How To Get Rid Of Bad Gut Bacteria – Everything You Need To Know

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By Thomas Youngerman

Reviewed by Juliana Tamayo, MS, RDN - Last Updated

How To Get Rid Of Bad Gut Bacteria

Stomach issues getting you down? It could be the result of having bad gut bacteria. These harmful microbes can impair cellular function, cause stomach discomfort, and even make you sick. So, how do you get rid of bad gut bacteria, while also promoting the good stuff that your body needs?

This article will explain just that! We’ll start with the complex, provide necessary definitions and explanations, and move to easier to understand methods to identify bad gut bacteria. We’ll help you determine if you might have harmful bacteria, and provide you with ideas and solutions for how to get rid of bad gut bacteria.

So, without further ado, let’s get started!

Trillions of Human Cells

Like every living organism, the human body consists of cells, the fundamental unit of life. We are complex beings, composed of trillions of human cells. Even a single-celled (unicellular) organism is elaborate as inside the cell, atoms make up molecules, and these, in turn, make organelles. Scientists estimate that we have about thirty trillion human cells that function together to form the human organism. To dramatically over-simplify, specialized cells form tissue, tissues form organs, organs form systems (digestive, circulatory, nervous), and systems function to form an organism. Cells are the building blocks of life. The actual number of cells in your body varies, determined by size, age, gender, health, and other environmental factors. 

The human body has multiple types (about 200 varieties) of specialized cells such as blood cells, epithelial cells, neurons, immune system cells, and fat cells, all of which play a vital role in the body. These cells are constantly dying while new ones are generated. When healthy, the human body is a marvel; it maintains a precise balance of aged and dying cells versus new cells. 

Human Cells

Trillions More of Bacterial Cells – the Microbiome

In addition to our 200 varieties of human cells, we have another estimated thirty-eight trillion cells that live in and on our bodies, known as the microbiome. The types of human microbiota include specific bacteria, fungi, viruses, and other microbes. Although the terms microbiome and microbiota are often used interchangeably, from a scientific viewpoint, there is a difference. The microbiome refers to the bacteria and their genes, while microbiota relates to microorganisms living in a specific environment. For our purposes, we refer to the gut microbiome or gut microbiota to depict the trillions of bacteria that reside in your gastrointestinal tract, primarily in the colon. 

The gut microbiome has a significant influence on our health, metabolism, and disease protection. More than 70% of your immune system is in the gut. Recent research has linked the microbiome to obesity, type 2 diabetes, autism, anxiety, and depression. An imbalance of healthy microbes in the intestines may also contribute to high blood sugar, high cholesterol, and other disorders.

Good Gut Bacteria vs. Bad Gut Bacteria

It’s ingrained that when we hear words such as bacteria or virus, we tend to think of exposure to something harmful; however, not all these microorganisms cause disease. Some bacteria are beneficial and provide essential functions for health. Others are considered probiotic; we rely on them to perform functions we may not be able to in their absence. Today, the preeminent expert in gut health, Dr. Steven Gundry, refers to these as our gut buddies, which we should supplement and nurture. 

There are also harmful microbes such as lectins, pathogens, and gut yeasts which can impair cell function and make us sick if the microbiota doesn’t control them. Our good bacteria do more than just aid in digestion and absorption – they also keep harmful bacteria in check.

A balanced microbiota with both beneficial and probiotic bacteria performs other essential functions, including protecting the gut lining and maintaining the correct pH to combat pathogens. An unhealthy and imbalanced gut microbiome can result in indigestion, weight gain, mood swings, poor sleep, reduced energy levels, and more. 


How to Tell if You Have Bad Gut Bacteria

Our preoccupation with gut and digestive health and the microbiome has given rise to a new service provided to help identify if you have harmful gut bacteria and specific types of bad bacteria. Yes, in some instances, it is a marketing ploy to help sell pre-and probiotics, but the information can also be beneficial for your health. Here are some of the companies providing this service:

  • Thryve
  • Ubiome
  • Psomagen
  • Genova
  • Daytwo
  • Sungenomics

This type of service analyzes your gut bacteria, recommends a diet of foods to eat and those to avoid, and prescribes a personalized probiotic blend to support your good bacteria and counteract the bad.

Common Symptoms of Bad Gut Bacteria

For those more interested in self-diagnosis, here are common symptoms of poor gut health and an imbalance of gut bacteria:

  • IBS, Irritable Bowel Syndrome, persistent stomach issues.
  • Occasional stomach issues such as gas, bloating, constipation, acid reflux.
  • Food intolerances, foods that trigger bloating, gas, diarrhea, abdominal pain.
  • Food allergies.
  • Skin irritations, psoriasis, and eczema.
  • Poor sleep quality, fatigue.
  • Uncontrolled weight gain or weight loss.
  • Food cravings, especially sugars.
  • Mood swings, anxiety, depression.
  • Migraine headaches, potentially due to the gut-brain axis.

Self-Diagnosis of Bad Gut Bacteria-Depression

Prevention and Treatment for Bad Gut Bacteria

As indicated above, poor gut health due to an imbalance of bacteria in the digestive tract can have a devastating impact on overall health and wellbeing. The resulting systemic inflammation can lead to autoimmune diseases, heart disease, asthma, rheumatoid arthritis, even cancer.  

