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Signs of host genetic regulation in the microbiome composition in cattle

View ORCID ProfileO. Gonzalez-Recio, I. Zubiria, View ORCID ProfileA. García-Rodríguez, A. Hurtado, R. Atxaerandio
doi: https://doi.org/10.1101/100966
O. Gonzalez-Recio
*Departamento de Mejora Genética Animal. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. 28040 Madrid, Spain
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I. Zubiria
†Departamento de Producción Animal. NEIKER-Tecnalia. Granja Modelo de Arkaute Apartado 46, 01080 Vitoria-Gasteiz, Spain
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A. García-Rodríguez
†Departamento de Producción Animal. NEIKER-Tecnalia. Granja Modelo de Arkaute Apartado 46, 01080 Vitoria-Gasteiz, Spain
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A. Hurtado
††Departamento de Sanidad Animal. NEIKER-Tecnalia. Berreaga 1, 48160 Derio, Spain
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R. Atxaerandio
†Departamento de Producción Animal. NEIKER-Tecnalia. Granja Modelo de Arkaute Apartado 46, 01080 Vitoria-Gasteiz, Spain
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ABSTRACT

Previous studies have revealed certain genetic control by the host over the microbiome composition, although in many species the host genetic link controlling microbial composition is yet unknown. This potential association is important in livestock to study all factors and interactions that rule the effect of the microbiome in complex traits. This report aims to study whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Data on 16S and 18S rRNA gene-based analysis of the rumen microbiome in 18 dairy cows from two different breeds (Holstein and Brown Swiss) were used. The effect of the genetic background of the animal (through the breed and Single Nucleotide Polymorphisms; SNP) on the relative abundance (RA) of archaea, bacteria and ciliates (with average relative abundance per breed >0.1%) was analysed using Bayesian statistics. In total, 13 genera were analysed for bacteria (5), archaea (1), and ciliates (7). All these bacteria and archaea genera showed association to the host genetic background both for breed and SNP markers, except RA for the genera Butyrivibrio and Ruminococcus that showed association with the SNP markers but not with the breed composition. Relative abundance of 57% (4/7) of ciliate analysed showed to be associated to the genetic background of the host. This host genetic link was observed in some genus of Trichostomatia family. For instance, the breed had a significant effect on Isotricha, Ophryoscolex and Polyplastron, and the SNP markers on Entodinium, Ophryoscolex and Polyplastron. In total, 77% (10/13) of microbes analysed showed to be associated to the host genetic background (either by breed or SNP genotypes). Further, the results showed a significant association between DGAT1, ACSF3, AGPAT3 and STC2 genes with the relative abundance Prevotella genus with a false discovery rate lower than 15%. The results in this study support the hypothesis and provide some evidence that there exist a host genetic component in cattle that can partially regulate the composition of the microbiome.

  • Abbreviations

    FDR
    False Discovery Rate
    NGS
    Next Generation Sequencing
    MAF
    Minor Allele Frequency
    OTU
    operational taxonomic units
    PC
    Principal components
    RA
    Relative abundance
    SNP
    Single Nucleotide Polymorphisms
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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    Posted January 17, 2017.
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    Signs of host genetic regulation in the microbiome composition in cattle
    O. Gonzalez-Recio, I. Zubiria, A. García-Rodríguez, A. Hurtado, R. Atxaerandio
    bioRxiv 100966; doi: https://doi.org/10.1101/100966
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    Signs of host genetic regulation in the microbiome composition in cattle
    O. Gonzalez-Recio, I. Zubiria, A. García-Rodríguez, A. Hurtado, R. Atxaerandio
    bioRxiv 100966; doi: https://doi.org/10.1101/100966

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