Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs
The gut microbiome plays an important role in the performance and health of swine by providing essential nutrients and supporting the immune system. Recent studies have demonstrated that the gut microbiome can explain part of the variation observed in growth, health, and meat quality. Feed efficienc...
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Elsevier
2025-03-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731125000369 |
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| author | P. Nuñez G. Martinez-Boggio J. Casellas L. Varona F. Peñagaricano N. Ibáñez-Escriche |
| author_facet | P. Nuñez G. Martinez-Boggio J. Casellas L. Varona F. Peñagaricano N. Ibáñez-Escriche |
| author_sort | P. Nuñez |
| collection | DOAJ |
| description | The gut microbiome plays an important role in the performance and health of swine by providing essential nutrients and supporting the immune system. Recent studies have demonstrated that the gut microbiome can explain part of the variation observed in growth, health, and meat quality. Feed efficiency is crucial in swine production, as feed cost account for more than 60% of total production costs. This study aimed to assess the relationships between the host genome, gut microbiome, and feed efficiency in Iberian pigs raised under intensive conditions. The specific objectives were to assess the mediating effects of the gut microbiome on feed efficiency and to estimate the direct and total heritability of feed efficiency. The data set included the feed conversion ratio (FCR) and residual feed intake (RFI) from 587 Iberian pigs, as well as the 16S rRNA gut microbial abundance from 151 of those pigs raised in a nucleus of selection. We reparametrised variance components from standard bivariate mixed models into recursive models to disentangle the microbiome’s mediating effect on feed efficiency. In our models, the host genome has direct effects on both the phenotype (G→P) and the gut microbiome (G→M). Additionally, there is an indirect effect of the host genome on the phenotype mediated by the microbiome (G→M→P). We identified a total of 14 taxa with relevant effects on FCR and 16 taxa with relevant effects on RFI. We categorised the gut microbiome into groups for potential practical application in pig farming. The gut microbes with relevant causal effects and low heritability can be manipulated through management interventions, while those microbes with relevant causal effects and moderate heritability can be targeted through selective breeding. Our findings indicate that incorporating microbiome data leads to a reduction in total heritability for both FCR and RFI. This study provides new insights into the link between the gut microbiome and feed efficiency, presenting practical methods to target microbes that can be influenced through selective breeding or management interventions. |
| format | Article |
| id | doaj-art-9e9e2155cbe44347a4900f4dfece3a46 |
| institution | DOAJ |
| issn | 1751-7311 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj-art-9e9e2155cbe44347a4900f4dfece3a462025-08-20T03:15:28ZengElsevierAnimal1751-73112025-03-0119310145310.1016/j.animal.2025.101453Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigsP. Nuñez0G. Martinez-Boggio1J. Casellas2L. Varona3F. Peñagaricano4N. Ibáñez-Escriche5Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de Valencia, Valencia 46022, SpainDepartment of Animal and Dairy Sciences, University of Wisconsin, Madison 53706, United StatesDepartment Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainInstituto Agrolimentario de Aragón (IA2), Universidad de Zaragoza 50013 Zaragoza, SpainDepartment of Animal and Dairy Sciences, University of Wisconsin, Madison 53706, United StatesInstituto de Ciencia y Tecnología Animal, Universitat Politècnica de Valencia, Valencia 46022, Spain; Corresponding author.The gut microbiome plays an important role in the performance and health of swine by providing essential nutrients and supporting the immune system. Recent studies have demonstrated that the gut microbiome can explain part of the variation observed in growth, health, and meat quality. Feed efficiency is crucial in swine production, as feed cost account for more than 60% of total production costs. This study aimed to assess the relationships between the host genome, gut microbiome, and feed efficiency in Iberian pigs raised under intensive conditions. The specific objectives were to assess the mediating effects of the gut microbiome on feed efficiency and to estimate the direct and total heritability of feed efficiency. The data set included the feed conversion ratio (FCR) and residual feed intake (RFI) from 587 Iberian pigs, as well as the 16S rRNA gut microbial abundance from 151 of those pigs raised in a nucleus of selection. We reparametrised variance components from standard bivariate mixed models into recursive models to disentangle the microbiome’s mediating effect on feed efficiency. In our models, the host genome has direct effects on both the phenotype (G→P) and the gut microbiome (G→M). Additionally, there is an indirect effect of the host genome on the phenotype mediated by the microbiome (G→M→P). We identified a total of 14 taxa with relevant effects on FCR and 16 taxa with relevant effects on RFI. We categorised the gut microbiome into groups for potential practical application in pig farming. The gut microbes with relevant causal effects and low heritability can be manipulated through management interventions, while those microbes with relevant causal effects and moderate heritability can be targeted through selective breeding. Our findings indicate that incorporating microbiome data leads to a reduction in total heritability for both FCR and RFI. This study provides new insights into the link between the gut microbiome and feed efficiency, presenting practical methods to target microbes that can be influenced through selective breeding or management interventions.http://www.sciencedirect.com/science/article/pii/S1751731125000369Feed conversion ratioMediation analysisModellingPigsResidual feed intakeStructural equation model |
| spellingShingle | P. Nuñez G. Martinez-Boggio J. Casellas L. Varona F. Peñagaricano N. Ibáñez-Escriche Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs Animal Feed conversion ratio Mediation analysis Modelling Pigs Residual feed intake Structural equation model |
| title | Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| title_full | Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| title_fullStr | Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| title_full_unstemmed | Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| title_short | Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| title_sort | applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs |
| topic | Feed conversion ratio Mediation analysis Modelling Pigs Residual feed intake Structural equation model |
| url | http://www.sciencedirect.com/science/article/pii/S1751731125000369 |
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