bovine cases and ... [more ▼]

Staphylococcus (S.) aureus is recognised worldwide as an important pathogen causing contagious acute and chronic bovine mastitis. Chronic mastitis account for a significant part of all bovine cases and represent an important economic problem for dairy producers. Several properties (biofilm formation, intracellular survival, capsular expression and group agr) are thought to be associated with this chronic status. In a previous study, we found the existence of two groups of strains based on the association of these features. The aim of the present work was to confirm on a large international and non-related collection of strains the existence of these clusters and to associate them with case history records. In addition, the genomes of eight strains were sequenced to study the genomic differences between strains of each cluster. The results confirmed the existence of both groups based on capsular typing, intracellular survival and agr-typing: strains cap8-positive, belonging to agr group II, showing a low invasion rate and strains cap5-positive, belonging to agr group I, showing a high invasion rate. None of the two clusters were associated with the chronic status of the cow. When comparing the genomes of strains belonging to both clusters, the genes specific to the group "cap5-agrI" would suggest that these strains are better adapted to live in hostile environment. The existence of these two groups is highly important as they may represent two clusters that are adapted differently to the host and/or the surrounding environment. [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 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), 200-229

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

Poster (2015, December 01)

To date, only a few studies have applied metagenomics to investigate the influence of different tillage regimes and types of crop residue management on soil microbial communities. These studies were ... [more ▼]

To date, only a few studies have applied metagenomics to investigate the influence of different tillage regimes and types of crop residue management on soil microbial communities. These studies were conducted under specific climates on soils characterized by particular land-use histories. A very different ecological context is to be found in certain areas of Western Europe, such as central Belgium, whose loess-derived soils are among the most fertile in the world and have long been used for intensive agriculture. Specific objectives were to determine diversity levels and changes in microbial community composition under different combinations of tillage regime (conventional vs. reduced) and crop residue fate (residue removal R- vs. residues left R+ on the field). As reduced tillage results in two contrasting zones (the first centimeters of soil are mixed each year, while the soil below remains unperturbed), we chose to perform the analysis at two depths: 0 to 5 cm and 15 to 20 cm. [less ▲]

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See detailMetagenomic insights into the dynamics of microbial communities in food
Kergourlay, Gilles ULg; Taminiau, Bernard ULg; Daube, Georges ULg et al

in International Journal of Food Microbiology (2015), 213

Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs ... [more ▼]

Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities. [less ▲]

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See detailFaecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Brévers, Bastien et al

in BMC Microbiology (2015), 15

Background The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been ... [more ▼]

Background The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been identified as an important cause of diarrhoea in horses. This study provides further information on the nature of the bacterial communities present in horses developing an episode of diarrhoea. The prevalence of C. difficile in hospitalised horses at the time of admission is also reported. Results Bacterial diversity of the gut microbiota in diarrhoea is lower than that in non-diarrhoeic horses in terms of species richness (p-value <0.002) and in population evenness (p-value: 0.02). Statistical differences for Actinobacillus, Porphyromonas, RC9 group, Roseburia and Ruminococcaceae were revealed. Fusobacteria was found in horses with diarrhoea but not in any of the horses with non-diarrheic faeces. In contrast, Akkermansia was among the three predominant taxa in all of the horses studied. The overall prevalence of C. difficile in the total samples of hospitalised horses at admission was 3.7 % (5/134), with five different PCR-ribotypes identified, including PCR-ribotype 014. Two colonised horses displayed a decreased bacterial species richness compared to the remaining subjects studied, which shared the same Bacteroides genus. However, none of the positive animals had diarrhoea at the moment of sampling. Conclusions The abundance of some taxa in the faecal microbiota of diarrhoeic horses can be a result of microbiome dysbiosis, and therefore a cause of intestinal disease, or some of these taxa may act as equine enteric pathogens. Clostridium difficile colonisation seems to be transient in all of the horses studied, without overgrowth to trigger infection. A large proportion of the sequences were unclassified, showing the complexity of horses’ faecal microbiota. [less ▲]

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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 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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