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AP Photo/Gero Breloer
Just you and trillions of your closest friends.

We’re home to trillions of cells that aren’t ours and they’re keeping us alive

By Katherine Ellen Foley

At any given time, you’re only about half your human self.

Living among our own 30 trillion cells are about 40 trillion bacteria according to a recent estimate—though others say we may have even more. (And there are also viruses and fungi). And though these microbes may get a bad name because they can cause illnesses, we also need them to function. They make up our microbiota, which has been compared to an entirely separate organ (paywall) because of all the jobs it carries out. (The microbiome is the collection of all the genetic information from our microbiota, but the two terms are often exchanged fluidly.)

Scientists have recently discovered that these microbes are almost everywhere on our bodies. In addition to the microbiomes on our skin, up our noses, and in women’s vaginal canals, they also cover our eyes, and have been even found in seminal fluid, according to research from earlier this year. And they’re so unique scientists have found that they can be used to identify different individuals.

Though researchers have been studying the microbiome for about a decade, they’re only just discovering the role it plays in our biology. The microbiome that lives in our gut—by far, our most extensive collection—affects just about every aspect of our health, from the nutrition we get from our food, to our immune systems, to our moods.

Break it down

“The most obvious way that we benefit from microbiota is from the chemical products they release (and we absorb) during the fermentation reactions they carry out in the gut,” Sonnenburg and his spouse, Erica, also a microbiologist at Stanford, write in The Good Gut. ”These chemical reactions allow us to salvage calories from food that would otherwise be wasted.”

Digestion starts when food touches our lips, travels down to our esophagus, and then sloshes around in our stomachs. The acid in our stomachs make it easier for nutrients to be absorbed in our small intestines. After it travels to the large intestine, where most of our gut microbiota reside, bacteria feed on the remains of the food we’ve consumed (you could say we’re eating for trillions), they release waste products that help us ingest the calories from our food and produce (paywall) some of the vitamins we can’t make on our own, like vitamin B12.

Gut microbes may also play a role in our weight. Different microbial communities may break down foods differently, leading to spikes in blood sugar at different times, according to a 2015 studyThis suggests that an individuals’ microbes play a major role in the success of diets. Additionally, higher gut populations of a microbe called Methanobrevibacter smithii have been linked (paywall) to higher levels of body fat. Scientists are still trying to find the link between specific species and weight, but doing so could lead to alternative therapies for obesity.

Body guards

The benign microbes we have in our gut act as a barrier for harmful microbes trying to reaching our cell walls, where they would be able to infect us. Having a large population of gut microbes—particularly in the large intestine, where most of these microbes live—can actually work to fight off harmful infections. Fecal transplants, which take a microbial population from a healthy individual and transfer it to a sick patient, can be used to treat some bowel infections, such as one caused by bacteria called Clostridium difficile, which causes sometimes fatal diarrhea.

Gut microbes also work with our immune cells to help train them how to react to various invaders. The Sonnenburgs refer to us as “bacteria-filled tubes”—our digestive tract is one long tube (about 25 feet), from mouth to anus. This tube offers the only exposure to the outside world our immune system receives. A diverse population of gut microbes train our immune cells on how to respond to various invaders, sparing us from immune responses which can make us almost as sick as an actual pathogen.

When the immune system overreacts to a benign threat, it can produce an inflammatory response, which can be one of the mechanisms behind auto-immune diseases, like allergies, irritable bowel syndrome and Crohn’s disease, or even multiple sclerosis. Certain microbes that frequent the small intestine in mice can signal (paywall) to some of our immune cells when to dampen their inflammatory response, making their chances of acquiring autoimmune diseases and allergies decrease ”in ways that no known drugs can,” according to the Sonnenburgs.

Mood management

Some research has suggested that the bacteria in our guts can even affect our brains.

The Sonnenburgs compare our gut microbiome to a drug factory: They produce chemicals that may directly or indirectly alter our brain chemistry. Some of the bacteria in our intestines produce serotonin, a chemical that helps different parts of our brains communicate, too little of which has been associated with depression. Other bacteria in our guts may affect (paywall) the amount of brain-derived neurotropic factor in our brains, low levels of which are also associated with anxiety and depression.

However, these associations quite often need to be taken with a grain of salt. “In general, the problem of causality in microbiome studies is substantial,” Rob Knight, a microbiologist at the University of California, San Diego, told Nature. “It’s very difficult to tell if microbial differences you see associated with diseases are causes or consequences.”

Still, it opens up interesting possibilities in a world that is increasingly dependent on pharmaceuticals. ““These bacteria could eventually be used the way we now use Prozac or Valium,”John Cryan, a neuroscientist at the University College of Cork in Ireland, told the Atlantic.

Maintaining your microbes

One of the best ways to maintain a healthy gut microbiota is to feed it right, explained Justin Sonnenburg. He and his spouse have found that diets high in natural fiber, like grains, fruits, and vegetables, can not only feed our own microbiomes well, but even those of our children and grandchildren. Studies have shown that high-fiber diets in pregnant mice have been linked to more populated gut microbiomes in their offspring.

Consuming foods that contain live cultures of beneficial bacteria, called probiotics or fermented foods also benefit your gut microbes. These are foods like kimchi, kombucha, yogurt, and miso. Though you can buy over-the-counter probiotics, these products aren’t particularly well-regulated. Sonnenburg said that a good rule when looking for healthy bacteria-rich food is to look in the refrigerated isle for these foods, because they need extra preservation. (Alcoholic beverages like beer and wine use fermentation in their production process; they don’t contain many useful live cultures of bacteria).

Lastly, don’t worry so much about staying clean: Exposure to microbes, especially those that are benign, can be a good thing because it keeps our own populated, and our immune system on its toes. When we interact with our friends, family, and coworkers, we’re almost certainly exchanging microbes. Certain activities, like gardening, hiking, or playing outside can expose us to all kinds of microbes we don’t normally encounter (although make sure your are not in an environment where you could be exposed to pesticides, Justin Sonnenburg warns). The Sonnenburgs even note that owning a dog can expose you to a different type of microbial community (though you should certainly not get a dog just for the microbial benefits, they add).