Suchergebnisse

The Krškopolje pig is the only indigenous Slovenian pig breed being still farmed. The breed is characterised by its rusticity and adaptation to the traditional farming system and has a black coat colour with a white belt across shoulders and forelegs. Despite the limited number of animals, the breed is on the way of becoming more sustainable due to the growing interest for local traditional breeds, in particular for organic farming. The objective of our study (made within project TREASURE) was to characterise the gut microbiota composition in 36 Krškopolje pigs raised by using three different diets: conventional feed, conventional feed supplemented with alfalfa pellets and organic feed supplemented with alfalfa hay. The gut microbiota composition of all pigs at two time points (155 and 228 days-ofage) was determined by resequencing the bacterial 16S gene in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime's open-reference OTU calling subsampled method following author's recommendations. NMDS and PERMANOVA analyses performed by the Vegan R package showed significant effects of dietary regime, showing that the organic feed produces a differentiation of the gut microbiota composition when compared with the other two diets and the two time points analysed. This pilot study illustrates the power of metagenomic analyses for the identification of effects of diets in the farming conditions of local European pig breeds. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

The Turopolje pig is a local porcine breed originating from Croatia characterised by its rusticity and adaptation to the traditional outdoor farming system linked to local oak forests. While this once-widespread breed was almost completely replaced by industrial breeds in the second half of the 20th century, there is growing interest on promoting its production in the framework of sustainable porcine production. The objective of our study (made in project TREASURE) was to characterise the gut microbiota composition in 24 Turopolje pigs raised outdoor by using a conventional feed vs a conventional feed supplemented with acorns. The gut microbiota composition of all pigs was determined by re-sequencing the bacterial 16S gene in an Illumina MiSeq device. Bioinformatics analyses were performed by using Qiime's open-reference OTU calling subsampled method following author's recommendations. NMDS and PERMANOVA analyses performed by using the Vegan R package showed significant effects of diet, showing that the acorn supplementation has a relevant impact on gut microbiota, notably by reducing richness and diversity. This result was confirmed in the differential abundance analysis which showed that 152 out of 1,466 OTUs were significantly different between the two groups. Interestingly, the predicted microbiota metabolic functions that were differentially abundant involved fatty acid and amino-acid metabolisms. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

The traditional raising system for Iberian pigs includes an open-air fattening period (montanera) where animals have a diet dominated by acorns. This system allows obtaining dry-cured products of unmatched quality. The most usual method for the verification of montanera products relies on assessing the particular backfat fatty acid composition after slaughter. Given that the advances on nutrition science makes feasible to emulate montanera meat products in an industrial farming environment, there is a growing need for the identification of complementary certification approaches. The objective of this study of TREASURE project was to evaluate the potential of gut microbiota composition analyses from faecal samples collected at slaughter as a new discrimination method of the montanera production system. Gut microbiota composition of 131 Iberian pigs (92 montanera and 131 commercial feeds) was determined by re-sequencing the bacterial 16S gene in an Illumina MiSeq device. Bioinformatic analyses were performed using Qiime's subsampled open-reference OTU calling method. NMDS and PERMANOVA analyses performed using the Vegan R package showed significant effects of diet and sampling batch on gut microbiota composition. The microbiota of montanera-raised pigs showed a tendency towards a reduced microbial diversity. Differential abundance analyses performed with the metagenomeSeq R package confirmed these differences by identifying 997 out of 1,703 OTUs whose abundance was significantly different between both systems. Our results suggest that the gut microbiota composition of Iberian pigs sampled at the slaughter could be used as a supplementary certification tool of traditional montanera Iberian pigs. Funded by European Union's H2020 RIA program (grant agreement 634476).

The traditional Iberian pig production system is characterized by a final open-air fattening period (montanera), in which the animals are fed acorns and grass, preceded by a growing period where the feeding is restricted to avoid undesirable weight gain. New growing diets based on olive agro-industrial by-products could be an alternative to avoid this restriction. The objective of the current study (of TREASURE project) was to analyse the effect of two growing alternative diets on the gut microbiota composition from faecal samples collected before and after montanera. Three diets, one incorporating dry olive pulp in the feed (DD), one incorporating olive cake in wet form (WD) and a control diet (CD) were supplied to 45 animals (15 per diet) during the growing period (45 to 95 kg of body weight). The gut microbiota composition of each individual was evaluated at two time points: before transition to montanera (95 kg) and at slaughter (160 kg). Microbiota analyses were performed by re-sequencing the bacterial 16S gene (V3-V4) in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime's open-reference subsampled OTU calling approach. The effect of diets on microbiota composition and diversity was evaluated using the Vegan package in R. Bray-Curtis distances, NMDS and PERMANOVA analyses showed significant effects on microbiota composition. WD caused an increase in microbiota diversity. In the second sampling point, differences in composition and diversity could be also observed after acorn supplementation. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

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 resequencing 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).