How to Naturally Increase Good Bacteria in the Gut 


Every individual carries within them a unique universe of microorganisms known as the gut microbiota. These microscopic creatures, which predominantly consist of bacteria, play a vital role in our health by assisting in digestion, producing essential vitamins, boosting our immune system, and even affecting our mood. Yet, not all bacteria in our gut are beneficial; there’s a constant tussle between ‘good’ and ‘bad’ microbes. 

So, how do we tilt the balance in favor of the beneficial bacteria? Typically, the answer might be probiotic supplements. These products contain live bacteria intended to boost the population of good bacteria in your gut. However, as health and fitness professionals, we often encounter individuals who either cannot or prefer not to take supplements or simply want to build a gut-health-promoting lifestyle before considering supplementation. 

This article is for those looking for natural strategies to enhance their gut microbiota. We will explore evidence-based lifestyle and dietary changes that can help increase the diversity and abundance of beneficial gut bacteria, promoting overall health and wellbeing. No pills, no powders – just simple, practical advice rooted in scientific research. 

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Before diving into specific approaches, it’s important to understand that promoting gut health isn’t solely about what you put on your plate. Yes, diet plays a major role, but there’s a broader lifestyle context that cannot be ignored. A holistic approach that encompasses sleep, physical activity, stress management, and hydration, in addition to diet, is key to fostering a diverse and healthy gut microbiome. 

Consider sleep, for example. Research reveals a bidirectional relationship between sleep and gut health. Poor sleep can disrupt your gut microbiota; conversely, an unhealthy gut can contribute to sleep issues. Similarly, regular physical activity is associated with a more diverse gut microbiota. 

Stress, both physical and emotional, can also affect the gut microbiota. Chronic stress may alter the diversity and composition of the gut microbiota, potentially leading to a range of health problems. Hydration, though often overlooked, also plays a role in maintaining the health of the gut. 

In this article, we will delve into each of these lifestyle strategies, exploring how they can be harnessed to naturally enhance the beneficial bacteria in our guts. But first, we will talk about some generalities of the microbiome and some signs and symptoms of a healthy gut.  

The Importance of the Gut Microbiome for Overall Health  

Often referred to as the body’s “second brain”, the gut microbiome is crucial for more than just digestive health. It plays an integral role in our overall health, influencing everything from metabolism and immunity to brain function and mood

Firstly, the gut microbiome aids in digestion and nutrient absorption. It assists in breaking down complex carbohydrates, producing essential vitamins like vitamin K and B-vitamins, and facilitating the absorption of certain minerals. 

But the role of the gut microbiome extends well beyond the digestive tract. Research has shown that it plays a crucial role in our immune system, with around 70% of the body’s immune cells found in the gut. The gut microbiome helps to regulate these immune responses, protecting against pathogens and preventing overactive immune responses, which could lead to autoimmune disorders. 

Moreover, the gut microbiome is intricately linked to our brain health. Through the gut-brain axis, our gut bacteria can influence our mood, behavior, and mental health. Studies suggest that an imbalanced gut microbiota may contribute to a range of neurological and mental health disorders, including anxiety, depression, and even neurodegenerative diseases. 

In essence, a healthy and diverse gut microbiome is integral to our overall health. By cultivating a flourishing gut ecosystem, we can nurture our physical and mental wellbeing, highlighting the importance of strategies that naturally promote beneficial gut bacteria. 

Signs and Symptoms of a Healthy Gut 

Recognizing a healthy gut can often be subjective and might differ somewhat from person to person, given our unique gut microbiomes. However, some general signs of a healthy gut include: 

