How healthy gut flora benefit animal welfare

Photography: Shutterstock


Gut bacteria play a key role in the physical health of humans and animals. Humans with healthy gut flora also benefit from improved mental health, but it is not known whether the same applies to animals. Wageningen University & Research is studying the link between the microbiome, the health of the gut and animal welfare.

Annemarie Rebel is head of the Animal Welfare & Health department at Wageningen University & Research and the project manager of the study on the role of the microbiome in the health of farm animals. This study is being carried out at Wageningen Livestock Research.

What does the term ‘microbiome’ mean exactly?

A variety of microorganisms, such as bacteria, viruses and yeasts, can be found in the intestines and respiratory tract and on the skin of humans and animals. The microbiome refers to all these microorganisms as a whole.

The microbiome consists of microorganisms such as bacteria, viruses and yeasts. Photo: Shutterstock

The microbiome differs between individuals, it changes in the course of a lifetime and it is resilient. How the microbiome evolves over time depends on your environment, diet and age. You can therefore use these factors to influence the microbiome.

Incidentally, plants and soil also have a microbiome.

What do we already know about the microbiome in the intestines?

Gut bacteria affect the development of the intestinal wall, which has consequences for the immune system and food digestion. The intestinal wall in turn influences the composition of the gut bacteria. If this system is no longer in equilibrium, that can lead to the excessive growth of potentially harmful bacteria, resulting in disease. What is more, the microbiome in the intestines is directly responsible for the digestion of fibres and production of important nutrients such as vitamin K, which is needed for clotting.

In humans, diet has a clear effect on the microbiome. It is now accepted that a healthy diet with plenty of fibre from vegetables, fruit, pulses, nuts and wholemeal products produces a different microbiome to a diet with less of these types of food. It transpires that changes in the feed for hens, pigs and calves also affect the gut immune system because they affect the microbiome in the gut. The effect is seen not just in the animals themselves but also in their offspring.

Furthermore, associations have been found in humans and mice between the microbiome in the intestines and certain intestinal diseases, obesity and mental disorders such as depression.

Researchers of Wageningen University & Research are looking into the link between microbiomes, the health of gut floras and animal welfare. The research aims to prove that food infuences behaviour and health. If so, farmers and feed producers can use food to select for health, resilience and behaviour.

What is the aim of your current study?

An animal in a state of good health and well-being is much more resilient and better able to cope with the challenges in its environment. That means the risk of an outbreak of an infectious disease is much smaller in healthy animals, and consequently humans run a smaller risk of catching these diseases. Healthy animals do not need so much medication either, which reduces the risk of resistance to antibiotics arising. That benefits both animals and humans.

The current study shows that there is a relationship between the microbiome in the intestines and the behaviour and well-being of the animal. It is not yet clear whether greater well-being leads to a change in the microbiome or whether a change in the microbiome improves well-being, but the fact that they influence one another is an important finding.

The microbiome differs between individuals, changes in the course of a lifetime and is resilient

Just a small change in the feed and/or environment can lead to a change in the microbiome. That can in turn have an effect on the immune system — and hence health — and on brain function — and hence behaviour. Our goal is to try and understand the link between the microbiome in the intestines, health, brain functions and behaviour.

What does this research project involve?

We are monitoring chickens and pigs over time. For example, we add enriching elements such as toys to the stall and study the effects. You have to do this carefully though: the enrichment must not lead to a change in eating patterns, otherwise you can’t tell whether the change in the microbiome is due to the welfare improvement or to eating the enrichment element. We study the behaviour of the animals in their stall. We use unobtrusive methods such as video images and sensors that measure body temperature. This lets us observe the animals’ behaviour without having to be physically present in the stall, which has the advantage that we don’t influence their behaviour.

We study both the ‘normal’ situation and the situation in which we give the animals more ‘challenges’. For example, we measure the degree of stress in a brief test situation in which we place new objects between the animals and then monitor their reactions.

The microbiome could give information about the health, brain function and behaviour of chickens. Photo: Wageningen Livestock Research

We determine the microbiome from the manure, with the help of DNA sequencing. We perform blood tests to see the impact on the immune system and we measure levels of the stress hormone cortisol. At the end, we will assess the intestinal tissue to determine developments in the immune system and the microbiome in the intestines. Finally, we will analyse all the results and investigate the relationships we find. We will be repeating the studies so that we can be sure the results are not just random chance. We minimize any discomfort for the animals during our studies. Many of the measurements are non-invasive, such as the analysis of the video images and manure samples. In addition, we always keep to the requirements for each particular species in terms of their surroundings and care, while all the changes we investigate are stall enrichments, in other words positive changes to their surroundings.

How can you determine whether an animal is happy based on your measurements and analyses?

That’s easier said than done. We use protocols for assessing animal welfare that have been drawn up for cattle, poultry and pigs. We look at the state of the animal’s coat or feathers and whether it has any injuries. We also check whether there is a decrease in negative behaviour such as pulling out feathers, biting tails or stereotypical behaviours such as pacing aimlessly in circles. Finally, we are looking at how positive behaviours start: how active is the animal, is the animal prepared to investigate new objects, how quickly does the animal approach the feeding trough?

A healthy animal is better able to cope with the challenges in its environment

We are also able to measure levels of cortisol, the stress hormone. The aim is to develop more non-invasive species-specific indicators that tell us whether an animal has a high level of well-being and positive emotions. Examples could be indicators in the manure, saliva, feathers or hairs. The researchers are busy developing these indicators.

Does it make much difference which animals you study?

Of course the animals differ in terms of their behaviour and physical makeup. However, the studies are largely similar. For example, investigating the genetics of bacteria is the same whether you are studying a pig or a chicken, or indeed a plant or soil.

Do you already have a picture of what the optimum microbiome looks like?

If only we did! It is fairly easy to identify gut bacteria that aren’t beneficial. However, we will need follow-up studies to determine what combination of bacteria maximizes well-being or growth or produces the best immune system.

What do you hope to achieve eventually with the follow-up studies?

Current production systems are geared to minimizing variation in animals’ diet and surroundings. Circular agriculture and climate-neutral production systems are the future but they entail much more variation for the animals. The farm animals will need to be more resilient to cope with this.

Annemarie Rebel is the project manager of a study on the role of the microbiome in the health of farm animals. Photo: Wageningen Livestock Research

We need to investigate how we can influence the microbiome in animals. Which changes in the feed and other factors that we want to make from a circular agriculture perspective will also have a positive impact on the microbiome, animal welfare and antibiotic resistance, and which changes would we be better off avoiding? Animals do have the capacity to deal with small changes, but we still need to make use of that capacity.

The ultimate goal is to have more resilient production systems with more resilient animals that are healthier and happier, make a major contribution to the implementation of circular agriculture and reduce the risk of infection for humans.

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