Your gut microbiome is your body’s frontline defense against disease. But, when harmful bacteria start to outnumber the beneficial ones, you may notice issues like bloating, digestive discomfort, and even weakened immunity. Learning how to starve bad gut bacteria through targeted diet and lifestyle changes helps rebalance your microbiome, support beneficial microbes, and promote a healthier, more resilient gut.
What are Pathogenic Bacteria?
Simply put, pathogenic bacteria are bacteria that can cause disease. Though they are usually harmless in small amounts, they can propagate by stealing nutrient sources from the rest of the microbiome and hijacking our genetic regulatory signals1.
Pathogenic bacteria are smart. Rather than fighting individually against the whole microbiome, they stay silent in our microbiome until they reach a large enough population, at which point they group together and spread disease.
They do this through a process called quorum sensing, in which they regularly send out special molecules (called autoinducers) as signals to be picked up by the rest of the pathogenic population. Once enough of these signals are in the microbiome, the pathogenic bacteria know that their population is large enough2, 39.
As a community, these bacteria can now:
- Evade immune responses by secreting toxins
- Target and eliminate specific competitors more effectively
- Create a biofilm (a cohesive “glob” of bacteria and carbohydrates) that is more resistant to stressors such as pH, temperature, and antibiotics2
What Do Harmful Bacteria Do in the Gut?
As mentioned above, one of the biggest issues with pathogenic bacteria is the toxins they produce. Here are some different types of toxins released by pathogenic bacteria and their negative effects:
Endotoxins, or lipopolysaccharides (LPS), are harmful substances found inside certain bacteria. These toxins are released into the gut when the bacteria die and break down, not while they are alive.
An abnormally high level of endotoxins, known as metabolic endotoxemia, increases the risk of diet-induced obesity due to insulin resistance. Insulin usually helps inhibit fat synthesis and regulates satiety (feeling full), but endotoxins reduce insulin’s effectiveness3.
Exotoxins are proteins secreted by harmful live bacteria that can disrupt natural cellular processes, leading to health issues like inflammation or infections. Diseases caused by exotoxins include:
- Colitis
- Typhoid
- Diphtheria
- Botulism
Exotoxins can also interfere with immune responses. Neutrophils, a type of immune cell, set out web-like “traps” to confine pathogenic bacteria and prevent them from spreading. However, a type of pathogenic bacteria called Streptococcus pyogenes releases exotoxins that prevent neutrophils from setting these traps.
This is just one example of the many interactions between pathogenic bacteria and immune cells. Other pathogenic strains have their own ways to evade immune responses and thrive4.
When pathogenic bacteria are present in high concentrations, they can negatively impact the microbiome by outcompeting beneficial bacteria. This can diminish many of the positive effects of a diverse microbiome, including:
- Decreased breakdown of foods indigestible by humans, leading to less nutrient absorption
- Reduced release of beneficial molecules produced by probiotic bacteria, such as short-chain fatty acids
- Weakening of the mucus gut barrier, which regulates toxins entering and exiting the gut
- Decreased ability of the gut to alert the immune system in case of infection
Not only can pathogenic bacteria outcompete probiotic bacteria, but some can also eliminate beneficial bacteria using cellular weaponry. They do this by stabbing competitors with a needle-like structure and injecting them with toxic proteins, thus killing them1, 38.
Finally, pathogenic bacteria can escape from the gut and infect the rest of the body through a process called translocation. When these bacteria adhere to the gut barrier, they can increase its permeability and pass through into the circulatory system. This can lead to infections not only in the gut but also throughout the body6.
How Can You Fight Off Bad Bacteria in the Gut?
Probiotic bacteria, when consumed orally, can strengthen the gut barrier by boosting mucus secretion and other barrier proteins. Mucus acts as a physical blockade between the inside of the gut and the outside, preventing pathogenic bacteria from escaping into the rest of the body7.
Probiotic bacteria also communicate with immune cells to prevent infections. They produce cytokines and chemokines, which are signalling molecules that activate immune cells and direct them toward fighting infections7.
