The Vital Importance of Healthy Gut Bacteria

Linked to everything from weight control to mental health, our gut bacteria is vital to our health—learn how to manage yours.


Asparagus is a good source of prebiotics—the food beneficial bacteria eat.

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Gut bacteria is the hot new area of scientific research, with a growing body of evidence linking widespread health issues—ranging from obesity and diabetes to rheumatoid arthritis, irritable bowel syndrome and depression—to the presence or absence of various microbes. While some of this research is very new, and science has a lot to learn about the connections between health and the microbes we carry around with us, it’s already clear just how much our gut bacteria matter to us.

So Many Microbes

What’s so important about the microbes in our bodies? To start with, there are a lot of them—we all carry trillions of bacteria in our gastrointestinal tracts (while a discussion of microbes in the human body might include fungi and viruses, most of the research we’re talking about in this article focuses on bacteria). These bacteria perform many critical functions, including digesting food and helping us absorb vitamins and medications. Gut bacteria also play a vital role in our immune systems, which influence our overall health in many ways.

One of the major sources of research on such bacteria is the Human Microbiome Project, run by the National Institutes of Health. Although the terms aren’t always used consistently in news articles, the “microbiome” is technically the collected genetic material of all the microbes in our bodies, while the microbes themselves are called the “microbiota.” The first phase of this ongoing project identified 10,000 species of microbes in the human body, some never known before. To learn about these microbes, scientists studied more than 200 healthy adults, taking samples from various parts of their bodies, including swabs from the skin, mouth and nose, as well as stool samples.

This research is uncovering a lot of interesting things. First, there is no universal “healthy” set of gut microbes; even among healthy people, there’s a wide variety in what’s present in gut bacteria. Each person’s microbiome is entirely unique.

Where do these differences come from? Science suggests many factors affect what our particular set of microbes look like, including environment, diet and antibiotic use. Some of our beneficial bacteria come directly from our mothers—we get many of them during passage through the birth canal. Children born vaginally appear to have greater diversity of microbes than those born through Cesarean section. Infants also get beneficial bacteria through breastfeeding.

Although all kinds of factors can shape what gut bacteria we end up with, our particular combination of microbes becomes stable surprisingly early—research suggests by age 3. However, some factors can shake that stable system, including dietary changes and treatment with antibiotics.

Antibiotics and Our Inner Ecosystems

While science still has a lot to learn about how our gut bacteria relates to health, some of the links are already well-established. One of the best understood of these issues is that taking antibiotics can seriously disrupt our gut microbe communities. While they are certainly beneficial—sometimes lifesaving—antibiotics kill both harmful and friendly bacteria in our guts. In this new environment, it’s easier for harmful bacteria to become established.

How exactly does this happen? One way to understand it is explained by a 2012 article in the journal Nature called “Diversity, stability and resilience of the human gut microbiota,” which makes the case that to better understand our gut bacteria, it’s useful to think of them as an ecosystem.

The article compares a low-bacteria system to bare soil in your yard, where there would typically be a lawn. The first species that move in are the weeds, by nature invasive plants that thrive when colonizing bare soil. In the same way, antibiotic treatments that disturb our gut bacteria (killing both beneficial and harmful microbes) can give microbes, which wouldn’t ordinarily be able to get a foothold, a chance to get established and make us seriously ill.

One of the best understood (and most graphic) problems with antibiotics and our gut microbes is the rise in infections with a strain of bacteria called Clostridium difficile, commonly called C. diff. Taking antibiotics puts people at higher risk for infection with this bacteria, which can cause severe diarrhea that has been linked to the death of 14,000 people in the U.S. each year. And while the numbers behind this issue are scary, it’s also noteworthy because of the treatment. This is one case where it’s possible to treat a sick person by giving them someone else’s microbes.

For people with serious C. diff infections that don’t respond to antibiotics, it’s becoming more common to have a “fecal transplant,” which involves bringing healthy bacteria from a donor into the gut of the sick person. Because of its effectiveness, and lack of other reliable options, it is quickly becoming a mainstream treatment. (If you want all the details about this procedure, you can find them in the book Gulp: Adventures of the Alimentary Canal by science writer Mary Roach, which has a whole chapter on it, as well as lots of other interesting—and sometimes gross—facts related to the digestive system.)

Researchers are also studying whether dietary consumption of very low levels of antibiotics—via meat from factory-farmed animals treated continually with antibiotics throughout their lives—alters our microbiota. Much more research is needed before we can come to a definitive conclusion, but some early studies suggest it’s a possibility. In a study published in the journal Nature, researchers from New York University treated mice with regular, low doses of antibiotics, similar to what farm animals receive. After seven weeks, the mice’s microbiota composition had changed and was different than a control group (they’d also gained 10 to 15 percent more fat mass). We don’t know if the trace levels of antibiotics we consume via the meat of antibiotics-treated animals is enough to alter our own microbiota, but scientists are starting to look into it. (You can read more about this topic in the 2013 Mother Jones article “Can Antibiotics Make You Fat?”)

Your Gut Microbes—and the Rest of You

One reason scientists find research into the microbiome so intriguing is because studies are turning up so many connections to our overall health. Some of the best understood issues pertain to our digestive systems. But research also suggests that this is just a starting place, and our gut bacteria have a much wider influence on our physical and mental health.

