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I'm A Microbiome Researcher: Here's The Difference Between "Good" & "Bad" Gut Bacteria

Christine Tara Peterson, PhD, RYT
September 6, 2023
Christine Tara Peterson, PhD, RYT
Ayurveda & Yoga Researcher
By Christine Tara Peterson, PhD, RYT
Ayurveda & Yoga Researcher
Dr. Christine Tara Peterson PhD AHP RYT is a highly accomplished practitioner and researcher in Ayurveda and Yoga. She has a background in Microbiology & Immunology, which she has integrated with her knowledge of Ayurveda and Herbal Medicine to become a renowned expert in the field.
woman holding gut
Image by Yazgi Bayram / iStock
September 6, 2023

The human gut, often referred to as the "second brain," is a complex ecosystem teeming with trillions of microorganisms, collectively known as the gut microbiota. This intricate community of bacteria, viruses, fungi, and other microorganisms plays a vital role in maintaining our overall health and well-being.

Among these microorganisms, there exists a balance between "good" and "bad" bacteria, each influencing various aspects of our health. As a microbiome researcher and clinician focused on gut health, I think about this balance often.

Let's explore the distinction between good and bad bacteria in the gut and delve into strategies to promote a healthy microbiota.

The good, the bad, and the balance

The gut microbiota is far from a monolithic entity; rather, it is a diverse and dynamic collection of microorganisms, each with its own set of functions.

"Good bacteria," sometimes referred to as probiotics, are beneficial microorganisms that aid in digestion, produce essential nutrients, and support a robust immune system.

We are more than what we eat. Rather, we are what we digest and absorb. These beneficial microbes help facilitate this process and enhance our digestive efficiency by degrading dietary nutrients. Subsequently, these beneficial bacteria produce metabolites that help maintain a healthy gut lining, which is crucial for nutrient absorption and protection against harmful invaders.

On the other hand, so-called bad bacteria, or pathogenic bacteria, are microorganisms that can disrupt the delicate balance of the gut microbiota and lead to various health issues under certain circumstances. Some of these bacteria are opportunistic viruses. Normally present in low abundance, under certain conditions like stress or poor diet, these viruses are able to seize the opportunity and increase their numbers, which leads to symptoms.

An overgrowth of bad or opportunistic bacteria has been linked to conditions such as irritable bowel syndrome (IBS)1, inflammatory bowel disease (IBD)2, and even obesity3. These bacteria can trigger inflammation, compromise gut barrier integrity, and produce harmful metabolites.

How to reduce undesirable bacteria in the gut

Maintaining a healthy balance of gut bacteria is essential for overall health. Here are some of my favorite strategies to help reduce bad bacteria in the gut:


Limit sugar and processed foods

A diet rich in processed foods, sugars, and unhealthy fats can fuel the growth of bad bacteria and has been linked to gut microbiome imbalances4. Harmful bacteria tend to thrive on sugars and simple carbohydrates, leading to an overgrowth that can disrupt gut health.

Limiting the intake of sugary and processed foods can help create an environment where beneficial bacteria can flourish. Reduce the consumption of these inflammatory foods that lack fiber and nutrient density. Switching to a diet high in fiber, whole grains, lean proteins, and a variety of fruits and vegetables can help create an environment less favorable for harmful bacteria.


Consider probiotics

Taking probiotic supplements or consuming foods rich in probiotics, such as yogurt, kefir, sauerkraut, and kimchi, can introduce beneficial bacteria to the gut and help crowd out bad bacteria. Probiotic supplements can also be useful in rebalancing the gut microbiota, especially after a course of antibiotics or during times of digestive distress5.

These supplements contain specific strains of beneficial bacteria that can help suppress the growth of harmful microbes. However, it's essential to choose reputable brands and consider a consultation with a health care professional before adding probiotics to your routine.