Just as pathogenic bacteria outcompete probiotic bacteria when in large amounts, probiotic bacteria can also keep pathogenic bacteria in check through competition. A healthy, balanced microbiome can effectively outcompete a larger number of pathogenic bacteria.
Some probiotics also release organic acids and bacteriocins, which are antimicrobial compounds. These substances directly suppress the growth of pathogenic bacteria in the gut, further enhancing the body’s defense against harmful microbes8.
It’s essential to consume a mix of different probiotics to maintain a balanced gut microbiome. Relying on a single probiotic species may not provide enough protection against various pathogens.
The two main types of probiotics crucial for safeguarding our body against pathogenic bacteria are Lactobacillus and Bifidobacterium. For example, Lactobacillus fermentum can competitively exclude Campylobacter jejuni, while Lactobacillus gasseri can do the same with Helicobacter pylori.
A diverse microbial community also naturally competes with bad bacteria for food, helping to keep bad bacteria populations in check9.
Taking prebiotics and incorporating fiber into your diet along with probiotics is necessary to maintain a diverse gut microbiome. Without prebiotics, your probiotics won’t be able to fight off bad bacteria.
Regular use of probiotics and prebiotics is crucial to protect our gut from pathogenic bacteria, rather than only taking probiotics when an infection arises. A healthy microbiome prevents disease, rather than curing it9.
Fighting Pathogenic Bacteria is Not Enough
In addition to pathogenic bacteria, we must also consider imbalances in our gut microbiome that can lead to chronic disorders, potentially detrimental to our long-term health. Maintaining a balanced microbiome is essential not just for warding off infections but also for preventing chronic conditions.
What is Gut Dysbiosis?
Gut dysbiosis refers to an imbalance in the diversity of gut bacteria10. One key indicator of this is the Firmicutes/Bacteroidetes (F/B) ratio. Firmicutes and Bacteroidetes are the two most common types of bacteria in your gut, making up 90% of all gut bacteria11. An irregularly high F/B ratio can lead to chronic disorders that impact your long-term health.
A high F/B ratio is often linked to obesity12. Studies from various countries show that obese individuals tend to have higher F/B ratios13, 14, 15, 16, 17. This is because Firmicutes bacteria are super efficient at extracting calories from food, which promotes weight gain18. They release enzymes that specifically target fat molecules.
Firmicutes bacteria also produce lots of short-chain fatty acids (SCFAs) that boost lipid and cholesterol synthesis after breaking down dietary fats. These SCFAs also slow down gut motility, giving the gut more time to absorb energy from fatty foods19, 20, 21.
In early human history, this relationship was beneficial, allowing for greater caloric absorption from meats and fats. But today, with more sedentary lifestyles, it often leads to weight gain.
The Damaging Effects of Western Diets
A Western diet, high in fats and sugars and characterized by frequent snacking, can harm our gut. The Western diet is broadly characterized with high consumption of the following foods:
- Refined sugars such as sweets, soft-drinks
- Animal fats
- Processed meats, especially red meat
- Refined grains
- Dairy products
- Pre-packaged and fried foods
- Food additives such as emulsifiers and sweeteners
These foods disrupt gut health by compromising the gut’s mucus lining and increasing gut permeability, a condition often referred to as “leaky gut.” This disruption occurs because excessive consumption of unhealthy fats and sugars can lead to inflammation and damage the cells that form the protective barrier of the gut.
This damage weakens the gut’s barrier, allowing harmful substances to leak into the bloodstream. One of these substances (as mentioned above) is lipopolysaccharides (LPS), which come from certain bacteria in the gut. When LPS enter the bloodstream due to a weakened gut barrier, they can trigger widespread inflammation throughout the body. This condition, known as endotoxemia, is linked to serious health problems like obesity, diabetes, and heart disease.
The balance of fatty acids is another problem. Omega-6 fatty acids, abundant in Western diets, promote inflammation, while omega-3 fatty acids—commonly found in fish and flaxseeds—are anti-inflammatory. A healthy diet should contain more omega-3s to keep inflammation in check, but Western diets often have too many omega-6s, further increasing gut problems.
