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Column: Do these (microbial) genes make me look fat?

Do these (microbial) genes make me look fat?

In the third instalment of ‘Just 10% Human,’ Daniel Sprockett looks at the effects that having different — or even no — microbes inside us can have on our health and our weight.


I’ve been discussing how extremely prevalent microbes are on our bodies and how important they are for the normal functioning of our immune systems. But what if they were missing? If we could completely get rid of all the microbes on a human being – what would happen?

And how would you go about ridding someone of all of their microbes in the first place?

Novelist Michael Crichton explored this idea in his 1969 best-selling science fiction thriller, The Andromeda Strain. The story begins with a military satellite returning to earth that brings with it a mysterious pathogen that causes a fatal blood-clotting disease. Eventually, the satellite is transported to a secret government laboratory in Flatrock, Nevada. A team of intrepid scientists and doctors are summoned to study the microbe (rumor has it that Jeremy Stone, the novel’s Nobel Prize-winning protagonist is modeled after Joshua Lederberg, who I discussed last week), but first they must descend through five levels of progressively severe sterilization and quarantine procedures which are designed to prevent any earthly microbes from mixing with the sample. Gaining entrance to Level V, the deepest and most secure level, requires days of broad-spectrum antibiotics, harsh ultraviolet and infrared irradiation, and repeated baths in strong disinfectants like biocaine, hexachlorophene, and xantholysin. (An interesting aside: while xantholysin inhibits the growth of many bacteria and fungi, it also promotes the growth of some Pseudomonas speciesbut that is a discussion for another column.)

As the research team arrives in Level V to begin studying the alien pathogen, they are as close to complete microbial sterilization as any human has ever been. But in reality, researchers are far more concerned with preventing infection than they are with contamination of a sample. In order to study the deadliest pathogens on the planet, like the Ebola Virus, scientists use what are called Biosafety Level 4 (BSL-4) laboratories. These labs have rigorous safety features designed to prevent the spread of microbes. There are only three BSL-4 labs in Australia, but scientists who work in them don’t need to be sterilized because, as I mentioned last week, our indigenous microbes actually help prevent infections by outcompeting potential pathogens.

So we can’t actually sterilise a living human, and even if we could, it wouldn’t be a very good idea. But scientists have worked out how to do the next best thing: breeding mice that are completely microbe-free. Researchers use these mice to study what happens when microbes are missing, but they can also colonize them with pure strains or simplified known mixtures of bacteria to figure out what each of type of microbe is doing. They’re commonly called gnotobiotic mice (Greek for “known–life”), because their microbial communities are completely known.

I’ve spent heaps of time working with normal lab mice, but I was completely blown away when I visited the gnotobiotic facilities at Stanford University last February. These mice are not just raised in germ-free environments; their entire bodies have been kept completely germ-free for several generations. Keeping them that way is a lot of work. These mice live out their lives in plastic and steel cages kept inside specially designed sterile isolators, with filtered air and long-sleeved gloves attached to the cages to allow scientists to work with the animals inside. The first generation of a new strain has to be sterilely delivered via Caesarean section and hand raised on synthetic milk. Further generations are commonly delivered via Caesarean section and then raised by adoptive gnotobiotic mothers, but fertilized embryos can also be surgically implanted into the uterus of a sterile mother. Everything, from their food and water, to their bedding, enrichment (toys and treats), and surgical tools must first be put through an autoclave, which is essentially an industrial-sized pressure cooker. All of this is done in strict accordance to detailed experimental guidelines laid out by the researchers and a committee of veterinarians and animal welfare officers.

Using gnotobioic animals is an enormous amount of work, but they have allowed researchers to identify what some of the 100 trillion indigenous microbes are doing while they’re in your body. For example, we now know that the guts of completely germ-free animals don’t mature properly. Intestines have finger-like projections called villi that help to increase intestinal surface area and make digestion more efficient. Microbes stimulate these villi to grow thicker, meaning that germ-free mice have less surface area than normal mice. Germ-free mice also have a larger caecum (the pouch at the beginning of the large intestine, where the appendix is attached), fewer intestinal blood vessels, and a thinner layer of mucus coating their intestines – all factors that affect digestion.

If you colonise these mice with microbes while they are still young, many of the negative effects of a microbe-free life can be ameliorated. But as it turns out, different groups of microbes can have variable effects on gut development, digestion, and host metabolism – making the whole system vastly more complex. For example, in one experiment, researchers used genetically altered mice as microbial donors. The mice had a mutation in the gene that codes for leptin, a hormone helps regulate appetite and metabolism. This mutation caused the mice to eat more and to become obese. When investigators transplanted gut microbes from the obese mice to gnotobiotic mice, they started rapidly gaining weight, even though these mice didn’t have the mutation in their leptin gene! By the end of the experiment, they had gained significantly more weight than a group of control mice that were colonized by microbes from normal mice, even though the two groups ate the same amount of food.

The differences in the microbial communities between lean and obese mice appear to be related to the relative abundance of two groups of microbes: Firmicutes and Bacteroidetes. Obese mice had communities with relatively more Firmicutes, while their leaner counterparts were instead enriched with Bacteroidetes. This pattern is also seen when you compare lean and obese human twins, as well as when you compare the gut microbes of the same person before and after weight loss. Scientists have identified that these different microbes can have a large effect on how efficiently you are able to extract energy from your food.

However, Firmicutes and Bacteroidetes are extremely broad categories of microbes. If we were making a similar comparison using animals, it would be like comparing vertebrates and invertebrates. Recent studies have revealed some of the more specific microbial interactions that may be impacting your weight. One experiment showed that if you feed obese mice (with the same mutation in their leptin gene) a bacterial species named Akkermansia muciniphila, the mice begin losing weight without changing their diet or level of exercise. Akkermansia is not in either of the groups Firmicutes or Bacteroidetes, though, and instead belongs to a group called Verrucomicrobia. This just goes to show that a complex trait like your weight is affected by lots of different groups of microbes, and that we are only beginning to understand how they impact one another.

Besides the obvious applications this may have for helping obese people lose weight, these findings could have a real impact on the way we treat malnutrition. One research group has begun focusing on a severe from of malnutrition called kwashiorkor, which is instantly recognizable by distended abdomens in young children. Researchers have found large differences in the gut microbiota of children afflicted by kwashiorkor from healthy children in the same families.

But they couldn’t be sure if these differences were causing the disease, or were simply a symptom of it. So they went one step further and colonised gnotobiotic mice with microbes from kwashiorkor patients. Incredibly, the mice quickly began losing weight! This suggests that there is something about the suite of microbes found in kwashiorkor patients that can’t extract energy and nutrients from food as well as other microbial communities. This was a very small study, but it begins to explain why certain nutritional interventions help some malnourished children, but not others. (For a more in depth discussion of this study, check out Ed Yong’s blog: Not Exactly Rocket Science.)

This is a very active field of research, and new tools are constantly being developed to unravel the complex network of interactions that tie microbial communities to the traits of their host and the foods they eat. We have established that the microbial communities in you gut can alter the way you process food, but we don’t yet know what it is about those communities specifically that contribute to weight gain or loss. It is possible for two identical twins with identical diets, to have very different weights and nutritional statuses if their gut microbiomes are substantially different. What is clear, though, is that weight loss or gain is not always a simple matter of balancing food intake against energy output.


Daniel Sprockett is a researcher at the Case Western Reserve University School of Medicine in Cleveland, Ohio. He currently resides in Double Bay with his wife, Andrea, while she completes a Master’s of International Public Health at the University of Sydney. Dan will return to the United States in September, when he begins his PhD in Microbiology and Immunology at Stanford University.