What Is Gut Flora? A Simple Guide to “Good,” “Bad,” and “Opportunistic” Bacteria

“Gut flora,” “good bacteria,” and “bad bacteria”—these are terms we often see on TV, in magazines, and on food packaging.

But when it comes to explaining them, many of us may find ourselves at a loss for words: “What exactly is flora?” “Is it better to have fewer bad bacteria?” “I’ve heard of opportunistic bacteria, but…”

In this article, you’ll learn three things:

• What “gut flora” is and why it’s called a “flower garden”
• What kinds of bacteria are referred to as good, bad, and opportunistic
• How to think about the often-mentioned “2:1:7” ratio

We’ll base our explanations as much as possible on medical and nutritional sources. Let’s take a look, step by step.

Gut flora is a “community” of bacteria living in the intestines

Gut flora refers to the many bacteria living in our intestines. Its formal name is the “gut microbiota” or “intestinal flora.”

It is often said to consist of about 1,000 species and 100 trillion bacteria. This figure is also given in a 2015 article by Professor Akira Ando of Shiga University of Medical Science, published in the Journal of the Japanese Society of Internal Medicine.

Why is it called a “flower garden”?

The bacteria are not scattered randomly throughout the intestines. According to the same article, each kind maintains its own “territory,” while together they form a single community.

The way different kinds of bacteria gather together resembles a flower garden where flowers of each variety bloom in clusters. That is why they are called “flora,” meaning “flowering plants.” The formal Japanese term, “sō” (叢), means “thicket” or “grassland.” Both terms describe bacteria living together in groups.

The number of bacteria varies depending on how they are counted

One thing to keep in mind is that the figure of “100 trillion” can vary.

In 2016, researchers published a paper recalculating the number of bacteria in the human body. They estimated that an adult man weighing 70 kg has about 38 trillion bacteria, weighing about 0.2 kg (PLOS Biology).

That’s quite different from the “100 trillion” figure often cited in the past. The numbers vary depending on how they are measured and calculated. Either way, however, an enormous number of bacteria live in our bodies.

The large intestine has the most bacteria

Bacteria are not present in equal numbers throughout the intestines. According to Professor Ando’s article, stomach acid greatly reduces the number of bacteria in the stomach. Their numbers then increase rapidly from around the end of the small intestine, reaching their highest levels in the large intestine.

It’s helpful to remember that discussions of gut flora are often referring to the bacteria in the large intestine.

“Good, bad, and opportunistic bacteria” are labels used to make things easier to understand

It would be difficult to memorize all 1,000 or so kinds of bacteria individually. So, a widely used approach is to divide them into three broad groups based on their functions: “good bacteria,” “bad bacteria,” and “opportunistic bacteria.”

The important thing to remember is that these are not formal medical classifications, but informal labels used to make things easier to understand. Lecture materials published by Kagawa Nutrition University also describe them as “informal terms.” Think of them as broad labels that group formally classified bacteria into three categories based on their functions.

Good bacteria: bacteria that produce acids and keep the intestines mildly acidic

Good bacteria are a group of bacteria said to have beneficial effects on the body. Representative examples include lactic acid bacteria and Bifidobacteria.

According to “Health and Longevity Net,” published by the Public Interest Incorporated Foundation for the Promotion of Healthy Longevity, good bacteria produce lactic acid and acetic acid, helping keep the intestines mildly acidic.

Why is acidity important? Professor Ando’s article explains that an acidic intestinal environment makes it harder for harmful bacteria such as Clostridium perfringens to multiply. It may help to think of good bacteria as creating an environment that is difficult for other bacteria to live in by producing acids themselves.

Bad bacteria: bacteria that produce substances harmful to the body

Bad bacteria are a group of bacteria said to have undesirable effects on the body. “Health and Longevity Net” lists Clostridium perfringens, staphylococci, and toxic types of E. coli as examples.

