Enteric microbiome host genetics and disease resilience

Profitability is determined by many different components of pig production. It has been suggested that the number of full value hogs sold off hog farms may be the most important factor affecting profitability (Boyd, 2012).

Pig mortality is an important factor in the number of pigs sold, and pig diseases play a major role not only in pig mortality, but also in the quality of pigs. Additional research agrees that diseases in pig production continue to reduce production and profitability (VanderWaal and Deen, 2018).

Treatments are expensive and vaccines are not 100% effective. It would then seem advantageous for pigs to possess a higher genetic merit for resilience to disease challenges, being less affected or recovering more quickly from infection caused by the disease. The economic impact of the disease is high (Cornelison et al., 2018), and the introduction of resilience measures in the goal of pig farming will increase the profits for producers.

One opportunity to impact disease resilience lies in studying the microbial community of the porcine enteric system, also known as the porcine gut microbiome. As examined by Kamada and colleagues (2013), a complex web of beneficial relationships exists between the enteric microbiome, the pig itself, and the enteric environment. This network is only beginning to be explored.

External factors can affect the type and size of microbial populations present, and these factors can alter the fitness of any of them if the relationships become unbalanced. For example, altered diet and administration of antibiotics can disrupt the microbial network and lead to intestinal colonization by harmful pathogens in an environment that was once balanced by beneficial bacteria. Therefore, a better understanding of how microorganisms contribute to the health and well-being of the pig is useful in combating disease problems.

One area of ​​interest related to the microbiome is quantifying the genetic control of the host (pig) over microbiome composition and identifying relationships between composition and disease resilience. Previous studies have identified variations in the type and abundance of bacteria present:

  • Estelle and colleagues (2014) identified a hereditary component to the abundance of certain bacterial types between individuals, ranging from very low (0.0) to very high (0.82), depending on the type of genus. Non-zero heritability estimates suggest that pig genes do play a role in the makeup of the microbiome.
  • An independent estimate would later be reported by Chen and colleagues (2018), with heritability estimates of up to 0.56 for bacterial abundance.
  • In addition, Estelle’s group identified strong genetic correlations between certain types of genera, suggesting symbiotic relationships between them.
  • Additional evidence for microbial influence on performance suggests that the vaginal microbiome may have a greater impact on reproductive performance (pre-weaning mortality and number of piglets weaned) than host genetics (Sanglard et al. , 2000).

Taken together, these results suggest the potential importance of the microbiome in the formation of phenotypes and the genetic role of a host (pig) in the makeup of the microbiome.

With evidence that host genetics play a role in the makeup of enteric microbial populations, a relevant next step is to consider genetic selection for microbiome makeup that supports pig health and productivity.

There is early evidence that immunity traits measured from blood composition are genetically correlated with the type of microbiota present (Estelle et al., 2014).

The microbiome has also been implicated in the impact on the efficiency of the vaccine response. Individual genetic variation has been documented in human and mouse populations, as well as between geographically separated human populations (Lynn and Pulendran 2017). A recent porcine example also hypothesized the influence of the gut microbiome on vaccine efficacy (Munyaka et al., 2020), where they confirmed a phenotypic relationship in the link between the vaccine response of Mycoplasma hyopneumoniae and the composition of the microbiome before vaccination. In their results, the abundance of certain types of genera might better predict vaccine results than others.

These results, coupled with evidence for the host’s genetic influence on the porcine gut microbiome, suggest a real opportunity to further improve natural resilience to disease through genetic selection for a favorable porcine gut microbiome.

Genesus joined this research by participating in a large-scale applied research project of Genome Canada in 2014. In terms of microbiome research to date, microbiome measurements on young pigs could potentially predict results of their vaccine response – which are then linked to immunity and potential susceptibility to disease.

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