Should mice be used to study the human gut microbiome?

In recent years, the trillions of bacteria living in our guts have risen from obscurity to stardom. Hyped press releases claim that probiotics and faecal transplants might one day treat almost everything, from bowel inflictions to obesity. These studies often involve mice, but are these rodents really a suitable model for microbiome research?

The gut microbiome has been associated with an ever-growing list of diseases, including obesity, diabetes and even mental disorders such as anxiety and autism. Much like the Human Genome Project around 15 years ago, the booming microbiome research field has promised to deliver new revolutionary treatments, some as simple as eating a yogurt. Perhaps inevitably though, history repeats itself. After a few years of frantic microbiome sequencing and many new biotech start-ups, microbiome researchers are now having to face the hard questions: are the changes in the gut microbiome associated with certain diseases a cause, or a consequence, of the disease? How on earth can bacteria in the gut affect other parts of the body, such as the brain? What are the molecular mechanisms behind all this?

E. coli bacteria thrive in the gut.

Studies in humans can at most reveal correlations between the microbiome composition and a given disease. For example: Bob is obese and happens to have a microbiome with lots of bacteria X, but John, who is slim, doesn’t. This suggests that bacteria X cause obesity, yet, there’s also a good chance that in fact it’s the other way round: obesity might somehow promote growth of bacteria X. Or maybe this type of bacteria thrives on Bob’s diet, or it simply prefers the unique environment of his gut.

It is virtually impossible, and unethical, to perform experiments in humans to explore causal hypotheses (does bacteria X cause obesity?) and control for confounding factors like diet and genetic background. Microbiome researchers have to use the next best thing: mice. There are, however, growing concerns within the scientific community that more often than not, data from mouse can’t be extrapolated to humans for clinical purposes. Or at least, not easily.

In a new study, Jeroen Raes and colleagues at the KULeuven University, in Belgium, carefully compared the human and mouse gut microbiomes to assess the strengths and pitfalls of this model system for studying microbiome-related diseases.

“Microbiome research, notably its association to inflammatory diseases, relies heavily on mouse models […]. It is essential to know the qualities and limitations of each model to choose the correct one to test specific hypotheses”, says Sara Vieira-Silva, one of the authors conducting the study.

Can mice recapitulate the human gut microbiome?

Mice are great for biomedical research. They share most of our genes, and have similar anatomy and physiology. With the many available genetic tools, scientists can easily and quickly discover the function of literally any gene in the mouse genome, and recapitulate human disease in a controlled experimental set up. So where’s the catch? The problem is that although mice and humans share many similarities, there are also many differences.

Rae’s team performed comprehensive statistical analyses for all gut microbiomes from mice and humans published to date. These new data tell us what types of bacteria live in the gut in various scenarios (disease, diet, genetic background…), as well as their relative abundance. The team first compared the gut microbiomes of healthy humans and mice. And the differences start here.

Human and mouse guts have predominantly two ‘families’ of bacteria—Bacteroidetes and Firmicutes—but within these groups, 85% of bacteria species found in mice are not present in humans. And the bacteria found in both? It appears their abundance in the gut also varies between mice and humans; when you’ve got a lot of a certain bacteria in mouse, you may find very little of it in humans, and vice versa. The authors stress that many of these differences could simply be a result of technical limitations, like methodology or interference from external factors (diet, age, etc).

Mouse models of disease

There are over 60 mouse models of Inflammatory Bowel Disease (IBD), but none fully recapitulates the disease. Even so, the changes in the gut microbiome of patients with IBD (when compared to healthy people) are similar to those observed in IBD mouse models. For example, there is a significant reduction in bacterial diversity in both IBD patients and IBD mouse models. However, some specific bacteria species will be more (or less) abundant in mouse but not in IBD patients. The same goes for obesity models. Overall, mice fed on high-fat diet, and also leptin-deficient mice, which cannot control their appetite, recapitulate the microbiome changes observed in obese people. But there are many discrepancies in the data, again likely due to external factors that are difficult to control, at least in human studies.

The conclusion? Well, mice are not people. Raes and colleagues warn microbiome researchers that extreme care should be taken when trying to extrapolate findings in mouse to humans. They should also make bigger efforts to standardise their protocols for animal handling and data analysis, and to share mouse models to eliminate any genetic variability that might skew the data.

“Most limitations of murine [mouse] models for fundamental microbiome research can be overcome by methodical study design and statistical testing: either eliminating or keeping track of possible confounders (e.g. diet variation, genetic background) and testing for their influence on the results”, says Vieira-Silva.

Nevertheless, the authors conclude, when it comes to understanding the causes and molecular mechanisms behind human disease, mouse models seem to fit the bill. “Although the mouse microbiota composition is not identical to the human's, most mechanisms of microbiota-host interaction will be shared between mice and humans” concludes Vieira-Silva. “Mice models allow us to study these mechanisms with direct controlled experiments, towards the ultimate aim of providing therapeutic solutions.”

