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Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs
BACKGROUND: The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9036775/ https://www.ncbi.nlm.nih.gov/pubmed/35468740 http://dx.doi.org/10.1186/s12711-022-00717-7 |
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author | Aliakbari, Amir Zemb, Olivier Cauquil, Laurent Barilly, Céline Billon, Yvon Gilbert, Hélène |
author_facet | Aliakbari, Amir Zemb, Olivier Cauquil, Laurent Barilly, Céline Billon, Yvon Gilbert, Hélène |
author_sort | Aliakbari, Amir |
collection | PubMed |
description | BACKGROUND: The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated. RESULTS: Estimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect. CONCLUSIONS: Our results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-022-00717-7. |
format | Online Article Text |
id | pubmed-9036775 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-90367752022-04-26 Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs Aliakbari, Amir Zemb, Olivier Cauquil, Laurent Barilly, Céline Billon, Yvon Gilbert, Hélène Genet Sel Evol Research Article BACKGROUND: The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated. RESULTS: Estimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect. CONCLUSIONS: Our results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-022-00717-7. BioMed Central 2022-04-25 /pmc/articles/PMC9036775/ /pubmed/35468740 http://dx.doi.org/10.1186/s12711-022-00717-7 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 Aliakbari, Amir Zemb, Olivier Cauquil, Laurent Barilly, Céline Billon, Yvon Gilbert, Hélène Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title | Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title_full | Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title_fullStr | Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title_full_unstemmed | Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title_short | Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
title_sort | microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9036775/ https://www.ncbi.nlm.nih.gov/pubmed/35468740 http://dx.doi.org/10.1186/s12711-022-00717-7 |
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