  1. Regular Bowel Movements: Regular bowel movements typically imply a healthy gut. The key word here is “regular,” which can vary from person to person. For some, regularity might mean a bowel movement every day, for others, it might be every other day. What’s important is that there’s consistency in your routine. Consistency and regularity in bowel movements signify a healthy digestive system. 
  2. Absence of Uncomfortable Symptoms: If you’re free from chronic bloating, gas, constipation, diarrhea, or heartburn, this is generally a sign of a well-functioning digestive system and a balanced gut microbiota.  
  3. A Well-Regulated Immune System: A healthy gut microbiota interacts with immune cells to help regulate the immune response. Therefore, not becoming sick frequently might indicate that your gut health is in a good state. Frequent illnesses, on the other hand, might indicate an imbalanced gut, as a healthy microbiome plays a crucial role in immune function
  4. Good Sleep: There is a two-way relationship between sleep and gut health. A balanced gut microbiota can influence the body’s sleep-wake cycle, help maintain a normal sleep pattern, and enhance sleep quality. Regular, restful sleep might indicate a balanced gut microbiome. 
  5. Healthy Skin: There is a complex relationship between gut health and skin health, but they communicate and affect one another via the gut-skin axis. Skin issues like eczema may be associated with a gut imbalance. Clear, healthy skin can be a sign of a healthy gut. 

Signs and Symptoms of an Unhealthy Gut 

Contrarily, there are also signs and symptoms that may indicate an unhealthy or imbalanced gut microbiome. These may include

  1. Digestive Issues: Chronic bloating, gas, constipation, diarrhea, or heartburn may all be signs of an imbalanced gut. These symptoms indicate that food is not being properly broken down or that harmful microbes might be present in your gut. 
  2. Food Intolerances: If you have difficulty digesting certain foods or experience symptoms such as gas, bloating, abdominal pain, or diarrhea after eating certain foods, it may indicate an issue with your gut bacteria. Difficulty digesting certain foods can be a sign of a gut imbalance. 
  3. Poor Sleep and Constant Fatigue: Disruption in the gut microbiota can affect your sleep cycle, leading to poor sleep and constant fatigue. Poor sleep can further lead to other health problems, including mental health issues. 
  4. Unintended Weight Changes: Unexplained weight loss or weight gain, despite not making significant changes to your diet or physical activity levels, may be a sign of an imbalanced gut. An unhealthy gut can affect the body’s ability to absorb nutrients, regulate blood sugar, and store fat. 
  5. Skin Irritation: Skin conditions like eczema, acne, or rosacea may be related to gut inflammation or a damaged gut. Inflammation in the gut caused by poor diet or food allergies can cause certain skin conditions. 
  6. Autoimmune Conditions: Recent research suggests that an imbalanced gut may increase systemic inflammation and alter the proper functioning of the immune system, which can lead to autoimmune diseases. 

8 Ways to Improve the Gut Microbiome, the Population of Health-Promoting Bacteria in the Gut 

Fiber First: Choose Natural Prebiotic-Rich Foods 

When it comes to fostering a healthy gut microbiome, fiber is your best friend. It plays a fundamental role in gut health as it feeds the beneficial bacteria, promoting their growth and activity. This nurturing relationship is where prebiotics come into play. 

Prebiotics are types of dietary fiber that act as food for your gut bacteria. They resist digestion in the upper gastrointestinal tract and reach the colon intact, where they are fermented by the gut microbiota. This fermentation process results in the production of short-chain fatty acids (SCFAs), such as butyrate, propionate, and acetate, which have numerous health benefits, including anti-inflammatory effects and strengthening the gut barrier. 

While it’s true that not all types of fiber function as prebiotics, many fiber-rich foods are high in prebiotic fiber. Foods rich in prebiotic fiber include fruits, vegetables, legumes, and whole grains. These foods provide the double benefit of offering a diverse range of fibers to feed different types of gut bacteria and also deliver other health-promoting nutrients. 

At the same time, it’s not just fiber that serves as a prebiotic. Other non-fiber nutrients, such as polyphenols found in foods like berries, tea, and dark chocolate, can also act as prebiotics, feeding beneficial gut bacteria. 

In essence, a fiber-first approach focusing on prebiotic-rich foods can help cultivate a thriving gut microbiome, enhancing the abundance and diversity of beneficial bacteria. 

Embrace Fermented Foods 

Fermented foods, while often associated with probiotics, don’t always deliver these beneficial bacteria in large quantities. This is because some fermentation processes, particularly those involving heat or certain preservation methods, may kill the probiotic organisms

Nevertheless, fermented foods are still a valuable asset for a healthy gut. While the probiotic content can vary, many fermented foods are rich in prebiotics. Prebiotics, as described above, are types of fiber that feed the beneficial bacteria in your gut, stimulating their growth and activity. 