Reference:

Nguyen T.L.A., A. Liston & J. Raes (2015). How informative is the mouse for human gut microbiota research?, Disease Models , 8 (1) 1-16. DOI: http://dx.doi.org/10.1242/dmm.017400

And edited version of this article was published in Lab Times on the 24-02-2015. You can read it here.

Interview with Nobel laureate Sir Tim Hunt

I recently spoke with Nobel laureate Sir Tim Hunt about the current research scene in Europe in an interview for Lab Times. We discussed topics such as research funding, gender inequality in academia and the publishing system. Below is a summary of his career and the full interview.

Sir Tim Hunt started his research career in 1964 at the University of Cambridge (UK) working on haemoglobulin synthesis under the supervision of Asher Korner. After obtaining his PhD in 1968, he spent a few years at the Albert Einstein College of Medicine in New York (US) working with Irving London, until he returned to Cambridge to teach and establish his independent research career studying translational control. In the late 1970s, he began teaching a summer course at the Marine Biological Laboratory, Woods Hole (US), where he began working with sea urchin and clam eggs. These experiments eventually led to the discovery of cyclins, a family of regulatory proteins that partner with cyclin-depent kinases (CDKs) to control the transition between cell cycle phases. For this breakthrough Hunt was awarded the Nobel Prize in Physiology or Medicine in 2001, together with Lee Hartwell and Paul Nurse for their work on CDKs in yeast. In 1990, Hunt moved his laboratory to the Clare Hall Laboratories at Imperial Cancer Research Fund (now London Research Institute/Cancer Research UK) where he carried out pioneering research on cyclins and cell cycle control until his recent retirement. He is a former Chair of the European Molecular Biology Organisation (EMBO) council, and currently member of the Scientific Council of the European Research Council (ERC), the Advisory Council for the Campaign for Science and Engineering (CaSE) and of the Selection Committee for the Shaw Prize in Life Science and Medicine.

You have recently retired from a long and prolific research career. How different is it to pursue a research career now, compared to when you started, or even just a couple of decades ago?

Hunt: I always like to joke that I am glad that I am not 20 something years old today, because I think it is much harder than when we started. When I started as a PhD student in 1964 our department didn’t have a Xerox machine, there were no calculators, you had to go to the library to read things and it was virtually impossible to analyse individual proteins because the SDS gel had not yet been invented. The tools were very blunt and the questions you could ask were corresponding limited; now the two are exceedingly sharp and the analytical procedures are absolutely awesome. […] When you look back at the papers of that era they were pretty simple, easier to understand in many cases. There was only so much you could do. I am appalled sometimes at some papers today; they are so data heavy, and I don’t think that makes them better papers. […] In terms of publication there is just much more competition these days, because the biosciences have been so successful; they consume about 2% of the growth national product in the US and the result is that there are thousands of competing young scientists. My generation is just on the point of retirement, and in the meantime we have all trained dozens of doctoral students and postdocs, each of which has trained their own students and postdocs, so this exponential growth is what caused all the problems, I would say.

And where do you think all this is heading?

Hunt: I really don’t know… Somewhere between 1990 and 2000 many of the outstanding problems of cellular, molecular and developmental biology were effectively solved. You do kind of wonder: how many really important problems are there in biology that remain? Of course there are hundreds of details but the last great frontier is how the brain works, there you have a very primitive partial understand of most of it. […] It is a pretty difficult problem.

Is the European Union currently taking the right measures to move European science forward?

Hunt: The old investigator-led grants are excellent and much better that top-down collaborative network grants, which are quite good fun but I don’t think it is a terribly good mechanism to hunt for the best science because the people aren’t really working together. When you really work with somebody you see them everyday, and here the idea is that you see one another once a year, or perhaps four times a year, it just doesn’t work. There are projects that might work, like these huge projects to sequence the human genome, the big science, but mostly I think that biology is still pretty small science that has to be carried out by committed individuals focusing on particular problems. I don’t know very many things that require that kind of effort.

What are the strengths and pitfalls of the European research community, when compared, for example, with research in the US?

Hunt: I think things have improved tremendously in Europe in the last few years. For example, in my field, the European Molecular Biology Laboratory (EMBL) has trained lots of people, not only in how to do science, but also on how to manage science and how to choose scientists. […] I believe very much in giving power to the young and not putting them under. I was given full autonomy and authority at a very young age, at 27 years old. I wasn’t running my own lab, I had friends around to help and I liked that. There is much more internationalization in Europe, good practice [of science] is much more diffused throughout. In the former communist countries, Poland, Bulgaria and places like that, they still have a long way to go but it is difficult to feed because any new talent that arises, very quickly migrates abroad. At the ERC we think about that a lot but we haven’t really taken steps to deal with it because it is against our principles. We say excellence only and that rules most of those people out, and it is understandable, they don’t have a good science base, and it is hard to see how they can build one.

