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Gut microbiota analyses for sustainable European local porcine breeds: A TREASURE pilot study

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J. Estellé et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

The study of gut microbiota and its effects on hosts has emerged as an essential component of host homeostasis and global efficiency. Besides host’s influence on gut microbiota, major quantitative and qualitative changes may occur in the composition of the intestinal microbiota due to the influence of diet and other environmental factors.
In accordance with the TREASURE project global aim of enhancing sustainability of production systems for local pig breeds, the objective of our task was to conduct a pilot characterisation of intestinal microbiota in order to test its usefulness to characterize several local European pig populations and their production systems. This approach has been applied to populations belonging to the following European traditional breeds: Gascon (France), Iberian (Spain), Krskopolje (Slovenia), Mangalitsa (Serbia), Moravka (Serbia) and Turopolje (Croatia). For each breed, faecal samples have been collected along different experiments performed in the TREASURE project targeting the comprehension of a particular traditional production system (e.g. open-air farming), management practice, or the comparison of breeds. In all experiments, the metagenomics technique employed is the re-sequencing of the bacterial 16S in an Illumina MiSeq system. Overall, the results have shown that the gut microbiota analysis is a promising approach for the characterisation of these local breeds, by allowing a deeper understanding of their production systems and potentially allowing the development of new certification approaches. Preliminary results will be summarized in this communication. Funded by European Union’s H2020 RIA program (Grant agreement no. 634476).

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2018

On the influence of host genetics on gut microbiota composition in pigs

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J. Estellé et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Gut microbial population acts in complement with its host through nutrient digestion and health of the gastrointestinal tract. Changes in microbiota composition may then lead to changes in nutrient digestibility. The present study aimed at determining the effects of dietary fibre content on gut microbiota composition and apparent faecal nutrient digestibility in pigs. Furthermore, the relationships between microbiota and digestibility coefficients were investigated. Growing-finishing pigs (from 35 to 74 kg mean body weight) were fed alternatively a low-fibre (LF) and a high-fibre (HF) diet during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period and faecal microbiota was collected at the end of each period for 16S rRNA gene sequencing. The two diets fed by the pigs could be discriminated using 31 predicting OTUs in a sparse partial least square discriminant analysis (mean classification error-rate 3.9%). Furthermore, microbiota was resilient to diet effect. Pearson correlations between microbiota composition and apparent digestibility coefficients of energy, protein, cellulose and hemicellulose emphasized the fact that in LF group, Clostridiaceae and Turicibacter were negatively correlated with protein and energy digestibility coefficients whereas Lactobacillus was positively correlated. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall components digestibility. In HF diet, no significant correlation between microbiota and digestibility was found. The present study demonstrates that 3 weeks of adaptation to a new diet seem to be sufficient to observe resilience in growing pigs gut microbiota. In addition, faecal microbiota can be used to classify pigs according to their diet. Because some bacterial family and genera are favourable to digestibility, this study suggests that manipulations of bacterial populations can improve digestibility and feed efficiency. This study is part of the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement no. 633531.

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2018

Impact of weaning age on gut microbiota composition in piglets

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F.R. Massacci et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Weaning is a crucial period of pigs, accompanied by nutritional, environmental and social stresses. Studies comparing different ages at weaning have shown that increasing weaning age improves wean-to-finish growth performances and reduces mortality. However, the impact of weaning age on the early-life establishment of the gut microbiota remains under-investigated in pigs. Our objective was to compare the gut microbiota composition of piglets weaned at different ages. 48 piglets were divided in 4 groups of 12 animals weaned at either 14, 21, 28 or 42 days-of-age.
Faecal samples were collected at 3 different time points: day of weaning, 7 days after weaning and at 60 days of age. Faecal DNA bacterial composition was assessed by sequencing the V3-V4 regions of the 16S rRNA gene.
Bioinformatic and biostatistical analysis showed that each weaned group had significant differences between the sample points through weaning transition, confirming that the gut microbiota changes before and after weaning. In addition, microbiota diversity increased according to weaning age, with piglets weaned at 42 days-of-age having a highest alpha diversity and richness. Interestingly, piglets weaned at 42-days maintained a more stable diversity until day 60. We show that late weaning leads to a higher diversity of potentially beneficial microbes prior to the crucial challenge of weaning and might thus provide a competitive advantage to piglets.

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2018

Construction et validation d’un premier catalogue de gènes du microbiome intestinal chez le porc

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50es Journées de la Recherche Porcine, 6 et 7 février 2018, Paris, p. 49-54, par Jordi Estellé (INRA) et al.

Le porc est une espèce importante en élevage comme en recherche biomédicale. Nous avons constitué un premier catalogue de gènes du microbiome intestinal par séquençage d’ADN fécal de 287 porcs originaires de France, Chine et Danemark. Ont été identifiés 7,7 millions de gènes microbiens non-redondants et 719 espèces métagénomiques. La moitié des gènes a pu être assignée au plan taxonomique ; 98% sont des gènes de bactéries pour lesquelles les phylums les plus représentés sont les Firmicutes (28,73%) puis les Bacteroidetes (9,28%). Le catalogue du porc partage cinq fois plus de gènes avec le catalogue humain qu’avec celui de la souris, confirmant que le porc pourrait être, dans certains cas, un meilleur modèle pour l’homme que la souris. Une analyse visant à identifier et quantifier l’abondance des gènes de résistance aux antibiotiques a reflété les pratiques courantes dans chaque pays ou élevage et montré que limiter l’usage des antibiotiques dans l’alimentation réduit massivement la charge en gènes d’antibiorésistance. Le séquençage d’ADN fécal d’animaux non représentés dans le catalogue (truies gestantes, jeunes porcelets) a permis de valider que le catalogue est perfectible mais largement utilisable de par sa couverture de la diversité microbienne. Ce premier catalogue de gènes du microbiome intestinal constitue une ressource majeure pour développer la métagénomique quantitative chez le porc et contribuer à la compréhension fine de la construction des phénotypes.

The first reference gene catalogue of the gut microbiome in pigs

The pig is an important species for food production and biomedical research. We have established a first gene catalogue of the pig gut microbiome by deep sequencing fecal DNA from a cohort of 287 pigs bred in France, China and Denmark. The catalogue contains more than 7.7 million non-redundant genes. A total of 719 metagenomic species was identified. Half of the genes could be taxonomically assigned, and 98% of them corresponded to bacteria. The most abundant phyla were the Firmicutes (28.73%) and the Bacteroidetes (9.28%). The pig and human catalogues share five times as many genes as the mouse and human catalogues, supporting the use of pigs for biomedical research. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems. Additional fecal samples from animals of various ages and physiological conditions (e.g. gestating sows, young piglets before and after weaning) were sequenced, and the results validated that the catalogue is perfectible but already provides a good coverage of microbial diversity. This first gene catalogue of the gut microbiome constitutes a highly valuable resource to implement quantitative metagenomics in pigs and to contribute to understand better the construction and plasticity of phenotypes.

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2018

Nouvelles technologies : des perspectives très prometteuses pour la sélection

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Tech Porc (FRA), 2017, n° 34, mars-avril, p. 40-42, par Joël Bidanel et Marie-José Mercat

Les recherches en matière de génomique s'accélèrent. La connaissance précise du génome, de sa gouvernance et le développement de nouveaux outils laissent entrevoir une accélération du progrès génétique sur de nouveaux caractères.

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2017

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

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Estellé et al., 48es Journées de la Recherche Porcine (FRA), 2-3 février 2016, Paris, p. 267-272

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.

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2016