According to Professor Ando’s article, Clostridium perfringens is one type of bacteria that breaks down proteins and produces harmful substances such as ammonia.

Opportunistic bacteria: bacteria that side with whichever group is dominant at the time

Opportunistic bacteria are a group that cannot be clearly classified as either good or bad. “Health and Longevity Net” gives Bacteroides and non-toxic types of E. coli as examples.

“Opportunistic” means taking the side that has the advantage in a given situation. “Health and Longevity Net” explains that opportunistic bacteria act similarly to whichever group—good or bad—is dominant.

Kagawa Nutrition University’s materials also describe them as bacteria that “usually do no harm, but can cause problems when the body becomes weak.” The wording differs somewhat between sources, but they agree that these are bacteria whose effects are not always the same.

Bacteria with the same name can belong to different groups

Here’s one thing to notice: “E. coli” appears in both the bad bacteria group (toxic types) and the opportunistic bacteria group (non-toxic types).

That’s because different types (strains) of bacteria called “E. coli” have different properties. This is a good example of how the three groups are only a rough guide. Knowing that the boundaries are not clear-cut can help you avoid being misled by information.

Think of “2:1:7” as a rough guide

A ratio often mentioned in discussions of gut flora is “2 parts good bacteria: 1 part bad bacteria: 7 parts opportunistic bacteria.” “Health and Longevity Net” also introduces this ratio as an ideal.

However, Kagawa Nutrition University’s materials state that “the ideal distribution of bacterial species varies from person to person.” It may be best to treat this figure as a rough guide to help you understand the concept, rather than a definitive answer that applies to everyone.

What the numbers tell us is that opportunistic bacteria are the largest group

The key point to notice is not the exact proportions, but that opportunistic bacteria make up the largest group.

Good and bad bacteria together account for about 30%. However, opportunistic bacteria make up the remaining 70%, and are said to act similarly to whichever group is dominant. Following the explanation in “Health and Longevity Net,” this means that the way the largest group functions also changes depending on whether good or bad bacteria are dominant.

The important idea is “balance”

This helps explain why people say that “balance is important for gut flora.”

It’s not about eliminating every last bad bacterium. Among the many bacteria present, the question is which group has the upper hand. Gut flora is often described in terms of this overall “balance.”

Gut flora differs from person to person—and changes over time

The kinds of bacteria in gut flora vary from person to person. According to Professor Ando’s article, gut flora is relatively stable in adulthood, with a pattern unique to each individual.

The foundations are shaped by the environment after birth

The same article also notes that studies comparing twins suggest that the environment from birth through weaning has a greater influence on how gut flora is formed than genetics.

It also changes with age

Gut flora also changes with age. According to Professor Ando’s article, Bifidobacteria are abundant in infancy, and the gut flora changes to the adult pattern around weaning. Then, from around middle age onward, Bifidobacteria decrease and Clostridium perfringens increase.

Diet and medication can also change it

It is explained that gut flora continues to change in adulthood under the influence of diet, antibiotics, and other factors.

In other words, gut flora is not fixed at birth and unchangeable. It is explained that its composition can change under the influence of diet, medication, and other factors.

What you can do every day: look at your meals from the bacteria’s point of view

From here, let’s move away from research and talk about everyday meals.

Professor Ando’s article explains that gut bacteria ferment dietary fiber and produce acids such as acetic acid. In other words, foods containing dietary fiber also serve as “food” for gut bacteria. Rather than doing anything special, try including foods like these in your daily meals, as much as is practical.

• Vegetables, beans, mushrooms, and seaweed: foods that contain dietary fiber
• Yogurt, natto, miso, and pickled vegetables: fermented foods made through the action of bacteria
• Foods containing oligosaccharides: Kagawa Nutrition University’s materials list onions and other foods as sources of nourishment for good bacteria

Kagawa Nutrition University’s materials describe consuming good bacteria as “probiotics” and consuming oligosaccharides, dietary fiber, and other substances that nourish good bacteria as “prebiotics.” The difference between “the bacteria themselves” and “food for the bacteria” is explained in more detail in this article.