What do you think of big science prizes like the Breakthrough Prize? Some people claim that junior scientists should receive this type of prize instead of established scientists. 

Hunt: I don’t know to be honest. You have to find a compromise. If you are a granting agency, you really do need to try to identify people who are successful and clever, and that will make good use of the money. There are a lot of funding agencies and in the past you feel that every person had to get a little piece of the cake, and in general, that meant that the food is spread too thinly. So I think that a bit of concentration is a good idea, but that then raises the question: how do you identify the good people? That is when the problems begin, because now we start talking about impact factor and things like that and everybody knows there are problems with that but nobody has found a satisfactory solution. We are good at judging science retrospectively but we are not good at judging science prospectively, because the future is always very hard to predict. The ERC does the best it can. We like to keep things very simple and in judging grant applications you give half the marks to track record of the applicant and half the marks to the project they propose. I think that is a pretty good ratio. You can’t just give money to people who have been successful in the past and say ‘do whatever you’d like’, I don’t think that sort of view is responsible although in some cases it will be fine. And likewise people can propose very fancy and clever research projects but when you look at their productivity you see that they are much better at writing grants than actually carrying out research. Somewhere between those two extremes lies the compromise.

How can we change the way scientists (and science) are perceived by the public?

Hunt: I don’t know, I think that is a very difficult question to answer. People always say that scientists must be encouraged to go out and explain what they are doing. I’m all for that, I try to do a little bit, I go and talk in schools and so forth. But nothing never really comes close to the experience of actually doing science, which is usually a rather peculiar random walk, mostly failure and the occasional few successes. But it doesn’t really explain why it is so wonderful and such good fun to do because in order to understand it you have to usually have first done a PhD in the subject and most people haven’t. I would find it difficult to explain to a quantum mechanics expert what I was doing and why I thought it was interesting. […] Science is really just a way of finding things out. You pursue a lot of false clues, you get misled and misinterpret things. And that is very hard to convey and unfortunately I think the teaching of science in school is very delusive…. They make it sound that there are some geniuses out there that figured everything out and then wrote it down in textbooks. And all you have to do is learn what it says in the textbooks and you will be a brilliant scientist, but we all know that textbooks are actually wrong in lots of places. And the alternative to that of course is: ok we won’t teach the kids what is known, we will let them find it all out for themselves. But if you have to find everything out for yourself it takes an awfully long time to discover anything. It is really important to have practical experience, but it is very difficult to give people practical experience of what it is really like to be pursuing a real live problem.

Do you think scientists are pressured to focus their research on ‘hot’ topics, like cancer or neuroscience?

Hunt: I think they are. It is the money issue; people tend to migrate in that direction because they have no choice. I don’t think it is a very sensible way to spend the money. I am a tremendous believer in fundamental research. When I look at the great breakthroughs, like the discovery of penicillin, that wasn’t produced by doctors wanting to make antibiotics, none of them realised it was possible. It was a tiny handful of basic researchers who were curious and figured out how to do it. I think this emphasis on translation research is very foolish, because it implies that we know everything that we need to know, and that is not true obviously. A good example is the case of gene therapy, which is much needed to treat genetic diseases and it doesn’t work very well because much more biological engineering is required. I think most biological fields are well populated, and if a breakthrough occurs they won’t fail to exploit them.

How would you explain to someone in one sentence that it is important to fund and encourage more basic research?

Hunt: I wouldn’t know how to begin! I think it is extremely difficult to justify because what you are really saying is ‘just pay me to have more fun’ and that works much better than paying me to do something I have no clue how to do.

In your opinion, why are women still under-represented in senior positions in academia and funding bodies? 

Hunt: I’m not sure there is really a problem actually. People just look at the statistics. I dare myself think there is any discrimination, either for or against men or women. I think people are really good at selecting good scientists but I must admit the inequalities in the outcomes, especially at the higher end, are quite staggering. And I have no idea what the reasons are. One should start asking why women being underrepresented in senior positions is such a big problem. Is this actually a bad thing? It is not immediately obvious for me that… is this bad for women? Or bad for science? Or bad for society? I don’t know, it clearly upsets people a lot.

What research area excites you at the moment?

Hunt: I am very excited by stem cell biology. I think the advances that have been made are just fantastic and I really hope that is something that will lead to people growing pancreas in a test tube and use them to cure diabetes, for example. I think that those advances have been absolutely spectacular, very, very interesting.

Interview by Isabel Torres

This interview was published in Lab Times on 4-07-2014 (print issue).