Furthermore, the fermentation process can make certain nutrients more bioavailable, meaning they are easier for your body to absorb and utilize. This is a significant advantage as it helps maximize the nutritional benefit of these foods. 

Fermented foods like yogurt, kefir, sauerkraut, kimchi, and kombucha also contain bioactive compounds produced during the fermentation process, which can have additional health-promoting effects. 

Multiple studies have found benefits of fermented foods on gut health. For example, consuming yogurt is associated with improved lactose digestion, enhanced immune responses, and may even provide protection against certain types of gastrointestinal diseases. Other fermented foods, like kefir and kimchi, have been linked to a range of health benefits, from improved digestion and inflammation reduction to enhanced immune function. 

To summarize, incorporating a variety of fermented foods into your diet can enrich your gut microbiome, making nutrients more bioavailable, and potentially improving your overall health. 

Stress Less, Flourish More 

Stress management is a crucial yet often overlooked aspect of promoting a healthy gut microbiome. Somewhat recent scientific advances have shed light on the bidirectional relationship between the gut and the brain, aptly termed the “gut-brain axis”. 

Chronic stress can disrupt this delicate balance, leading to alterations in the gut microbiota, which in turn can influence mental health, mood, and cognitive function. Additionally, stress-induced alterations to the gut microbiome can compromise the intestinal barrier, leading to increased gut permeability, sometimes referred to as “leaky gut,” which has been associated with numerous health problems. 

Multiple studies have shown that practices aimed at reducing stress, such as mindfulness, yoga, and regular exercise, can positively influence the gut microbiome. A study published in the journal Brain, Behavior, and Immunity showed that mindful meditation reduced inflammatory biomarkers, which may have positive effects on the gut microbiome. 

Regular physical activity has also been associated with increased diversity and stability of the gut microbiota, which is a key marker of gut health. 

Sleep, another vital aspect of stress management, also plays a significant role in maintaining a healthy gut. Sleep deprivation or irregular sleep patterns can disrupt the gut microbiota, while conversely, a healthy gut microbiome can promote better sleep. 

In short, managing stress through mindfulness practices, exercise, and maintaining regular sleep patterns can significantly contribute to a healthier and more balanced gut microbiome. 

Get Moving: The Power of Exercise in Shaping Your Gut Health 

The potent influence of physical activity on health is well-established, but recent findings reveal that its benefits extend to our gut microbiome as well. Exercise can enhance the diversity and richness of our gut bacteria – key indicators of gut health. 

Studies have found that individuals who lead physically active lives have a more diverse gut microbiota than those who are sedentary. This diversity can help improve the resilience and functional capacity of the microbiota, aiding in digestion, vitamin synthesis, and protection against harmful pathogens. 

Exercise also aids in reducing inflammation, improving immune function, and enhancing the strength of the intestinal barrier – all factors that contribute to a healthy gut. 

Research comparing professional athletes to controls found that the athletes, who engaged in long-term, high-intensity exercise routines, had a more diverse gut microbiota, highlighting the potential of physical activity in modulating gut microbiota. 

While more research is needed to determine the ideal types and amounts of exercise for optimal gut health, regular moderate-intensity exercise appears to be beneficial. 

Adding regular exercise to your routine can promote a healthier and more diverse gut microbiome, contributing to better overall health. 

Sleep Well to Feed Your Gut 

Sleep is far more than a mere period of rest. It is a critical time when your body carries out vital repair, recovery, and cognitive processes. One of the lesser-known roles of sleep is its effect on your gut microbiome. Sleep can significantly influence the diversity and composition of your gut bacteria. 

Research suggests that people who are sleep-deprived or have disrupted sleep patterns often have an altered gut microbiota. For example, a study published in Molecular Metabolism found that just two nights of partial sleep deprivation could result in changes to the gut microbiota, including decreased bacterial diversity. 

Conversely, a healthy gut microbiome can also promote better sleep. Emerging research indicates that a balanced gut microbiome can enhance sleep quality by producing and regulating various substances involved in the sleep-wake cycle, such as melatonin and serotonin. 

