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Microbiote intestinal chez le porc : paramètres génétiques de sa composition et liens avec des caractères immunitaires

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FR

L’objectif de cette étude est d’estimer les paramètres génétiques de la composition du microbiote intestinal chez le porc Large White et d’étudier les covariations entre cette composition et des paramètres immunitaires et de croissance. Dans le cadre du projet Sus-Flora, nous avons caractérisé la diversité du microbiote fécal pour 518 porcelets âgés de 60 jours, par séquençage d’une région variable du gène bactérien codant l’ARNr 16S. Nos premiers résultats ont mis en évidence une prédominance des genres bactériens Prevotella puis Oscillibacter, Dialister, Roseburia et Treponema. Des valeurs d’héritabilité comprises entre 0,13  0,08 et 0,55  0,16 ont été estimées pour l’abondance relative de 19 genres bactériens parmi les plus fréquents, démontrant ainsi une part génétique significative de la composition du microbiote intestinal chez le porc. Des corrélations génétiques positives et négatives sont identifiées entre abondances des taxons bactériens. Des covariations positives et négatives ont été trouvées entre des paramètres de formule sanguine (taux de monocytes, éosinophiles, plaquettes) et l’abondance des genres Prevotella, Roseburia, Dialister. Nous montrons également, pour un sous-groupe de 31 animaux, que la composition du microbiote intestinal se stabilise après 36 jours d’âge et que les animaux se séparent en deux groupes sur la base de la composition de leur microbiote intestinal, évoquant les entérotypes identifiés chez l’homme. Ces deux groupes, dominés par le genre Prevotella ou les Ruminococcaceae, sont retrouvés à 60 jours d’âge, avec la cohorte des 518 porcelets.

ENG

Pig gut microbiota: genetic parameters and links with immunity traits of the host

Our objectives were to estimate genetic parameters of the gut microbiota composition in French Large White pigs, and to uncover co-variations between the abundances of microbial communities and immunity or growth parameters of the host. In the framework of the Sus-Flora project, we characterized the diversity of the faecal microbiota of 518 60 day-old piglets by sequencing a variable region of the ribosomal 16S gene. Our first results have shown that the genera Prevotella, followed by Oscillibacter, Dialister, Roseburia or Treponema are dominant in the porcine faecal microbiota. Heritability values ranging from 0.13  0.08 to 0.55  0.16 were estimated for the relative abundance of 19 of the most common bacterial genera, highlighting the contribution of the host genome to the shaping of the gut microbial ecosystem. Regularized canonical correlations and sparse Partial Least Squares analyses highlighted both positive and negative correlations between immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. The establishment of microbial diversity in the gut was assessed by following a subset of 31 piglets at 14, 36, 48, 60 and 70 days of age. We showed that the gut microbiota composition was stabilized after 36 days of age. In addition, a stratification of the 31 piglets in two groups was observed after weaning, suggesting the existence of enterotypes as observed in humans. These two enterotype-like clusters were primarily distinguished by the levels of unclassified Ruminococcaceae and Prevotella, respectively. These two enterotype-like clusters were also found in the cohort of 518 60 day-old piglets.

2016

Etude de la capacité immunitaire chez le porc Large White : recherche de marqueurs génétiques liés à l'expression des gènes dans le sang

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Poster.

FR

En élevage porcin, les schémas de sélection cherchent à produire des animaux plus robustes afin, notamment, de réduire l’usage des antibiotiques. Nous avons engagé des recherches qui visent à qualifier la compétence immunitaire des animaux et étudions l'architecture génétique de paramètres immuns dans des populations d'animaux cliniquement sains. Nous avons déjà montré que de nombreux paramètres immunitaires sont héritables (Flori et al. 2011) et que le transcriptome du sang est informatif pour quantifier certains d'entre eux (Mach et al. 2013). Notre objectif est maintenant d'identifier des marqueurs génétiques associés à la variation d'expression des gènes dans le sang.

ENG

Analysis of the immune capacity in Large White pigs: search for genetic markers linked to the variation of gene expression in the blood

Combining animal production performances and health traits is a main issue in livestock farming. Blood is emerging as a source of biological information linked to the health and physiological state of each individual. Furthermore, it is an interesting surrogate tissue for animal phenotyping because its sampling is almost non-invasive and reproducible. We have already shown that several immune parameters are heritable and that the blood transcriptome is informative to quantify some of them. In this study, our aim was to identify genetic markers associated with gene expression variations in the blood, based on an expression genome-wide association study (eGWAS) using 243 Large White pigs at 60 days of age. Each pig was genotyped with the Illumina iSelect 60K Chip and the blood transcriptome analysis was performed by using a custom gene expression 8X60K microarray (Agilent Technologies). 4,591 significant associations between one SNP and one probe were found, including 62% cis-associations (the associated SNP is in a window of 2Mb surrounding the probe). Among the 3,419 probes with at least one associated SNP (eQTL), 70% had a cis-eQTL and 89% could be assigned to a porcine gene. The eQTLs were found to be linked with the expression of one to 51 genes. The genomic regions surrounding the eQTLs correspond to candidate regions to further study the genetic architecture of immunity trait variations in pigs, and contribute to paving the way towards a qualification of the individual immune capacity for translational research in precision pig farming.

2016

Gut microbiota composition in swine: genetic parameters and links with immunity traits

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Poster.

The intestinal microbiome plays a major role in host's physiology and homeostasis. It participates in the immunological barrier against infections, helps to develop and mature the immune system, and contributes to extract nutrients and energy from food. Despite large scale studies in human, little is known on gut microbiota composition and potential associations with individual traits in livestock species. The objective of this study was to estimate the genetic parameters of the gut microbiota composition and analyze its links with immunity traits in French Large White pigs. A cohort of 60 days old piglets was assessed for fecal microbiota composition by pyrosequencing the 16S rRNA gene. First results on 299 piglets showed a predominance of Prevotella followed by Oscillibacter, Dialister, Roseburia and Treponema. Among a set of 63 genera, 7 had low (0.1<h2<0.2), 15 medium (0.2<h2<0.4) and 8 high (h2>0.4) heritabilities for abundance variations. At the genetic level, the relative abundance of Prevotella, Oribacterium, Selenomonas, Dialister and Megasphaera were found positively correlated with each other and tended to be negatively correlated to other genera. Finally, regularized canonical correlations (rCCA) and sparse Partial Least Squares (sPLS) analyzes highlighted both positive and negative correlations between various immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. In this report we demonstrate for the first time that the gut microbiota composition in swine is influenced by the genetics of the host. In addition, we have found covariations between microbiota composition and immunity traits. These results pave the way for studying the microbiota as a new component of phenotype construction in pigs. Microbiota parameters together with zootechnical and immunity traits will help to better decipher the driving forces that shape animal performances and robustness.

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2014

Immunité des porcelets : importance du colostrum

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Le porcelet naît sans protection immunitaire. Il est donc primordial qu'il acquière très rapidement une immunité via la prise colostrale. La protection acquise par le porcelet dépend de la quantité d'anticorps présents dans le colostrum et de sa capacité à l'absorber.

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2013

Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation

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Background: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual’s immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics.
2011