Good Bacteria, Bad Bacteria & Gut Microbiome: Understanding Probiotics and Everyday Diet

What Are Good Bacteria, Bad Bacteria and Opportunistic Bacteria?

Our intestines are home to an enormous number of microorganisms. Together, these communities are known as the gut microbiota, gut microbiome or intestinal microbiota, and their composition varies from person to person depending on factors such as diet, age and environment.

When reading about gut bacteria, you may often come across the terms “good bacteria,” “bad bacteria,” and “opportunistic bacteria.”

These terms have traditionally been used as a simple way to describe the complex world of intestinal microorganisms. They are generally explained as follows:

• Good bacteria: Bacteria involved in potentially beneficial activities, including the production of substances such as lactic acid and acetic acid
• Bad bacteria: Bacteria that, under certain conditions, may be associated with the production of less desirable metabolic compounds
• Opportunistic bacteria: Bacteria whose behaviour may change depending on diet, the surrounding gut environment and other conditions

Lactic acid bacteria and bifidobacteria are among the microorganisms commonly described as “good bacteria.”

Modern gut microbiome research goes beyond these three simple categories and also considers bacterial species and strains, interactions between microorganisms, diet and the surrounding environment.

The Gut Microbiome Is a Network of Diverse Microorganisms

In the past, suggested ideal percentages of “good,” “bad,” and “opportunistic” bacteria were sometimes presented as a guide to a healthy gut.

Current research shows that the composition of the gut microbiota can vary considerably even among healthy individuals.

For this reason, researchers increasingly look beyond fixed percentages and focus on which microorganisms are present and what roles they may play.

There Are Many Different Types of E. coli

When people hear the name Escherichia coli or E. coli, they may immediately think of harmful bacteria.

In reality, there are many different types of E. coli. Some live naturally in the human intestine, while certain strains have characteristics that can make them pathogenic.

In other words, the broad name “E. coli” includes bacteria with different characteristics.

This is one of the interesting aspects of studying the gut microbiome. Rather than looking only at the name of a microorganism, it can be more informative to consider which strain is present, the environment it lives in and what it is doing there.

How Are Gut Bacteria Related to Our Everyday Diet?

The gut microbiota is studied in relation to many factors, including diet, age, environment, sleep, physical activity, stress and medication use.

One of the factors most closely connected with everyday life is diet.

Some components of the food we eat are not fully digested and absorbed in the small intestine and instead reach the large intestine, where they can be used by gut microorganisms.

One important example is dietary fiber.

Certain types of dietary fiber can be fermented by gut bacteria, producing substances known as short-chain fatty acids.

Short-chain fatty acids include acetate, propionate and butyrate. Butyrate, in particular, is an important energy source for cells lining the colon, and the relationship between short-chain fatty acids and intestinal function continues to be widely studied.

Modern microbiome research therefore looks not only at which bacteria are present, but also at what those bacteria use and what substances they produce.

Bringing Fiber, Fermented Foods and Fruit Into Everyday Meals

When thinking about the gut microbiome, everyday food choices are one of the easiest places to begin.

Dietary fiber is found in many foods, including vegetables, fruit, legumes, seaweed, whole grains and mushrooms.

There are many different types of dietary fiber, and gut bacteria do not use them all in exactly the same way. Including a variety of plant-based foods can naturally bring more diversity to your everyday diet.

Fruit and Dried Fruit as Everyday Options

Fruit provides dietary fiber as well as a range of vitamins, minerals, polyphenols and other naturally occurring compounds.

Pectin, found in foods such as apples and citrus fruits, is one type of dietary fiber. Human studies have also investigated fruits such as kiwifruit in relation to digestive function and bowel habits.

Fruit can be enjoyed fresh or in dried form.

Because much of the water has been removed, dried fruit has a more concentrated flavour. Its sugars and energy are also more concentrated, so portion size is worth keeping in mind.

Fruit tea made with fruit and herbs is another way to enjoy natural fruit aromas, gentle acidity and flavour as part of a tea break.

Fruit tea can be enjoyed primarily for its aroma and flavour, while whole fruit and dried fruit can be enjoyed as foods that contain dietary fiber.

You might enjoy a fragrant fruit tea during a relaxing break and choose fresh or dried fruit as a snack, depending on the occasion and your preferences.

Fermented Foods Are Another Way to Explore Microorganisms

Foods produced with the help of microorganisms, such as yogurt, natto, miso and kimchi, are known as fermented foods.

