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Of Mice & Men

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By Claire Thompson

Are mouse models of immune disorders of the human gut, such as inflammatory bowel disease, reliable? And can probiotic supplements keep us healthy?

The intestine is a place where man and microbe meet. From the moment we are born, bacteria colonise our intestines, entering via the food we eat and from contact with our environment.

As a consequence, the vast surface area of the intestine is continually exposed to bacteria. Those that take up permanent residence are collectively referred to as the gut microbiota, many of which are beneficial and perform important functions, such as assisting us with digestion and synthesising vitamins that we require but cannot make ourselves. In addition to these good bacteria are other microbes that are less helpful and even capable of causing disease.

In order to cope with this onslaught, the intestine is also the home to a highly adapted immune system. Indeed, the majority of the body’s immune cells are located within the intestine. These cells can be in contact with a bacterial community of more than 100 trillion cells amassed from hundreds of different species.

Yet our immune system is sophisticated enough to recognise friend from foe. It is able to strike a balance, tolerating the presence of some bacteria while eliminating others. How the immune system is able to do this is not yet fully understood.

Gut microbes are able to trigger important processes within the body. For example, the development of the immune system is incomplete in germ-free animals, and even the architecture of the intestine is altered.

The influence of the gut microbiota is not restricted to the intestine. Gut bacteria regulate various aspects of drugs metabolism and energy storage. Given their contribution to such a variety of physiological and metabolic processes, it is therefore unsurprising that gut bacteria have such a large influence on our health.

So what happens when we fail to get along with our bacterial inhabitants? Upheaval in our gut community and changes in the way we respond to our gut bacteria are thought to be responsible for chronic inflammatory diseases of the intestine.

Inflammatory bowel disease (IBD) affects thousands of Australians and has no known cure. IBD encompasses two conditions, both involving inflammation of the intestine. While Crohn’s disease can occur in any part of the intestine, ulcerative colitis affects only the large intestine. Patients with these diseases also show changes in the composition of their gut bacterial communities. Might we able to improve a patient’s health by changing their gut community back to a healthy state?

There is one major obstacle to achieving this. We still do not understand enough about the gut microbiota to be able to define what “healthy” is.

One potential characteristic of a healthy gut community is stability of the types and abundance of different bacterial species in the intestine over time. Studies of gut bacteria in healthy humans have found that their intestinal communities remain stable over time, but patients with IBD have relatively unstable communities.

What controls the stability of the gut community? We know that the immune system plays a large part in regulating the gut microbiota. Therefore, it is likely that it also plays a role in generating gut stability.

In diseases such as IBD, it is thought that the immune system reacts inappropriately to the gut microbiota, causing inflammation and damage to the intestine. This response may be to blame for the relative instability in the gut community of IBD patients. A greater understanding of the role of the immune system in gut stability might give us an insight into how diseases such as IBD are caused and how we might better treat them in the future.

Mice are commonly used to study many human diseases, including IBD. They are a good model for studying immune function as their genetic background can be controlled, and “knockout” mice that do not expresses certain genes can be generated.

Several immune-knockout mouse strains have been developed that in some respects resemble human IBD and show similar symptoms. However, little is known about how well they reflect IBD in humans. One major problem is that we do not know how similar the dynamics of the mouse gut microbiota is to that of humans. Are the gut communities of mice also stable?

To address this question, we examined how parts of the innate immune system affect gut stability in mice. We measured the stability of the gut microbiota in four different strains of mice: two standard laboratory strains and two that lacked different components of the interferon signalling system.

Interferons play a role in a variety of immune functions, and interferon signalling is crucial for the host immune response to bacterial, parasitic and viral infections. As a consequence, mice that lack parts of this pathway are more prone to infection. Since interferon signalling also regulates the response of intestinal epithelial cells to inflammation, would the absence of these components influence the stability of the gut community?

Our first aim was to gain access to the mouse gut microbiota. Hidden away in the large intestine, gut bacteria are difficult to examine. While it would be ideal to take a sample directly from inside the intestine, by doing so, we would disrupt the community and inadvertently cause changes in its composition.

A far less intrusive method is to collect faeces. From these samples we can amplify the bacterial DNA and produce a profile of the different types of bacteria in the mouse gut.

What we found was that each of the mice in our study had a unique profile, indicating that each possessed its own distinctive gut community. A similar observation has been made in other mammals, such as humans and pigs. However, by comparing the profiles from individual mice we observed that, unlike in humans, the gut microbiota of mice was not stable – the profiles changed over time. This was true for all the mice in our study whether they had a fully functioning immune system or not.

Why might there be less stability in the mouse gut compared with humans?

1. Firstly, the mouse intestine is anatomically different from the human gut – both the length of the colon and the time taken for food to pass through the intestine is considerably shorter.

2. Laboratory mice are inbred for many generations. Inbreeding affects immune function, and this might influence the way in which the mouse responds to its gut bacteria.

3. Laboratory mice live in a clean environment, with sterilised food and bedding. As a result they come into contact with far fewer bacteria than they would in the wild.

These aspects would all influence the way that the mice interact with their gut communities and could potentially lead to instability.

While all the mice in our study showed a degree of instability in their gut microbiota, the greatest instability occurred in mice that did not express the interferon regulatory factor 9 (IRF9), suggesting that this gene may be potentially involved in maintaining the composition of the gut microbiota. These mice also had significantly more immune cells, such as T cells and neutrophils, in their intestinal tissue. IRF9 is a component of the interferon signalling pathway, and when activated it promotes the expression of certain genes that are important in immune responses. However, its role is yet to be fully defined and it may play a part in other signalling pathways. Our findings make it an interesting target for future studies.

We still have a lot to learn about our bacterial communities and what makes them so important to health. There is considerable interest in being able to modify our gut communities to treat certain diseases or to improve the way the gut functions, such as by adding beneficial gut microbes in the form of probiotic cultures, or taking prebiotics that encourage the growth of beneficial microbes that already exist in the gut.

However, the stable nature of our gut microbiota makes it extremely resistant to these modifications. For example, although probiotic cultures can be bought in most supermarkets, we still do not understand how to turn these beneficial but transient microbes into permanent members of the gut community without having to continually ingest them.

Therefore, discovering what makes the human gut community so resistant to change is a step towards being able to take charge our gut communities.

Claire Thompson completed this research as a PhD student at the University of Sydney’s School of Molecular Bioscience. She is now a postdoctoral fellow at the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany.