Unveiling the Hidden Impact of Domestication on Animal Health

Every day, we interact with domesticated species, those that have been tamed and/or cultivated for human use. We do this through playing with our pets or eating the food we buy from the grocery store. By choosing specific traits, like larger fruit or body size, we adapt plants and animals to be useful to us. This process also changes how these species look and behave. In animals, these changes can include lighter coat colors, smaller tooth and brain size, and different ear and tail shapes. Even their behavior can change, becoming tamer and displaying juvenile behavior for longer. Inside their bodies, there are changes as well, such as those to the gut microbiome: the bacteria in an animal’s digestive tract. Some bacteria are needed to help digest food, but the gut can also be infected by harmful bacteria. The gut microbiome thus affects an animal’s health and survival. Therefore, it is important to understand the changing relationship between animals and their gut microbiomes during domestication. 

In this study, we focused on domestic pigs. Pigs make up a large percentage of agricultural animals. Pigs also serve as biomedical models for humans in medical research. Both domestic and wild pigs are available for us to compare. We know that domestic and wild pigs have different types of gut microbes. Additionally, among domestic pigs, different breeds can also have different types. However, we don’t know how differences in husbandry (care) or herd conditions shape the gut microbiome or the functions it provides for pigs. 

By changing the gut microbiome, domestication also likely changes the interactions between pigs and their microbes. For domestic pigs, how the gut microbiome supports the pig’s immune system is particularly important. Domestic pigs can transmit diseases and antibiotic-resistant bacteria to humans. Additionally, sick pigs provide lower quality meat, increasing costs for both farmers and customers who end up paying more for less. Understanding how changes in the gut microbiomes from domestication impact immune functioning is vital. 

We investigated how domestication affects both the gut microbiome and animal immune system in wild and domestic pigs from different environments. We collected fecal and blood samples from wild pigs as well as captive pigs from zoos. We also sampled domestic pigs from organic (free-ranging), research (captive), and commercial industrial (captive) farms. We looked at differences in pig genetics (wild vs. domestic), husbandry conditions (outdoor foraging and living vs indoor housing), and across herds or locations. We then used two DNA sequencing methods to identify the microbes and their genes in the various pig gut microbiomes. Genes are like tools that do different things. “Sequencing” or reading the genes encoded in their DNA helps us identify which tools the microbes have in their toolbox. We also measured the concentration of some pig immune molecules and explored their relationship with the gut microbiome.

 Our results showed that the type of gut microbes as well as their gene content differed across genetics, husbandry, and herds. Pigs which were more closely genetically related had more similar microbiomes. The biggest differences in the types of genes their gut microbes used were between wild and domestic pigs. This might be because pigs had to adapt to new diets during domestication. New diets required their microbes to use new genes in their toolbox to break down food. For instance, compared to domestic pigs, wild pig microbiomes had more genes for breaking down carbohydrates. Wild pigs eat a larger diversity of plants and insects than domestic pigs. Their microbiomes may have evolved to break down a wide range of complex carbohydrates. In contrast, domestic pig gut microbiomes had more genes for breaking down starch and sugar. This may be because domestic pigs consume mainly corn and grain-based diets high in starch. Our results suggest that domestic pig gut microbiomes have adapted to a starch-rich diet, while no longer using some genes typically used to digest a wild diet. 

Domestication includes changes in both the evolution of animal genetics as well as changes in an animal’s environment. We observed that some microbial features, such as the genes for breaking down food, depended on if a pig was genetically wild or domestic. Other features could be shaped by environmental factors. We found that husbandry conditions had the greatest impact on the types of microbes present in the gut. Potential harmful bacteria, or pathogens, also differed across husbandry practices of domestic pigs. Domestic pigs from research and industrial (captive) farms had many pathogens. In contrast, very few free-ranging domestic pigs had any potential pathogens. Possibly the stress and high-density living conditions of captive farms lead to more pathogens as well as more transmission between pigs. Domestic pigs’ microbiomes generally had more antibiotic resistance genes compared to wild pigs, but this wasn’t true of all domestic pigs. Free-ranging domestic pigs had fewer antibiotic resistance genes in their microbiomes compared to domestic pigs from research and industrial farms. 

We also found herd-specific factors. The number of pathogens differed across herds within some husbandry groups. Local factors distinct to each herd (e.g. interactions with other animals, climate, and the physical environment) may shape what pathogens exist in the environment and how well they can colonize pigs. Likewise, some herds within each husbandry group had more antibiotic resistance genes compared to others. 

Living conditions also shaped the pigs’ immune system. The immune system is very complex, but we can measure the concentrations of proteins called cytokines to better understand different parts of immune health. We observed that pigs with outdoor access had higher concentrations of the cytokine TNF-α compared to pigs without outdoor access. TNF-α is a pro-inflammatory cytokine, meaning it activates the immune system. Exposure to the natural environment through outdoor living could increase TNF-α and activate the immune system. These data, along with other unreported data, show that domestication may be linked to changes in the pigs’ immune system, possibly through changes in the gut microbiome. Without measuring other cytokines, however, we are not sure yet what our results mean for the health of these pigs. 

Altogether, our results highlight microbiome and immune differences between wild and domestic pigs as well within different types of domestic pigs. Our study is one of the first to show how husbandry conditions and herd-specific factors shape not only the microbiome but also the pig immune system. These results may help us use the microbiome to keep domestic pigs healthy and prevent diseases from spreading, among pigs and to humans. 

Written By: Sahana Kuthyar

Academic Editor: Chemical Engineer

Non-Academic Editor: Operations Manager

Original Paper

• Title: Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population

• Journal: Journal of Evolutionary Biology

• Date Published: 1 December 2023

Please remember that research is done by humans and is always changing. A discovery one day could be proven incorrect the next day. It is important to continue to stay informed and keep up with the latest research. We do our best to present current work in an objective and accurate way, but we know that we might make mistakes. If you feel something has been presented incorrectly or inappropriately, please contact us through our website.