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Updated: Jun 22, 2025

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Driving gut microbiota enterotypes through host genetics.

Catherine Larzul1, Jordi Estellé2, Marion Borey3

  • 1GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France. catherine.larzul@inrae.fr.

Microbiome
|June 29, 2024
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Summary

Host genetics influence gut enterotypes in pigs, impacting their functionality and growth. Selecting for specific enterotypes can enhance piglet growth, demonstrating the potential for breeding programs to utilize host genetics and microbiota for improved animal health.

Keywords:
EnterotypeGenetic selectionGeneticsGut microbiotaHeritabilityHolobiontMetagenomicsPig

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Area of Science:

  • Animal Science
  • Microbiology
  • Genetics

Background:

  • Enterotypes, microbial ecosystems in the gut, are linked to environmental factors but host genetic influence is understudied.
  • Previous work identified two distinct pig enterotypes: Prevotella-Mitsuokella (PM) and Ruminococcus-Treponema (RT).

Purpose of the Study:

  • To investigate the role of host genetics in shaping pig enterotypes.
  • To explore functional differences between enterotypes and their impact on growth traits.

Main Methods:

  • Established distinct pig lines selected for PM or RT enterotype prevalence over three generations.
  • Analyzed fecal microbiota composition and growth performance.
  • Utilized shotgun metagenomics and KEGG Orthology database for functional analysis.

Main Results:

  • Selection successfully increased enterotype prevalence and associated bacterial abundances across generations.
  • The PM enterotype showed less diversity but enhanced piglet growth post-weaning compared to the RT enterotype.
  • Functional analysis revealed PM enterotype enrichment in starch/polysaccharide metabolism and RT enterotype in nucleoside/peptide/nickel transport, with potential differences in branched-chain amino acid metabolism.

Conclusions:

  • Enterotypes are functional ecosystems that can be selected via host genetics.
  • Holobionts, encompassing host and microbiota, should be considered units of selection in breeding programs.
  • Findings support a holistic approach integrating host genetics, microbiota diversity, and enterotype functions for understanding holobiont adaptation.