The microorganisms involved, fermentation methods and resulting compounds differ from one food to another.

For example, natto is produced using natto bacteria, while various lactic acid bacteria are used in yogurt production.

Looking beyond the general term “fermented food” and learning which microorganisms are involved and how they transform the food can make familiar fermented foods much more interesting.

Everyday Lifestyle and the Gut Microbiome

Along with diet, researchers are also studying the relationships between the gut microbiota and lifestyle factors such as sleep, physical activity and stress.

In everyday life, some basic habits to consider include:

• Combining a variety of vegetables, fruits, legumes and whole grains
• Including foods that contain dietary fiber
• Drinking enough fluids for your individual needs
• Getting an appropriate amount of sleep
• Staying physically active within a comfortable range
• Paying attention to changes in your diet and how you feel

Because the gut microbiota varies greatly from person to person, it is useful to look at your overall diet and lifestyle over time rather than focusing on a single food.

Medications such as antibiotics are also studied for their effects on the gut microbiota. Antibiotics play an important role in treating bacterial infections, so when they are prescribed, they should be used according to the instructions of your doctor or pharmacist.

What Are Probiotics? And How Are They Different From “Good Bacteria”?

Once you begin learning about good bacteria, another term you are likely to encounter is “probiotics.”

In everyday conversation, probiotics are sometimes used almost interchangeably with “good bacteria,” but the term probiotic has a more specific internationally accepted definition.

Probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.”

In this definition, the “host” refers to the person or other organism receiving those microorganisms.

One important point when learning about probiotics is which specific microorganism is being discussed.

Rather than looking only at broad groups such as lactic acid bacteria or bifidobacteria, probiotic research often needs to be considered down to the level of the specific strain.

Different Strains Can Have Different Characteristics

When a product or article mentions “lactic acid bacteria,” it can be easy to imagine that all of these microorganisms are essentially the same.

In reality, there are many different types of lactic acid bacteria, and within them are many different strains. Even microorganisms belonging to the same species may have different characteristics depending on the strain.

When looking at an individual probiotic, it is useful to check the strain used, the number of microorganisms, the study population, intake conditions and the research that has been conducted.

In other words, understanding probiotics means looking at which microorganism has been studied and under what conditions.

Fermented foods and probiotics also have different definitions.

As discussed in our previous article on natto, fermented foods are made through the activity of microorganisms. Probiotics, on the other hand, refer to specific live microorganisms considered in relation to their strain and the conditions under which they have been studied.

Starting with the familiar idea of “good bacteria” and then learning about species and strains can make the concept of probiotics much easier to understand.

Summary: Look Beyond “Good” and “Bad” to Understand the Gut Microbiome

The terms “good bacteria,” “bad bacteria,” and “opportunistic bacteria” provide a simple starting point for understanding the complex world of the gut microbiome.

Current research shows that gut microbiota differs from person to person and that many different microorganisms exist and interact with one another. Researchers continue to study their relationships with diet, age, sleep, physical activity and the environment.

In everyday life, a varied diet that includes vegetables, fruits, legumes, grains and fermented foods can provide a broad range of foods and nutrients. Fruit, dried fruit and fruit-based teas can also bring different flavours and experiences to everyday eating and drinking.

As you learn more about the gut microbiome, familiar terms such as lactic acid bacteria and bifidobacteria naturally lead into a deeper understanding of probiotics and fermented foods.

Moving beyond the simple labels of “good” and “bad” bacteria and looking at the relationship between microorganisms, food and everyday life can offer a new perspective on the meals we eat every day.

Important Note

This article is intended to provide general educational information about good bacteria, bad bacteria, gut microbiota, the gut microbiome, dietary fiber, fermented foods and probiotics. It is not intended to diagnose, treat, cure or prevent any disease. If symptoms such as abdominal pain, diarrhea or constipation persist, or if you experience blood in the stool, unexplained weight loss or severe abdominal pain, please seek medical advice.

The research and general definitions discussed in this article do not indicate the effects or functions of any individual products displayed elsewhere on this page.

References

1. Hill C, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology. 2014.
2. Marco ML, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology. 2021.
3. NIH Office of Dietary Supplements. Probiotics Fact Sheet for Health Professionals.
4. Valdes AM, et al. Role of the gut microbiota in nutrition and health. BMJ. 2018.
5. Makki K, et al. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host & Microbe. 2018.