Updated: August 28th, 2023

By Mary Berger, Nutrition & Integrative Health AOC Herbal Medicine Student


Maintaining adequate gut health is important as it influences the health of the rest of the body. If your gut is not digesting, absorbing, and assimilating the food you eat, then the rest of the body will suffer. In the United States, 60-70 million people are affected by some type of digestive disease. Some of the more common ones include reflux (GERD), stomach ulcers, chronic constipation, and/or chronic diarrhea, which may fall under irritable bowel syndrome, hemorrhoids, celiac disease, and inflammatory bowel conditions. The prevalence of these disorders seems to be on the rise. It has been demonstrated that sometimes a disruption in the environment of your gut can lead to some of these disorders as well as other diseases that don’t exhibit gut-related symptoms.

What is gut health?

What is a gut and what makes it healthy?

Your “gut” includes all the parts of your digestive tract: the mouth, esophagus, stomach, pancreas, liver, gallbladder, small intestine, large intestine (colon), and rectum.

But there’s more to your gut than your own tissues. You also have about 100 trillion bacteria living inside it! These bacteria play such an influential role in your overall health that they are often called the “forgotten organ.”

Many of the bacteria in your gut are “friendly,” meaning they support your overall health. Some gut bacteria are “bad” because they can make you sick and increase your risk for certain health problems even depression. This is why understanding how to kill bad gut bacteria is so important.

Gut health refers to how well-balanced these bacteria are and the overall function of your digestive system. Factors like stress and poor diet can throw off the balance between good and bad gut bacteria.

A look inside the gut

Inside the gut, there is a living ecosystem of bacteria known as the microbiome. The microbiome consists of good bacteria that promote health and bad bacteria that can lead to an unhealthy state. The health of your microbiome can be affected by antibiotic use,since antibiotics can kill both the good and bad bacteria. A person taking antibiotics needs to replenish their gut vitality through probiotics—either by eating fermented foods or by taking a supplement. Probiotics are good bacteria that help restore the gut to a healthy balance of good bacteria (also called intestinal flora). Additionally, these positive or good bacteria need to be fed in order to stay alive. Food for good bacteria is called prebiotics.

Herbs as probiotics

Probiotics are live organisms” that can survive in your digestive tract and offer proven benefits to your health. According to the National Institute on Minority Health and Health Disparities, certain herbs may offer extra health benefits due to the colonies of friendly bacteria living on them.

One study by Montenegro et al (2015) found that a traditional Japanese herbal blend called Juzen-taiho-to—which includes cinnamon, ginseng, and licorice—contains bacteria that support the immune system.

What is fascinating is that herbs can act as prebiotics for our microbiome. Some of the good bacteria that make their home in the gut include species such as Bifidobacterium, Lactobacillus (think yogurt), and Bacteroides. Bacteria in your gut that can lead to disease include Citrobacter freundii and Klebsiella pneumoniae. The study by Peterson et. al. (2018) examined if herbs typically used in Ayurvedic medicine for gut conditions could alter the development and the quantity of certain species of bacteria. The herbs examined here were slippery elm, licorice, and a combination of three dried fruits termed triphala. These herbs have been used to treat inflammatory conditions such as ulcerative colitis, Crohn’s disease, GERD (hyperacidity), and membranes that might be compromised in any way.


Triphala may be one of the best herbs for leaky gut. Used in traditional Ayurvedic medicine for centuries, triphala is an herbal blend of three plants: amla (Indian gooseberry), Bibhitaki, and Haritaki. Triphala contaias a mild laxativens important nutrients and antioxidants and can alleviate gastrointestinal distress such as bloating, constipation, and abdominal pain. Triphala is typically employed to help heal the epithelial lining in the gut, to enhance barrier function (keeping the gut from becoming leaky), and to improve absorption of nutrients.

Licorice root

Licorice root is often used to help with irritation by providing a protective cover over the membrane lining, and to help decrease inflammation. Research including a double-blind study by Raveendra et al (2011) reveals that licorice root contains plant compounds that can alleviate stomach discomfort. Another study by Hajiaghamohammad et al (2016) found that licorice root helped eliminate a bad gut bacteria called H. pylori, which can cause peptic ulcers.

Slippery elm

Finally, slippery elm is used for healing the mucous membranes in the gut. Slippery elm has been shown to improve bowel movements in patients with irritable bowel syndrome (Hawrelak and Meyers, 2010), alleviate heartburn, and provide an antioxidant effect in inflammatory bowel conditions like Crohn’s (Langmead et al, 2002).

