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International audience; Pig gut microbiota displays high inter-individual variability and it remains an open question to determine to what extent its taxonomic composition relies on host genetic determinism and not only on environmental conditions. We carried out a study to demonstrate coevolution of the host and its gut microbiota established one month post-weaning, by directional selection over two generations. The gut microbiota was characterized by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal samples collected on 60-day-old Large White piglets. Amplicon sequence variants were inferred from amplicon data and the microbial community was further studied at the genus level. Based on the stratification of the initial population (generation G0) according to the two major pig enterotypes, characterized by relative overabundance of either Prevotella and Mitsuokella or Ruminococcus and Treponema, we used the relative abundance of these four genera as selection criteria. From the G0 population of 317 piglets, we selected 6 males and 30 females per line and produced two successive generations (G1 and G2) of approximately 130 pigs per line. We consistently confirmed a moderate heritability for each of the selected genera (h²=0.3 to 0.4). We also estimated the heritability values of the relative abundances for 64 additional bacterial genera, which ranged from 0.1 to 0.5. We showed significant differences between the two lines in the relative abundance of the four bacterial genera at G1 (P

Pig gut microbiota displays high inter-individual variability and it remains an open question to determine to what extent its taxonomic composition relies on host genetic determinism and not only on environmental conditions. We will illustrate links between host genetics and gut microbiota composition by reporting results from different experiments carried out on Large White pig cohorts. Under similar controlled feeding and environmental conditions, we have shown that the gut microbiota after weaning can be consistently classified into two enterotypes by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal DNA. The two enterotypes are characterized by either an overabundance of the genera Prevotella and Mitsuokella or Ruminococcus and Treponema. We explored the contribution of host genetics to the gut microbiota composition by estimating genetic parameters and by launching a directional selection based on the enterotype assignment of 60-day-old pigs. Calculated heritabilities of the relative abundance of fecal microbiota bacteria genera and the response to selection confirmed a significant contribution of host genetics to microbiota variability. The results on this ongoing selection experiment should help to investigate coevolution of the gut microbiota with its host.

L'histoire de la génétique animale est ancrée dans celle des hommes et des femmes qui, depuis le début de l'agriculture, ont oeuvré pour sélectionner des animaux adaptés à leurs besoins. Le développement de la génétique quantitative avec des méthodes statistiques de plus en plus performantes, le déploiement de la génétique moléculaire et des biotechnologies du génome depuis la découverte de l'ADN, l'essor de la génomique depuis le séquençage des génomes, ont progressivement dessiné des champs de recherche variés et complémentaires. La recherche en génétique animale est ainsi nourrie par l'accumulation de nouvelles connaissances et par le renouvellement des approches méthodologiques. Dans le contexte actuel de transition agroécologique et sociétale, les objectifs de sélection se diversifient, conduisant à élargir le panorama des caractères étudiés, à explorer les interactions avec des approches systémiques, à tenir compte de nouvelles échelles d'analyse, à favoriser la diversité génétique, à caractériser finement les liens en génotypes et phénotypes pour améliorer la précision des prédictions. Il sera important d'acquérir une vision intégrative à la fois des questions posées et des approches à déployer pour y répondre. Il sera attendu de favoriser des formations qui couplent science des données et biologie, avec un éclairage apporté par les enjeux sociétaux et environnementaux.

Additional file 3 Fig. S2. 3D BAC center-to-center distances in resting and activated swine macrophages. Cumulative frequency graphs of the normalized center-to-center distances between: (i) MHC class III (TNFα) and SSC7 centromere in red; (ii) MHC class II (SLA-DRA) and SSC7 centromere in green. Pairwise comparisons (p-values) of cumulative 3D distance distributions in resting and activated macrophages (Student’s t-test) are indicated in each graph.

Additional file 4 Table S2. Comparison of gene expression level in resting macrophages. mRNA expression level, analyzed by RT-qPCR, were pairwise compared with one-way ANOVA model with repetitions.

Additional file 5 Fig. S3. Schematic representation of the method used to define the conformation of each allele: given that r1 and r2 are the radii of two fluorescent spots, when the 3D distance between two spot centers (d1) is greater than r1 + r2, the allele is assumed to be decompacted (D), whereas when the 3D distance (d2) between two spot centers is less than r1 + r2, the allele is assumed to be compacted (C).