If an ounce of prevention is worth a pound of cure, let’s first discuss those protocols to maintain gut health, supporting your beneficial microbes naturally.

Common Sense Protocols to Maintain a Healthy Gut

As is common to so many health regimens, lifestyle plays an essential role in good gut health. However, there are some protocols specific to gut health we highlight first:

  • Avoid sugary, processed, and fast foods.
  • Eat smaller meals more frequently. 
  • Eat more fiber.
  • Avoid unnecessary antibiotics.
  • Avoid artificial sweeteners.
  • Chew your food thoroughly.
  • Eat more fermented foods.

Food to Maintain Healthy Gut

Lifestyle also has a significant impact on gut health:

  • Maintain a healthy, diverse diet: whole foods, plant-based foods, and grass-fed sources of protein. 
  • Consider a vegan or vegetarian diet.
  • Exercise.
  • Avoid tobacco products and limit alcohol intake.
  • Get sufficient, quality sleep.
  • Avoid or restrict stress as possible.

Treatment Regimens for Bad Gut Bacteria

The most prevalent treatments for those with poor gut health and an excess of harmful gut bacteria are pre-and probiotics, postbiotics, digestive enzymes, and avoiding certain foods that may trigger stomach distress. Gut health testing companies provide a list of foods to be avoided and a personalized program of probiotics. 

Pre-, Pro-, and Postbiotics for Gut Health

Most people are familiar with probiotics; they are Dr. Gundry’s gut buddies, healthy bacteria, living organisms in dietary supplement form. As the fastest-growing segment in the natural product industry, probiotics are proven to improve gut health, address intestinal inflammation, and support your immune system. Some of the more common types of probiotics used in the supplement space are Bifidobacterium, Lactobacillus, Streptococcus, Saccharomyces, and Bacillus. When selecting a probiotic, it’s essential to know they are measured in (CFUs) colony-forming units. This indicates the number of viable (living) cells in the supplement at the time of consumption.

Some of the more respected brands in the probiotic category include:

Pre-, Pro-, and Postbiotics for Gut Health-Gundry MD

Prebiotics are fiber-rich microorganisms that feed and support the healthy bacteria, the probiotics, in your gut. The combination of pre-and probiotics is often referred to as a synbiotic relationship, which improves the activity and survival rate of beneficial microorganisms. One of our favorite pre-and probiotic products is Daily Synbiotic, from Seed. The company uses an ingenious delivery system featuring a capsule within a capsule. The outer capsule contains the prebiotic formula, while the inner capsule delivers the probiotics, over 53 billion AFUs/CFUs.

Postbiotics are a newer segment of the microbiome category; they are the waste products, metabolites, or short-chain fatty acids (SCFAs) leftover after probiotics feed on certain types of fiber molecules. Researchers believe postbiotics may prove to be beneficial in improving overall digestive health. GundryMD’s Bio Complete 3 was one of the first commercial products to incorporate a prebiotic, probiotic, and postbiotic in one formulation. 

Digestive Enzymes

Nutritional supplements that contain the following digestive enzymes in some combination; Lipase, Protease, Amylase, Cellulase, Papain, or Bromelain. Enzyme supplements typically provide relatively fast relief for symptoms of stomach issues, such as gas, bloating, constipation, and heartburn.

Other Popular Microbiome Ingredients

Several other ingredients used frequently in microbiome support products include the amino acid L-glutamine, Magnesium, Licorice Root, Bio-Perrine, and Fish Oils. Glutamine and Magnesium help maintain immune health and aid indigestion. Fish Oils are healthy fats known to address systemic inflammation. Licorice Root is a commonly used ingredient as it helps to soothe gastrointestinal discomfort. Bio-Perrine is universally accepted for its ability to aid in absorption.

One last segment of gut health we would be remiss to skip is protecting the stomach lining. Research tells us that increased intestinal permeability (leaky gut) can play a role in certain conditions such as celiac disease, Crohn’s disease, and irritable bowel syndrome (IBS). The typical Western diet, intestinal bacteria, and systemic inflammation can lead to cracks in the stomach wall allowing toxins to enter the bloodstream resulting in numerous adverse outcomes. Gundry MD has introduced a product, Total Restore, featuring many of the ingredients cited above but sans pre- or probiotics to protect the gut lining. 

In Summary: Getting Rid of Bad Gut Bacteria

We hope we have delivered our promise of helping you identify and determine if you suffer from poor gut health and harmful gut bacteria and provided common-sense protocols to prevent or rid yourself of any imbalances.

We believe that if you take care of your gut health, you will be amazed at your level of general health and wellbeing.

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Thomas Youngerman

Thomas Youngerman is an entrepreneur and author in the health and wellness space with extensive experience in the supplement industry. He has owned multiple sports nutrition stores and served as the Category Manager and Director of Business Development for a regional chain of nutrition stores. Thomas created a successful line of men’s healthy aging supplements that was distributed in GNC, The Vitamin Shoppe, and Kroger, and later sold to a West Coast corporation. Thomas was previously a certified nutrition coach. He has a strong understanding of nutrition, supplement formulations, DSHEA, cGMP, and FDA regulations.