Turns Out, Your Gut Flora Do a *Whole Lot More* Than Help You Digest Your Food

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The path to good gut health may look a little different for everyone, but it doesn't have to be complicated. Find out how to balance your microbiome, manage digestive conditions, and keep your gut on the up and up, and hear from people who've dealt with GI issues and come out the other side. Get Your Gut Check

The concept of gut health is really having a moment these days. If your social media feeds have been swarmed with gut health supplements, drinks for gut health, or even foods promoting it, you’re not the only one. But what does gut health really mean, and how can we achieve it?

When you hear the words “gut flora," you might imagine something blossoming inside your stomach. Well, that’s not totally wrong. The word “flora” is actually Latin for “flower." So while there aren't actual flowers growing in your gut, there are important, healthy bacteria flourishing within your intestines that play a major role in your health, i.e., your gut flora.

Experts In This Article

Here, doctors explain what exactly gut flora is, how it affects your overall health, and ways that you can actually help improve it.

What is gut flora, aka your microbiome?

Gut flora, also known as the microbiome, is basically the bacteria composition of your gut, says Khoi Vu, MD, a family medicine physician and founder of Revitalife Medical Center. In order for your microbiome to be healthy, it needs to have the right balance of "good" and "bad" bacteria (yup, both of 'em). And when your gut flora is balanced, it's connected to better health overall.

The gut microbiome exists in your large intestine and requires a balance of about "80 percent good bacteria and 20 percent bad bacteria," says Dr. Vu. While "starch and sugar increase bad bacteria, eating fermented, fibrous foods and taking probiotic supplements increase good bacteria," he adds.

There are other types of microbiomes within our bodies, too, says Alessio Fasano, MD, chief pediatric gastroenterologist at Massachusetts General Hospital and member of the Viome Scientific Advisory Board. The gut microbiome, as we've learned, is located in the large intestine (aka, colon) but there are also oral, skin, vaginal, and lung microbiomes, among others.

“An average human microbiome has about 50 trillion microbes from more than a thousand different species; most are bacteria, but we also live with archaea, viruses, fungi, protozoa, and parasites,” says Dr. Fasano, all of which are fairly normal for most people. Talk about a diverse community!

How do gut flora develop?

The moment we’re born, our gut flora starts to develop, says Joseph Lamb, MD, an internal and functional medicine specialist, and medical director for Nature’s Sunshine Products.

“As soon as babies are born, their microbiome begins to develop," he adds. "Just being part of the world and being exposed to a non-sterile environment helps a baby to develop a healthy microbiome.”

Turns out, the first moments of a baby's life are crucial to developing a healthy microbiome. Often, this can depend on how a baby is birthed. For example, “a mother with a healthy vaginal microbiome, who delivers her child vaginally, gives her child a probiotic boost that can play a major role in the child developing a healthy microbiome,” says Dr. Lamb.

In fact, a September 2019 study in Nature compared the microbiota of babies born vaginally versus C-section. Results showed that babies born vaginally had a higher initial concentration of healthy bacteria, while babies born via C-section had a higher concentration of unhealthy bacteria.

The study also found that babies born vaginally had more bacteria diversity after the first few weeks of life. And remember: A more diverse microbiome tends to be a healthier microbiome, per Dr. Lamb. (Though it's perfectly okay if you or your baby were born via C-section; there are plenty of opportunities to grow a healthy microbiome after birth!)

As we grow up, the microbiome changes based on our behaviors. Factors like diet, exercise, your environment, and taking antibiotics can all shape your microbiome.

“The food you eat and environment in which your gut microbes live can greatly affect their behavior and, in turn, your health,” says Dr. Fasano. “A balanced gut microbiome, created through a personalized diet and a low-stress environment, can improve health and well-being.”

And the more we age, the more gut flora evolves, especially for older adults, adds Dr. Fasano. This is often when we see food tolerances and digestion functions change. “This change may require extra energy for your body to break down sugar, which can contribute to certain age-related diseases, too," he says.

