Bacteria – The Good, the Bad, and Your Gut

If you’re like most people, the very thought of bacteria makes you reach for your hand sanitizer. But when it comes to your gut, bacteria can actually be your friend.

This friendly bacteria, also known as gut flora or microbiota, plays a key role in the overall well being of a variety of different body functions, including your weight, immune system, digestive health, and even your mood!

Bacteria Basics

There is a mix of both good and bad bacteria living in your body. Your gut has an entire colony of good bacteria living in it. There are trillions of bacteria within the gut and intestinal tract. To give you an idea, together they add up to between three and four pounds.

Bacteria starts to develop in the body at birth, and the types of bacteria depend on the food the baby ingests. There are many different types of bacteria, and each person has a unique composition of bacteria, similar to a fingerprint.

In an effort to learn more about the microorganisms and bacteria living within the body, the National Institute of Health launched the Human Microbiome Project (HMP) in 2007. The goal of this five-year initiative was to identify the various strains of bacteria in the body and the role they play in disease and health. Much of what we know today about gut flora is the result of this project.

Gut Flora and Your Health

So what does this bacteria do? Plenty. The most well-know functions of gut flora have to do with the digestive system. When your biome is diverse and balanced, it can:

  • Help digest and absorb important nutrients from food
  • Help fend off harmful bacteria and toxins
  • Regulate bowel movements
  • Help eliminate gas and bloating

The role of gut flora in your health goes way beyond digestion. As scientists study gut flora, they have found that the ecosystem within our guts plays a crucial role in other systems, too.

Immune System

Studies have found that gut flora helps keep harmful pathogens at bay. One way it does this is by reinforcing the protective barrier that keeps toxins from leaking from the GI tract and into the bloodstream. It also helps keep the pH level of the gut acidic. This is important because bad bacteria, such as salmonella and e. coli, can’t survive in an acidic environment.

While the gut flora affects the immune system, your immune system also affects your gut flora. When the immune system is weakened, entire composition of your gut flora changes and can lead to issues such as inflammatory bowel syndrome, as shown in one study. Another study confirmed the relationship between the gut and the immune system, linking underdeveloped gut flora to malnutrition and inflammatory bowel syndrome.

Mental Health

The gut and brain have a strong connection, thanks to the enteric nervous system (ENS), sometimes called the “gut brain.” Responsible for controlling digestion, it communicates with the brain. Scientists have found that when the GI tract is irritated, the ENS sends signals to the brain that can trigger depression and other mood changes.

Not only does a balance of healthy gut bacteria keep the blues away, but it also keeps your brain functioning normally. One study showed that antibiotics (which work by killing both good and bad bacteria in the body) that kill gut bacteria also stop the growth of new brain cells.


Gut flora can also help you fit into your skinny jeans. A healthy balance of flora in the gut can curb food cravings, make you less likely to overindulge. Additionally, one study found that having a diverse balance of bacteria in the gut is associated with lower body fat.

Pro and Prebiotics

One of the best ways to keep the gut flora balanced and functioning properly is through diet. Pre and probiotics, which are ingested through the foods we eat, play a vital role in keeping the gut flora balanced.


If you’ve ever seen a yogurt commercial, you’ve probably heard of probiotics. According to the International Scientific Association for Probiotics and Prebiotics (ISAPP), a probiotic is a "live organism that when administered in adequate amounts, confers a health benefit on the host."

Probiotics are the live bacteria found naturally or added in certain foods, infant formulas or dietary supplements. Probiotics help balance the amount of good and bad bacteria in the gut, keeping your internal biome healthy and diversified.

Probiotics also help your body replenish good bacteria after it has been lost. A loss of good bacteria is common after taking antibiotics, for example. Taking a probiotic can help defend good bacteria and replace it if it has been lost.

Taking probiotics is also associated with weight loss. One study found that women who took a probiotic supplement lost twice as much fat and were more successful at maintaining their weight loss than those who took a placebo. Keep in mind that this doesn’t mean the probiotic itself was the main reason the weight loss occurred. However, the probiotic might have affected weight loss by helping normalize the digestive process or other factors.

According to ISAPP, there's also evidence that certain probiotics can:

  • Reduce antibiotic-associated diarrhea
  • Treat infectious diarrhea
  • Improve mild to moderate irritable bowel syndrome and other digestive symptoms
  • Help manage symptoms associated with poor digestion of lactose
  • Reduce colic symptoms and reduce risk of eczema in infants
  • Decrease some common infections, including those of the respiratory tract, gut, and vaginal tract


Prebiotics are different from probiotics, but they also play an important role in the gut. Prebiotics are non-living dietary fibers that can’t be digested by the body. They act as a natural fertilizer to probiotics, helping them thrive and multiply.

Prebiotics are particularly important because probiotics are fragile and can be killed by stomach acid and heat. The body does not destroy prebiotics, and they can help protect probiotics by encouraging a healthy environment for growth.

Getting Enough Good Bacteria

Alone, prebiotics and probiotics are great for your health. Together, they’re even more powerful, creating an unstoppable bloat-busting, fat-fighting, mood-boosting team.

Regularly eating foods that are high in pre and probiotics can help ensure your gut flora is balanced. Common foods that contain the highest amounts of probiotics include yogurt, soft cheeses, dietary probiotic supplements, etc.

Prebiotics are plant-based and found in many different foods including raw vegetables like chicory root, asparagus, dandelion roots, onions, and leeks.

What about fermented foods?

Although all fermented foods are made through the action of live microorganisms, the final food product may or may not contain live microorganisms. So contrary to misconception, not all fermented foods are technically "probiotic foods" by definition of ISAPP. Many of the processes used to make fermented foods such as heat treatment or filtering can "kill" or remove live microorganisms from the final product. Examples of fermented foods include tempeh, kefir, kombucha, kimchi, and sauerkraut. While there may be some health benefits associated with the consumption of fermented foods such as kefir, kombucha, kimchi, and sauerkraut--when studied, they haven't been found to meet the required evidence level for probiotics to be considered true probiotic foods. To know for sure if a fermented food, you can look on the label to see if live bateria have been added as an ingredient afterward and if so, at what dose it has been added. You can also contact the manufacturer to confirm. 

In addition to eating foods that are high in pre and probiotics, there are other things you can do to balance your gut flora, including:

  • Take supplements. Supplements are particularly helpful for those who are lactose intolerant or vegan and don’t want to down yogurt every day. Look for supplements that contain Lactobacillusand Bifidobacterium, which are two strains of bacteria associated with the greatest health benefits, and supplements that contain at least 10 billion live organisms per dose.
  • Skip added sugar & artificial sweeteners. As if you needed another reason to cut back on your sugar intake, sugar creates an environment in the gut that helps bad bacteria thrive, leaving less room for the good guys. In fact, a study from Oregon State University found that an increase in sugar and fat in the diet altered the bacteria composition in the gut that led to significant losses in cognitive function and memory.
  • Cut back on meat. Diets that contain animal protein have been shown to feed a “bad” bacteria that is linked to increased inflammation in the gut. Skip the embarrassing gas and uncomfortable bloating by cutting back on red meat and getting more plant-based proteins into the diet.

As you can see, not all bacteria are bad. When it comes to your gut, good bacteria is on your side, helping you get and stay trim, happy, and healthy.


Written By: Jill Overmyer
Edited By: Scarlett Full, in-house Registered Dietitian

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