For one thing, gut bacteria are tied into our immune systems, with all sorts of obvious and less obvious connections. One area of study is investigating possible links between gut bacteria and autoimmune disease. For example, recent research suggests there’s a connection between one particular type of gut bacteria and rheumatoid arthritis. Gut microbes also appear to have a role in the low-level inflammation (an immune system response) associated with diabetes and obesity. Evidence also shows a potential brain-gut connection: New research has found connections between microbes and mental-health conditions, including depression, anxiety and autism.

Is there a time coming when you might get a fecal transplant to treat obesity, or a treatment with a particular microbe to deal with anxiety, or the symptoms of autism? It might sound far-fetched, but all of those things have already been tried on mice with positive results. Recent studies have found that the right bacteria can help make anxious mice calmer, obese mice leaner and reverse autism-like symptoms.

But there’s still a lot to learn, and whatever medical treatments might someday be available, most of what we can do now to positively affect our gut bacteria (and the wide range of health issues related to them) centers on diet.

Eat for a Healthy Gut

To help sort out the current recommendations on eating for good gut health, I spoke to two dietitians who are particularly interested in gut bacteria. The first is Jo Ann Hattner, a registered dietitian and nutrition consultant at Stanford University, and author of the book Gut Insight: Probiotics and Prebiotics for Digestive Health and Well-Being. The other is Kristi King, a spokesperson for the Academy of Nutrition and Dietetics, and a pediatric dietitian at Texas Children’s Hospital, who specializes in nutrition counseling and chronic intestinal disorders. Both offered similar recommendations.

First, think plants. Have you heard the phrase “a healthy, plant-based diet?” Probably so, because a diet high in plant-based foods (fruits, vegetables, soy, nuts, seeds, etc.) is frequently recommended by nutrition experts, including Hattner and King.

Two commonly cited benefits of this type of diet include lowering our risk for heart disease and diabetes, but if that’s not enough to sell you on the benefits, it turns out that it might also help nourish a healthy gut ecosystem. Many studies focus on diversity, or lack of diversity, in our gut. (Think of biodiversity in the ecosystem.) And it turns out one simple way to nurture our gut microbe diversity is through…you guessed it: a healthful diet. According to that 2012 Nature article, decreased microbial diversity has been linked “to a diet that is high in fat and sugar compared with one that is low in fat and plant-based.”

Add Live Culture Foods. You can support a healthy microbiome by eating beneficial bacteria—two of the best-studied are Lactobacillus and Bifidobacterium. You know these beneficial bacteria as probiotics. “Everyone has good bacteria, but sometimes we have to add a little more to maintain gut health,” King says.

To find foods with probiotics, look for foods labeled as having “live cultures,” Hattner says. Yogurt, kefir and soy “dairy” products labeled as having live cultures should be the easiest to find.

You can also get probiotics from supplements—while some health professionals question the efficacy of probiotic supplements compared with food, few raise issues with their safety for healthy adults. Hattner suggests getting probiotics from food, but if you do turn to supplements, research to make sure what you’re getting is effective (read “Take Your Bacteria!” for our recommendations). King says if you’re not getting probiotics from food, a supplement isn’t going to hurt.

You can also make traditional, live-culture foods at home, including homemade (not canned—that process kills both good and bad bacteria) sauerkraut, pickles and kimchi. An excellent resource for making these foods is Wild Fermentation by Sandor Katz.

Plus, eat prebiotics (even more plants!). And here’s another way we can nourish the beneficial bacteria in our guts—we can feed them. “Prebiotics are actually food for the probiotics, food for the good bacteria,” King says. “Ultimately it’s a fiber that we don’t break down all the way and the bacteria eat at it.”

Two compounds that specifically encourage the beneficial bactria are oligosaccharides and inulin. Oligosaccharides are found in breast milk, so babies get both a probiotic and a prebiotic while nursing. Inulin is an ingredient being added to a lot of convenience foods so they can be advertised as having prebiotic benefit, but a long list of natural foods contain these compounds, too. High on Hattner’s list of prebiotic foods are onions, garlic and leeks; other familiar options include bananas, asparagus, beans, whole wheat and rye.

Hattner says we should eat prebiotics every day. Probiotics help introduce beneficial bacteria, but prebiotics help keep them healthy. She says, “I always tell my students that bacteria have to eat, too.” And if they like to eat garlic and leeks, why not add a few more to your menu?

Digest This!

Want to learn more about your gut? As mentioned elsewhere in this article, a practical guide to gut health is the book, Gut Insight: Probiotics and Prebiotics for Digestive Health and Well-Being by Jo Ann Hattner.

See some of the news coming out of the National Institutes of Health-funded, Human Microbiome Project. The director of this project, Martin J. Blaser, has a new book, Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

Want to find out what’s in your own gut? It’s possible through the American Gut project: This citizen science project collects samples from volunteers, who also donate $99 to cover testing costs. Or, you could just read about what writer Michael Pollan had to say about this experience for The New York Times magazine. There’s also a series of essays from the director of this project, Jeff Leach, called Honor Thy Symbionts.

Megan E. Phelps is a freelance writer based in Lawrence, Kansas. She eats ridiculous amounts of her favorite probiotic food (yogurt) and her favorite prebiotic (garlic).