In-vitro Methods

Using in-vitro (outside the human body) methods, the authors found that these herbs helped promote the abundance of certain species of bacteria. Triphala significantly increased the abundance of bacteria Acidaminococcus and Sutterella. Slippery elm had the greatest impact on bacteria belonging to the family of Clostridium. Licorice demonstrated an increase to Bacteroides. This demonstrates that the herbs used can act as prebiotics to increasing numbers of good bacteria. In addition, licorice root was able to decrease the population of potential opportunistic invaders Enterococcus faecalis and Klebsiella pneumoniae. These potential disease-causing bacteria have been linked to the development of a leaky gut (intestinal permeability).

Future studies in human subjects will help clarify the effect of herbal medicine on gut health. But current laboratory studies help us understand how and why herbs have such an instrumental role in overall well-being.

By restoring gut flora, herbal plants (and the probiotic bacteria found on them) can maximize the body’s ability to absorb nutrients and eliminate toxins. In this way, herbs for gut health benefit many parts of the body, not just the digestive tract.

Antibiotics and Gut Health

Antibiotics are types of medications used to fight bacterial infections and kill bad bacteria in the gut, bloodstream, and elsewhere in the body.

Like most medications, antibiotics come with side effects. According to the U.S. National Library of Medicine, these side effects may include nausea, diarrhea, yeast infections, and skin rashes. Side effects and adverse reactions can happen because of the way these powerful drugs affect gut health.

How antibiotics impact gut health?

Doctors figured out how to get rid of bad gut bacteria by creating antibiotics. Unfortunately, antibiotics also tend to kill some of the good bacteria in your gut. This throws off gut health and may allow unhealthy bacteria like C. difficile to grow out of control. C. difficile infections can cause severe diarrhea, gut tissue damage, or even death in extreme cases.

How to replenish good bacteria after antibiotics?

If a doctor prescribes you antibiotics, it’s important you take these medications exactly as prescribed, even if you start to feel better. Improperly taking antibiotics can lead to antibiotic resistance, which means bacteria evolve so that they can’t be killed by the drug anymore. These antibiotic-resistant bugs can then go on to infect other people and make them sick, sometimes fatally.

That said, taking antibiotics can be incredibly harsh on your gut health. If your imbalanced gut isn’t restored, you may be at risk for future health problems. To replenish good bacteria in your gut after taking antibiotics, focus on maintaining healthy lifestyle habits, such as:

  • Exercising
  • Managing stress
  • Not smoking
  • Maintaining a healthy diet rich in fruits, vegetables, and probiotic herbs (while avoiding refined sugar, alcohol, and processed foods)
  • Getting enough sleep


So many factors influence your gut health, including stress, exercise, exposure to environmental toxins, and perhaps most importantly your diet. Modern research has now confirmed what centuries of Ayurveda and other traditional medicine practices have inherently known for years—that certain herbs and herbal blends can promote gut health. If you believe you’re struggling with a leaky gut or poor gut health, consider adding herbs to your healthy lifestyle.

Frequently Asked Questions about Herbs and Gut Health

How to kill bad gut bacteria?

You can kill bad gut bacteria and support healthy bacteria in several ways. Diet may be one of the most important and most effective. Focus on eating plenty of fruits and veggies, which are rich in fiber and micronutrients that healthy bacteria need to grow. You can also add herbal remedies to your healthy lifestyle for an added benefit.

How to improve your gut microbiome in a day?

Your gut microbiome (the population of bacteria living in your digestive tract) is frequently changing in response to your food, environment, stress level, and so on. It may take more than one day to change your gut microbiome, but research suggests a healthy diet rich in plants and herbs can rapidly improve your gut health.

What happens if you don’t restore gut health?

If you don’t restore gut health, harmful bacteria can flourish and grow in your digestive tract. This can lead to health problems such as C. difficile infections. Poor gut health has also been linked to an increased risk of chronic diseases, including gastrointestinal disorders, depression, and obesity.



1) Prebiotic Potential of Culinary Spices Used to Support Digestion and Bioabsorption. Evid Based Complement Alternat Med. 2019; 2019:8973704. Peterson CT, Rodionov DA, Iablokov SN, Pung MA, Chopra D, Mills PJPeterson SN. PMID: 31281405; PMCID: PMC6590564.

2) Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease. J Altern Complement Med. 2018 Jul; 24(7):656-665. Peterson CT, Sharma V, Uchitel S, Denniston K, Chopra D, Mills PJPeterson SN. PMID: 29565634; PMCID: PMC6065514.