The bacteria in our guts are indispensable. They help us fight off other, more harmful bacteria and aid in digestion and nutrition. But scientists are also now finding evidence that when our microbial ecosystems fall out of balance, they can end up related to all sorts of problems — obesity, allergies, and possibly even some mental illnesses.

The science around our bodies' "microbiomes" is still quite young — too young to inform medical treatments in most cases. Scientists can't yet draw a direct link between a specific microbe and obesity, or suggest the best diet for the community living in your gut. But what researchers are finding is that these microbes might influence our health far more than anyone realized.

Here are four ways that the microbes in our guts may be messing with us.

1) Obesity

When researchers compare the gut microbes of obese and non-obese people, they do find some differences in certain types of bacteria. And it's at least possible that the microbes in our guts may influence how much energy various people can extract from food. That could make it one factor of the many that can work together in various ways to cause obesity. Still, this is just a correlation. So how do scientists figure out what's causing what?

One way researchers try to pin down causal links is to study "germ-free" mice. These are mice raised in sterile environments that have no bacteria of their own. Researchers can then selectively give them bacteria and see what happens.

One 2013 study from Jeffrey Gordon's lab at Washington University School of Medicine published in Science showed that giving these germ-free mice the bacteria from an obese person's gut made the mice themselves gain weight.

And there was a twist: When these mice with obese-people-microbes were then introduced to gut bacteria from lean people, they could maintain a healthy weight — as long as they ate a healthy diet. (By contrast, mice remained heavier if they were given lean-people gut bacteria and also ate poorly.)

In another study published in August of 2014, researchers found that disturbing the normal gut microbiomes of young mice caused them to gain a ton of weight later on. Transplanting these mice's gut microbes into germ-free mice ended up transferring weight gain, as well. This suggests that the gut microbes were indeed the cause of the extra weight.

That said, we still don't know an awful lot of what's going on here. We don't know precisely what types of bacteria or what features of a bacterial ecosystem are influencing obesity in these mice. And we still don't really know if gut microbes are playing a causal role in obesity in humans. And this science certainly isn't anywhere near a treatment or cure for obesity, either.

2) Allergies

One of the ideas that researchers are exploring right now is the possibility that being overly hygienic early in one's life can throw off a person's immune system — leading to health problems such as allergies and asthma throughout childhood and beyond. This is known as the "hygiene hypothesis." And gut microbes are potentially involved here, too.

A child's gut ecosystem is in a state of fairly flexible development until about age two or three, when it becomes more stable. That means that events in those early years could have big consequences for who's living in your gut later in life — and that could include any microbes picked up from family members, surfaces, dirt, pets, and food. (What foods you eat could also influence which microbes like living in your gut and eating those foods, too).

So, for example, studies have found that children born via vaginal delivery have fewer allergies in subsequent years. Some researchers think that may be because they picked up certain helpful microbes from the vagina while physically being delivered through the vaginal canal. Another study has found that infants who have a less diverse array of microbes in their guts are more likely to become children who have allergies years later.

Researchers are now doing experiments in mice to better understand how allergies and gut microbes might be related. For example, in August of 2014, a team based at the University of Chicago published a study in which they essentially made mice really sensitive to peanuts — it's a model for peanut allergies in people. The scientists then found out that giving the mice a certain type of bacteria made the peanut sensitivity go away. That's not to say that this bacteria will necessarily cure anything in humans, but it's promising.

3) Diabetes

Researchers have conducted several studies comparing the gut bacteria of people with and without type 2 diabetes — and found some differences. However, this is still a correlation, so it's unclear if the gut bacteria are helping to cause diabetes or vice versa.

But the results are intriguing. For example, two studies that sequenced the genetic material of gut microbes in people with and without diabetes were published recently in Nature — and they came up with fairly similar results. The gut microbes of people with diabetes showed differences in genes related to things like starch and sugar metabolism. This suggests that gut microbes may be playing a role here — since diabetes is a problem characterized by high blood sugar. Still, this research is young.

4) Brain disorders and mental health

Scientists are also beginning to find some intriguing suggestions that what's going on in our guts could be influencing our brains, as well.

For example, several studies have shown that germ-free mice exhibit behavior that's considered bolder and less anxious than mice raised more conventionally. What's more, giving these mice microbes during early development makes their behavior less bold. (These results aren't a reason to advocate for germ-free humans, but it does show that there might be some sort of relationship between gut microbes and anxiety, in general.)

Scientists have been finding possible links between gut microbes and other disorders, as well. For example, in a 2013 study published in the journal Cell, researchers showed that a type of mouse with symptoms similar to those of autism-spectrum disorder had some different gut microbes than healthy mice. When researchers fed these mice a particular microbe, they ended up with fewer symptoms.

Now, a word of caution: these are very early findings. And it's particularly difficult to extrapolate from a mouse to a human — especially when it comes to brain research. A mouse can't verbally tell you if it's feeling anxious, for example. However, scientists are definitely continuing to work in this area, hoping to find new ways to prevent and treat problems in people.

Further reading:

9 questions you were too grossed out to ask about the bacteria living on you

There is no ‘healthy’ microbiome

Gut feelings: the future of psychiatry may be inside your stomach

Is being too clean making us sick?