The National Sleep Foundation recommends that adults aim for 7 to 9 hours of sleep per night. Consistent, high-quality sleep can support your gut microbiome and contribute to overall health. 

Maintaining regular sleep patterns, practicing good sleep hygiene (such as maintaining a cool, dark, quiet sleep environment and establishing a relaxing pre-sleep routine), and prioritizing sufficient sleep can significantly contribute to a healthier and more balanced gut microbiome. 

Quench Your Gut by Staying Hydrated 

While it’s widely known that staying hydrated is crucial for overall health, the impact of hydration on the gut microbiome is less commonly discussed. However, adequate hydration plays an essential role in promoting a healthy gut and supporting optimal microbiome function. 

Water is integral for digestion. It helps break down food so your body can absorb nutrients, and it softens stool, which helps prevent constipation. Chronic constipation can disrupt the balance of bacteria in the gut, leading to a decreased diversity of gut microbiota. 

Moreover, staying hydrated helps maintain the mucus lining in the intestines. This mucus lining is one of the first lines of defense against the ‘bad’ gut bacteria and toxins, and it’s also home to many beneficial bacteria. Dehydration can disrupt this protective layer, potentially leading to a range of gut issues, from simple discomfort to more serious conditions like increased gut permeability

There isn’t a one-size-fits-all approach to water consumption, as the ideal amount depends on individual factors like age, sex, weight, physical activity level, and overall health. However, a general guideline is to aim for at least 8 cups (64 ounces) of water per day. This can come from beverages like water and tea, as well as from water-rich foods like fruits and vegetables. 

In short, adequate hydration supports digestion, maintains the protective mucus lining of your gut, and promotes a healthy, balanced gut microbiome. 

Plant Power for Your Gut: Trade Animal-Based for Plant-Based Foods 

The food choices we make significantly influence our gut microbiome’s composition and function, and thus our overall health. Notably, a plant-based diet, rich in fruits, vegetables, legumes, whole grains, nuts, and seeds, can provide exceptional benefits to your gut microbiome. 

Plant-based diets are rich in dietary fiber, which acts as a prebiotic, providing the necessary nourishment for beneficial gut bacteria to thrive. This fiber-driven nourishment results in the production of short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate, which have a host of health benefits. These SCFAs help maintain gut barrier integrity, reduce inflammation, and regulate the immune system. 

Moreover, plant-based diets typically offer a wider variety of foods, which can help increase the diversity of the gut microbiota – a key marker of gut health

In contrast, diets high in animal-based foods, particularly red and processed meats, have been associated with negative alterations in the gut microbiota. For instance, a study published in the journal Nature showed that a diet high in animal-based products could lead to an increase in bile-tolerant bacteria and a decrease in bacteria that metabolize dietary plant polysaccharides. 

However, it’s important to note that incorporating plant-based foods into your diet doesn’t necessarily mean you must completely exclude animal-based foods to achieve good gut health. It’s about maintaining a balance that leans heavily toward plant-based foods, which can help sustain a healthier and more diverse gut microbiome. 

Choose PUFAs Over Saturated Fats 

When it comes to fats and the gut microbiome, not all fats impact the gut in the same way. The type of fat you consume can significantly influence the composition and function of your gut bacteria, affecting your overall health. 

Saturated fats, primarily found in animal-based foods and some plant oils, have been linked to negative changes in gut microbiota. Studies show that diets high in saturated fats can reduce the diversity of gut bacteria, promote the growth of harmful bacterial strains, and increase gut inflammation. 

On the other hand, polyunsaturated fatty acids (PUFAs), particularly omega-3 fatty acids, appear to have a positive effect on the gut microbiome. Omega-3 fatty acids, found in fatty fish, walnuts, flaxseeds, and chia seeds, can increase the abundance of beneficial gut bacteria and reduce inflammation. 

For instance, a study published in The Journal of Nutritional Biochemistry found that a diet rich in omega-3 fatty acids could increase the abundance of beneficial bacteria, such as Bifidobacterium, which is known to promote gut health. 