"The food you eat and environment where gut microbes live can greatly affect their behavior, and, in turn, your health." —Alessio Fasano, MD, gastroenterologist

How your gut microbiota benefit your body

The gut microbiome is made up of trillions of microbes in the gastrointestinal tract, and they play pivotal roles in various aspects of your health, says Dr. Fasano. One obvious aspect is your digestion: “These microbes aid in breaking down food, synthesizing essential vitamins, and neutralizing harmful compounds, contributing directly to nutrient absorption and overall digestive efficiency," he notes.

But you might be surprised to learn that whatever’s going on in your gut is likely affecting other parts of your health, too. That includes your mood, energy levels, and immune health. There’s even a communication network of nerves that exist between the brain and the gut—called the gut-brain axis, per the Cleveland Clinic. This communication network allows your brain to influence the functionality of your intestines, aiding immune function, nutrient absorption, and digestion, says Dr. Lamb.

“It also allows your gut to influence your brain, specifically your cognition, mood, and mental health. Studies have shown that microbiome composition, and even specific microbes, can influence things like anxiety and stress,” says Dr. Lamb, pointing to a May 2019 review in General Psychiatry.

All that is to say, a healthy gut microbiome is deeply connected to many aspects of your health, including your mental well-being and brain function. So if we want to live our best lives, it helps to treat our gut flora well.

Health problems linked to unhealthy gut flora

Because gut health is so intertwined with overall health, it stands to reason that unhealthy or unbalanced gut flora can contribute to larger health issues, too. The most obvious being conditions like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), says Dr. Lamb.

An unhealthy microbiome can also leave your gut inadequately protected from potentially harmful substances.“This impaired barrier function may contribute to chronic inflammation, 'leaky gut' syndrome, and autoimmune challenges, as well as increased incidence of depression, asthma, allergies, and other potential health problems,” says Dr. Lamb.

Serious chronic diseases like heart disease, diabetes, high blood pressure, and cancer can also be linked to a lack of beneficial bacteria in the gut, Dr. Fasano says.

The medical term for this imbalance of bacteria is dysbiosis, which an April 2015 study in the International Journal of Molecular Sciences linked with many chronic conditions, including IBD, obesity, cancer, and autism.

It’s also true that unhealthy gut flora can lead to symptoms that affect your daily life, such as digestive issues, bloating, diarrhea, fatigue, poor mood, and a low immune system, says Dr. Vu.

How can you improve your gut flora?

There are some things you just can't control when it comes to your microbiome, like how you were born, or living in an area where you're more likely to catch a foodborne illness. But there are a few lifestyle changes you can make to improve your gut flora, and help not just your digestive health, but your overall health, too.

Focus on whole foods

The best way to improve your gut flora is by eating more non-processed, nutrient-dense foods. “You are what you eat, so try to eat more living, organic, or fermented foods and take a probiotic every day,” says Dr. Vu.

And the best diet for gut health? A balanced one. Try including the following foods to increase gut flora, per the Mayo Clinic:

  • Fruits (like bananas and berries)
  • Gut healthy smoothies (with things like flax seeds, chicory root, fruits, and veggies)
  • Vegetables (like leafy greens, artichokes, asparagus, and garlic)
  • Legumes
  • Whole grains (like oats, barley, rye, and wheat)
  • Kefir (a fermented yogurt-like drink)
  • Yogurt with live cultures
  • Sauerkraut
  • Kimchi
  • Tempeh (fermented soybeans)
  • Sourdough, or other gut healthy bread

This doesn't mean you have to totally give up your favorite foods that might be considered "unhealthy," though; it's all about balance. It's just that eating too much ultra-processed food (think: sugary drinks, packaged snacks and desserts, frozen and fried foods) will throw off your microbiome and kill off good bacteria, says Dr. Vu.

Ultimately, it's best to find the right eating style for you. There's no one-size-fits-all approach, says Dr. Fasano. And if you have specific dietary concerns, it may be worth working with a registered dietitian to make sure you're hitting your nutrient needs.

Limit antibiotics

Antibiotics are medications that treat bacterial infections, and are quite literally known to save our lives, per the Cleveland Clinic. They can wipe out illnesses like strep throat, UTIs, skin infections, and more.