Manage stress

Stress can have a significant impact on the gut microbiota. Chronic stress may lead to an imbalance in gut bacteria, favoring the growth of harmful microbes6. Practices such as meditation, deep breathing exercises, yoga, and mindfulness can help reduce stress and promote a healthier gut environment, as I share in this scientific review article7.


Prioritize sleep

Prioritizing quality sleep is essential for overall health, including a balanced gut microbiota. Poor sleep patterns can disrupt the gut microbiota and lead to an increase in harmful bacteria8. Strive for seven to nine hours of restful sleep each night to support a balanced gut environment.


Stay hydrated

Adequate hydration is crucial for maintaining a healthy gut. Staying adequately hydrated supports proper digestion and helps support the health of the gut lining, promoting a healthy gut environment or microbiome. Water helps transport nutrients, support digestion, and maintain the mucosal lining of the intestines. A well-hydrated gut is better equipped to flush out toxins and prevent the growth of harmful bacteria. Aim to drink plenty of water throughout the day to support optimal gut function.

How to increase beneficial bacteria in the gut

Fostering the growth of good bacteria is equally important for maintaining a balanced gut microbiota. Here's how to increase the presence of beneficial bacteria:


Incorporate fermented foods

In addition to probiotic supplements, incorporating fermented foods like kombucha, miso, and tempeh into your diet can introduce a variety of beneficial bacteria strains to your gut.


Embrace prebiotics

Prebiotics are nondigestible fibers that serve as food for good bacteria. Foods like garlic, onions, leeks, bananas, and asparagus are excellent sources of prebiotics and can promote the growth of beneficial microbes.

Medicinal herbs and spices are also prebiotics and excellent ways to increase your fiber consumption. I love incorporating fresh herbs and spices into cooking and have even published extensively on the prebiotic effects of medicinal herbs9 and spices10 on our gut microbes.


Prioritize plant-based diversity

Eat a wide variety of plant-based foods to help increase the number and diversity of good gut microbes. A varied and plant-focused diet can provide a wide range of nutrients and compounds that feed beneficial gut bacteria.

Phytonutrients found in fruits, vegetables, and herbs have been linked to promoting the growth of specific strains of good bacteria11. Legumes, whole grains, nuts, and seeds are excellent sources of phytonutrients and fiber that can support the growth of beneficial microbes. Aim to include a broad spectrum of colorful plant-based whole foods to provide nourishment for a diverse microbiota.


Get regular exercise

Regular physical activity has been shown to positively influence the gut microbiota12. Exercise can enhance the diversity of gut bacteria and promote the growth of beneficial strains. Aim for a combination of aerobic exercises, yoga, and strength training to support a healthier gut.

The takeaway

The balance between good and bad bacteria in the gut is crucial for maintaining digestive health, supporting the immune system, and preventing various health issues. Remember that progress takes time, and small, sustainable changes can lead to substantial improvements over the long term. By steadily adopting a diet focused on whole, plant-based foods, incorporating probiotics and prebiotics, managing stress, and making lifestyle adjustments, we can nurture a thriving community of beneficial bacteria in our gut and promote overall well-being.

Christine Tara Peterson, PhD, RYT author page.
Christine Tara Peterson, PhD, RYT
Ayurveda & Yoga Researcher

Dr. Christine Tara Peterson PhD AHP RYT is a highly accomplished practitioner and researcher in Ayurveda and Yoga. She has a background in Microbiology & Immunology, which she has integrated with her knowledge of Ayurveda and Herbal Medicine to become a renowned expert in the field.

With extensive training from some of the most distinguished Ayurvedic clinicians and doctors, Dr. Peterson is committed to promoting individualized and evidence-based approaches to healthcare. Her research on the gut microbiome and Ayurvedic medicine has made significant contributions to the field, while her clinical work focuses on gut and nervous system disorders, women’s health, and personalized care. She is the author of You Are What You Digest.

You can connect with Christine on her website or on Instagram and Facebook @instituteforvedicresearch.