This doesn’t mean you should completely eliminate saturated fats from your diet but rather maintain a balance favoring PUFAs, especially omega-3 fatty acids. It’s important to remember that moderation and diversity in diet are key to supporting a healthy and diverse gut microbiome. 

Microbiome & Gut Health FAQs 

How can I increase good bacteria in my gut quickly? 

The fastest way to increase beneficial bacteria in your gut is by adjusting your diet. Consuming a variety of fiber-rich, plant-based foods can provide the necessary prebiotics that these bacteria need to thrive. Fermented foods, like yogurt, sauerkraut, and kefir, can also help increase beneficial bacteria. Diet, in combination with probiotic supplements and your doctor’s support, can help to swiftly re-establish your microbiota balance.  

What eliminates bad bacteria in the gut? 

A diet rich in fiber, plant-based foods, and fermented foods can help maintain a healthy balance of gut bacteria and limit the growth of harmful bacteria. Regular physical activity, stress management, adequate hydration, and sufficient sleep can also contribute to a healthy gut environment. 

How do you build a population of good bacteria in your body? 

Building a population of good bacteria in your body is similar to increasing gut bacteria. A balanced diet rich in fiber, plant-based foods, and fermented foods, along with healthy lifestyle habits, will create an environment in which beneficial bacteria can flourish.

What is the fastest way to restore gut microbiome? 

A diverse diet rich in plant-based foods, especially those high in fiber, is one of the fastest ways to restore gut microbiome. Incorporating probiotic-rich foods like yogurt and kefir, or prebiotic-rich foods such as onions, garlic, and bananas can also help restore gut microbiome. A diverse diet rich in plant-based foods, especially those high in fiber, is one of the fastest ways to restore gut microbiome. Incorporating probiotic-rich foods like yogurt and kefir, or prebiotic-rich foods such as onions, garlic, and bananas can also help restore gut microbiome. 

How long does it take to “fix” an unhealthy gut? 

The timeline for improving gut health varies for each individual and depends on several factors, such as diet, lifestyle, and the existing state of gut health. Some studies suggest that noticeable changes can occur within a few days of making dietary changes. However, for a significant and lasting improvement, consistent healthy habits over weeks to months may be required. 

What promotes the health of “good” gut bacteria? 

A diet rich in diverse, fiber-rich foods can promote the health of “good” gut bacteria. This includes whole grains, legumes, fruits, and vegetables. Fermented foods, which are rich in probiotics, also promote good gut bacteria. Lifestyle factors such as regular exercise, adequate sleep, proper hydration, and stress management also support gut health. 

How do I get my gut bacteria back to normal after an illness or antibiotics? 

Antibiotics can disrupt the gut microbiota. Post-antibiotics, you can help restore your gut microbiota by consuming a diet rich in fiber and fermented foods. Additionally, ensure you stay hydrated, get enough sleep, manage stress, and engage in regular physical activity. In some cases, a healthcare provider might recommend a probiotic supplement. 

Main Takeaways 

Your gut microbiome is a dynamic and vital aspect of your health, with far-reaching effects that extend beyond digestion. It’s integral to your immune function, mental health, metabolic processes, and even your body’s capacity to process nutrients from food. Enhancing your gut microbiome naturally isn’t just about what you eat—it’s about how you live. 

A well-rounded approach to gut health incorporates diverse, fiber-rich, plant-based foods and a moderate intake of healthy fats. However, our gut microbiome is influenced by more than just our diet. Factors like regular physical activity, proper sleep, adequate hydration, and effective stress management are equally critical. These lifestyle factors can contribute to a healthier, more balanced gut microbiome, fostering an environment where beneficial bacteria can flourish. 

By adopting these strategies, we can cultivate a healthier gut microbiome without relying on supplements. A healthy gut microbiome supports digestive health and also contributes to overall wellbeing, from mental health to disease prevention. Remember, small but consistent changes can have a significant impact over time, so take those initial steps toward improving your gut health today. 

The journey toward optimal gut health is a marathon, not a sprint. Every positive choice you make, every balanced meal you eat, every workout you complete, and every good night’s sleep you get brings you one step closer to better gut health. And better gut health brings you one step closer to better overall health. 

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