In many cases, antibiotics are good for us when we’re sick, but they shouldn’t be overused, says Dr. Vu.

Using antibiotics too often or for too long can potentially harm your gut health by wiping out essential bacteria. (Don't forget, we need both good and "bad" bacteria for our overall health.)  It can also cause our bodies to become resistant to antibiotics, leading to poor immune health, per the Mayo Clinic.

Take probiotics and prebiotics

One quick way to improve gut health is to use probiotics, says Dr. Lamb.

“Probiotics are healthy, living bacteria that can potentially colonize the gut, leading to a rapid change in microbiome composition and potentially improving gut health,” he adds.

With so many supplements out there, picking a probiotic may feel intimidating. Dr. Lamb suggests choosing a probiotic with a broad spectrum of different bacterial strains. Look for the number of colony forming units (CFUs) on the label; the average product will have about 1 to 10 billion CFUs, per the National Institutes of Health.

Another way you can improve your gut health is by taking prebiotics or eating prebiotic-rich food (think: fruit, veggies, legumes, whole grains). "Prebiotics basically serve as food for specific groups of healthy bacteria," says Dr. Lamb. The most well-known prebiotic is fiber.

“Eating a diverse range of fibers, particularly soluble fibers, gives the healthy microbes that break down fiber a competitive advantage. This allows them to out-compete other bad bacteria and improve microbiome health,” he adds.

While both probiotics and prebiotics are effective, prebiotic fibers take a little longer to start working. “It can take 90 days or more for prebiotics to really have an effect on microbiome diversity," says Dr. Lamb. But if you eat them (or take prebiotic supplements) consistently, they can have a major positive effect on your microbiome composition and diversity, he adds.

Ideally, taking or eating foods rich in both probiotics and prebiotics each day will have the greatest effect on your microbiome health, adds Dr. Lamb.

See a doctor about symptoms

Don't brush off digestive symptoms like bloating, indigestion, constipation, or diarrhea. Especially if you think you have a virus, fungal infection, parasite, or other unhealthy bacteria, Dr. Vu says it's best to see your doctor to get treated properly.


What kills gut bacteria?

Lifestyle choices and medications can kill gut bacteria—both good and bad bacteria, says Dr. Vu. If your diet consists of a lot of ultra-processed foods, it will likely cause some good bacteria to die. The same is true if you take antibiotic medications for prolonged periods of time.

There is also some research to suggest that medications like antidepressants, statins (to lower cholesterol), and proton pump inhibitors (for acid reflux) can also mess with your gut microbiota, and potentially kill off good bacteria, per a January 2017 review in Gut Microbes.

If you take any of these medications, talk to your doctor about ways to preserve your gut health while on them.

What is bad bacteria in the gut called?

There are several strains of unhealthy bacteria. "Bad" bacteria in the gut can be categorized as staphylococcus, streptococcus, and clostridium, says Dr. Lamb. These strains are harmful and can cause a number of severe illnesses if left unmanaged.

That said, if you develop any concerning symptoms like vomiting, diarrhea, stomach cramping, and fever, call your doctor. You may have an underlying infection that needs to be treated with specific antibiotics.

—reviewed by Jennifer Gilbert, MD, MPH

Well+Good articles reference scientific, reliable, recent, robust studies to back up the information we share. You can trust us along your wellness journey.
  1. Shao, Y., Forster, S.C., Tsaliki, E. et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574, 117–121 (2019). https://doi.org/10.1038/s41586-019-1560-1
  2. Yang, Beibei et al. “Effects of regulating intestinal microbiota on anxiety symptoms: A systematic review.” General psychiatry vol. 32,2 e100056. 17 May. 2019, doi:10.1136/gpsych-2019-100056
  3. Zhang, Yu-Jie et al. “Impacts of gut bacteria on human health and diseases.” International journal of molecular sciences vol. 16,4 7493-519. 2 Apr. 2015, doi:10.3390/ijms16047493
  4. Imhann, Floris et al. “The influence of proton pump inhibitors and other commonly used medication on the gut microbiota.” Gut microbes vol. 8,4 (2017): 351-358. doi:10.1080/19490976.2017.1284732

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