Additional file 6 Table S3. Nucleus-by-nucleus analysis of pairs of allele conformations and of the effects of LPS/IFNγ activation.

Additional file 1 Fig. S1. BAC probe specificity control by 2D-FISH on porcine metaphases. (a) class I (SLA-1, SBAB-490B10) in green; class II (SLA-DRA, SBAB-591C4) in red; and class III (TNFα, SBAB-493A6) in yellow. (b) porcine chromosome 7 centromere in red (SBAB-437A9). (c) BAC probe specificity control by 2D-FISH on human metaphases: class I (HLA-A, RP11-192H11) in green; class II (HLA-DRA, RP11-379F19) in red; and class III (TNFα, RP11-184F16) in yellow.

Additional file 2 Table S1. Mean values of 3D normalized center-to-center distances and angles calculated using center-to-center distances.

Additional file 7 Fig. S4. Schematic representation of genes positioned inside survival zones (SZ) as determined by the application of the three-loci algorithm. The probable positioning of three genes (blue, red and green dots) is represented in two cells as an example (in cell 1 shown by dotted lines, and in cell 2 by continuous lines). The different positions of each gene make it possible to define its SZ represented by a circle of the same color. The radius of the circle defined for each locus is denoted by Rb for the blue dot, Rr for the red dot and Rg for the green dot.

The ambition of the Foresight was to rethink the place, the roles of livestock and how it should be transformed to fully contribute to the development of more sustainable agri-food systems. It is also to identify cross-disciplinary research themes that explore promising fronts of science or methodologies to solve knowledge locks. The foresight was managed by a group of 15 researchers and mobilized a hundred researchers. Based on an analysis of the context and the drivers for the evolution of the systems, we propose a new conceptual framework to think about innovations. Livestock farming must be part of circular agri-food systems in which it must contribute, beyond an increased efficiency of production factors, to the preservation of the quality of the resources and to the production of a food at an affordable price. Systems need to be rethought to be climate-smart and to respond to the health and welfare challenges of animals and people, rethink the linkages between livestock, crop production and territories to maximize recycling and rethink livestock linkages, processing and consumption of these livestock products. Innovations should be based on the principles of agro-ecology supplemented by those of the circular economy and mobilizing levers of (bio) technologies and organizational innovation. The text describes 4 major scientific priorities with their research issues and produces recommendations for an action plan; L’ambition de l’Atelier de Réflexion Prospective sur l’élevage a été de repenser la place, les rôles de l’élevage et en quoi il doit se transformer pour contribuer pleinement au développement de systèmes agri-alimentaires plus durables ainsi que d’identifier des thématiques de recherches interdisciplinaires permettant d’explorer des fronts de science ou méthodologiques porteurs d’avenir pour lever les verrous de connaissances. La réflexion a été animée par un groupe de 15 chercheurs et a mobilisé une centaine de chercheurs. A partir d’une analyse du contexte et des drivers d’évolution des systèmes nous proposons un nouveau cadre conceptuel et des voies de progrès pour penser l’élevage de demain. L’élevage doit s’inscrire dans le cadre de systèmes agri-alimentaires circulaires dans lesquels il doit contribuer, au-delà d’une efficience accrue des moyens de production, à la préservation de la qualité des ressources et à la production d’une alimentation à un prix abordable. Il faut repenser les systèmes pour qu’ils soient climato-intelligents et répondent aux enjeux de santé et du bien-être des animaux et des hommes ; repenser les liens entre élevage, production végétale et territoire pour maximiser les recyclages et repenser les liens entre élevage, transformation et consommation de ces produits de l’élevage. Les innovations doivent être basées sur les principes de l’agro-écologie complétés par ceux de l’économie circulaire et par la mobilisation des leviers des (bio)technologies et de l’innovation organisationnelle. Le texte décrit quatre grandes priorités scientifiques avec leurs enjeux de recherche et produit des recommandations pour un plan d’action.

Additional file 3: Figure S3. Venn diagram showing the overlap in the differentially abundant OTUs before and after weaning for each weaning group.

and which often tend to be obese. The SLAdd (DD) minipig line was created by the NIH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. In this report, we characterized the physiological status of a herd of French DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. Three datasets were produced, i.e. complete blood counts (CBCs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (NAFLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome.

International audience