Things to keep in mind

Consuming a lot of dietary fiber or oligosaccharides at once may cause loose stools or bloating, depending on your constitution and condition. Add them gradually and see how your body responds.

Also, if digestive symptoms persist, don’t try to manage them through diet alone; consult a medical professional. If you have a chronic condition or take medication, consult your doctor about changes to your diet as well.

Frequently asked questions

Q. Should I try to eliminate bad bacteria completely?

The sources cited in this article do not discuss eliminating bad bacteria. They focus on which group—good or bad—is dominant. Also, “good” and “bad” are informal labels used to make things easier to understand; the groups are not clearly divided. Rather than thinking simplistically that “bad bacteria are all bad,” it’s better to consider the overall balance.

Q. Can I find out the proportions of bacteria in my own gut flora?

Many gut bacteria are difficult to extract and grow. For this reason, research uses methods that examine DNA (according to Professor Ando’s article). If you have concerns about your gut health, consult a doctor.

Q. Do I need to get close to the “2:1:7” ratio?

As mentioned earlier, the ideal proportions are said to differ from person to person. Rather than making the numbers themselves your goal, use them as an opportunity to review your overall daily diet.

Summary: Gut flora is a “flower garden where many kinds of bacteria live”

Here are the three main takeaways:

• Gut flora is a community of many bacteria living in the intestines, especially the large intestine. The way they gather in groups by type is compared to a flower garden (flora).
• Good, bad, and opportunistic bacteria are informal labels based on their functions. Opportunistic bacteria, the largest group, are said to act similarly to whichever group is dominant.
• “2:1:7” is a rough guide. The ideal proportions vary from person to person. What matters is the idea of overall “balance.”

One thing you can do today is check whether your meals include foods containing dietary fiber, such as vegetables, beans, or seaweed, as well as fermented foods. Try looking at your meals from the perspective of the bacteria in your gut.

You may also find these related articles helpful.

• How are kestose supplements different from lactic acid bacteria and Bifidobacteria supplements? A guide to “food” versus “the bacteria themselves”
• What causes constipation, and where in our daily lives does the cause lie?

Why not add kestose to your daily gut-health routine?

The information above is general information about gut flora. It does not demonstrate the effects of kestose.

Aidaya Shoten’s kestose is made with 100% kestose, an oligosaccharide that nourishes good bacteria. It is an oligosaccharide consisting of three sugar units, the smallest unit. The product contains 30 sachets of 3 g each. Use one sachet per day as a guide, adding it to yogurt or a drink. It has a mildly sweet taste.

• Kestose, 3 g × 30 sachets (one-time purchase)
• Kestose, 3 g × 30 sachets (subscription)

Please see the product page for details, including pricing.

This article provides general information about diet. It is not intended to diagnose, treat, or prevent disease. If you have health concerns, a chronic condition, or persistent symptoms, please consult a doctor.

Sources

• Akira Ando, “Types and Colonization of Intestinal Bacteria: Their Hidden Functions as an Organ,” Journal of the Japanese Society of Internal Medicine 104(1):29–34 (2015) https://www.jstage.jst.go.jp/article/naika/104/1/104_29/_pdf
• Public Interest Incorporated Foundation for the Promotion of Healthy Longevity, “Health and Longevity Net: What Is the Intestinal Microbiota (Gut Flora)?” https://www.tyojyu.or.jp/net/kenkou-tyoju/kenko-cho/chonai-saikin.html
• Kagawa Nutrition University, Web Lecture 5, “The Power of the Intestinal Microbiota” (author: Toshiko Ota) https://llab.eiyo.ac.jp/ions/wp_dr/wp-content/uploads/2023/04/%E3%82%A6%E3%82%A7%E3%83%96%E8%AC%9B%E5%BA%A75.pdf
• Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology (2016) https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533