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Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet
BACKGROUND: Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive e...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9327178/ https://www.ncbi.nlm.nih.gov/pubmed/35896976 http://dx.doi.org/10.1186/s12711-022-00742-6 |
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author | Déru, Vanille Tiezzi, Francesco Carillier-Jacquin, Céline Blanchet, Benoit Cauquil, Laurent Zemb, Olivier Bouquet, Alban Maltecca, Christian Gilbert, Hélène |
author_facet | Déru, Vanille Tiezzi, Francesco Carillier-Jacquin, Céline Blanchet, Benoit Cauquil, Laurent Zemb, Olivier Bouquet, Alban Maltecca, Christian Gilbert, Hélène |
author_sort | Déru, Vanille |
collection | PubMed |
description | BACKGROUND: Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet. Fecal samples were collected at 16 weeks of age to sequence the V3–V4 regions of the 16S ribosomal RNA gene and predict DE with near-infrared spectrometry. The proportions of phenotypic variance explained by the microbiota (microbiability) were estimated under three OTU filtering scenarios. Then, microbiability and heritability were estimated independently (models Micro and Gen) and jointly (model Micro+Gen) using a Bayesian approach for all traits. Breeding values were estimated in models Gen and Micro+Gen. RESULTS: Differences in microbiability estimates were significant between the two extreme filtering scenarios (14,366 and 803 OTU) within diets, but only for all DE. With the intermediate filtering scenario (2399 OTU) and for DE, microbiability was higher (> 0.44) than heritability (< 0.32) under both diets. For two of the DE traits, microbiability was significantly higher under the high-fiber diet (0.67 ± 0.06 and 0.68 ± 0.06) than under the conventional diet (0.44 ± 0.06). For growth and FE, heritability was higher (from 0.26 ± 0.06 to 0.44 ± 0.07) than microbiability (from 0.17 ± 0.05 to 0.35 ± 0.06). Microbiability and heritability estimates obtained with the Micro+Gen model did not significantly differ from those with the Micro and Gen models for all traits. Finally, based on their estimated breeding values, pigs ranked differently between the Gen and Micro+Gen models, only for the DE traits under both diets. CONCLUSIONS: The microbiota explained a significant proportion of the phenotypic variance of the DE traits, which was even larger than that explained by the host genetics. Thus, the use of microbiota information could improve the selection of DE traits, and to a lesser extent, of growth and FE traits. In addition, our results show that, at least for DE traits, filtering OTU is an important step and influences the microbiability. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-022-00742-6. |
format | Online Article Text |
id | pubmed-9327178 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-93271782022-07-28 Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet Déru, Vanille Tiezzi, Francesco Carillier-Jacquin, Céline Blanchet, Benoit Cauquil, Laurent Zemb, Olivier Bouquet, Alban Maltecca, Christian Gilbert, Hélène Genet Sel Evol Research Article BACKGROUND: Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet. Fecal samples were collected at 16 weeks of age to sequence the V3–V4 regions of the 16S ribosomal RNA gene and predict DE with near-infrared spectrometry. The proportions of phenotypic variance explained by the microbiota (microbiability) were estimated under three OTU filtering scenarios. Then, microbiability and heritability were estimated independently (models Micro and Gen) and jointly (model Micro+Gen) using a Bayesian approach for all traits. Breeding values were estimated in models Gen and Micro+Gen. RESULTS: Differences in microbiability estimates were significant between the two extreme filtering scenarios (14,366 and 803 OTU) within diets, but only for all DE. With the intermediate filtering scenario (2399 OTU) and for DE, microbiability was higher (> 0.44) than heritability (< 0.32) under both diets. For two of the DE traits, microbiability was significantly higher under the high-fiber diet (0.67 ± 0.06 and 0.68 ± 0.06) than under the conventional diet (0.44 ± 0.06). For growth and FE, heritability was higher (from 0.26 ± 0.06 to 0.44 ± 0.07) than microbiability (from 0.17 ± 0.05 to 0.35 ± 0.06). Microbiability and heritability estimates obtained with the Micro+Gen model did not significantly differ from those with the Micro and Gen models for all traits. Finally, based on their estimated breeding values, pigs ranked differently between the Gen and Micro+Gen models, only for the DE traits under both diets. CONCLUSIONS: The microbiota explained a significant proportion of the phenotypic variance of the DE traits, which was even larger than that explained by the host genetics. Thus, the use of microbiota information could improve the selection of DE traits, and to a lesser extent, of growth and FE traits. In addition, our results show that, at least for DE traits, filtering OTU is an important step and influences the microbiability. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-022-00742-6. BioMed Central 2022-07-27 /pmc/articles/PMC9327178/ /pubmed/35896976 http://dx.doi.org/10.1186/s12711-022-00742-6 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Déru, Vanille Tiezzi, Francesco Carillier-Jacquin, Céline Blanchet, Benoit Cauquil, Laurent Zemb, Olivier Bouquet, Alban Maltecca, Christian Gilbert, Hélène Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title | Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title_full | Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title_fullStr | Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title_full_unstemmed | Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title_short | Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
title_sort | gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9327178/ https://www.ncbi.nlm.nih.gov/pubmed/35896976 http://dx.doi.org/10.1186/s12711-022-00742-6 |
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