Frequent snacking in Western diets also plays a role. Constant eating doesn’t give the gut a chance to rest or heal, disrupting the natural process where the gut lining regenerates during fasting periods. This continuous activity prevents the gut from healing and recovering, making inflammation worse over time41.
On the other hand, a fiber-rich, plant-based diet helps keep the gut healthy by encouraging the growth of good bacteria. These beneficial bacteria help repair the gut lining, reduce inflammation, and maintain overall gut health.
What Diet Should You Follow to Prevent Dysbiosis?
Eating a diet rich in whole, fiber-rich plants foods supports a healthier gut microbiome and helps prevent dysbiosis.
Foods To Eat
- Whole fruits and vegetables, such as bananas, berries, broccoli.
- Legumes and pulses, like chickpeas, lentils, butter beans.
- Whole grains, like oats, quinoa and buckwheat.
- Nuts and seeds, like walnuts, almonds and flaxseeds.
- Fermented foods, like miso, sauerkraut and kimchi.
A diet high in plant-based foods encourages the growth of beneficial bacteria like Bacteroidetes (lowering the F/B ratio). These bacteria excel at breaking down complex carbohydrates, providing energy and promoting a balanced gut environment. Studies have shown that populations consuming plant-dominated diets, such as those in Burkina Faso, have higher levels of Bacteroidetes compared to those on Western diets27.
Maintaining a balanced F/B ratio through a fiber-rich diet can reduce low-grade inflammation and alleviate symptoms of chronic conditions like irritable bowel syndrome (IBS), obesity, and chronic fatigue syndrome28. Moreover, incorporating moderate amounts of healthy fats from sources such as olive oils, legumes, and nuts can further support overall well-being29.
Foods To Avoid
- Ultra-processed foods, such as ice-cream, soft drinks, ready meals and meal replacement shakes.
- Refined sugars and artificial sweeteners, such as high fructose corn syrup, sucralose, and aspartame.
- Red and processed meats, such as beef, pork, lamb, veal, goat, hot dogs, hams and canner meat.
- Foods high in unhealthy fats, such as bacon, fatty meat cuts and heavy cream.
- Excess sodium, such as in packaged snacks, canned soups and processed meats.
Avoid or minimize intake of ultra-processed foods, refined sugars, red and processed meats, and foods high in unhealthy fats, as these can disrupt the gut microbiota and promote the growth of harmful bacteria.
The Role of the Gut Microbiome in Food Cravings
Obviously, shifting to a healthier diet isn’t always straightforward. We’ve all had those sudden cravings for junk food, whether it’s a cheeseburger, fries, or something else. Part of the reason why this happens lies in the intricate relationship between your gut microbiome and food cravings.
When certain bacteria don’t receive their preferred food, they release toxins in the gut that can cause discomfort or even pain by binding to cell receptors in the gut lining. On the flip side, other bacteria release neurotransmitters like dopamine (the feel-good hormone), which can lead to cravings for the foods that feed them31.
The vagus nerve, which connects the gut to the brain, transmits signals that influence emotional responses and food cravings. Studies indicate that individuals with different food preferences, such as those who crave chocolate, have distinct gut microbiomes. Consuming a diet that supports a healthy microbiome can reduce cravings for unhealthy foods and foster a preference for nutrient-dense, fiber-rich options25, 30, 32.
Specific Probiotics To Regulate Imbalances
A high F/B ratio can be managed by consuming Lactobacillus and Bacillus bacteria, as well as Saccharomyces yeasts. For instance, Lactobacillus rhamnosus and Lactobacillus sakei were found to reduce F/B ratios and fat mass in obese mice by releasing conjugated linoleic acid (CLA)33.
Lactobacillus paracasei, paired with a xylooligosaccharide prebiotic, reversed the negative effects of a high F/B ratio in obese mice. This highlights the importance of prebiotics in addressing gut health issues by providing nourishment for probiotic bacteria34. Similarly, Saccharomyces boulardii also showed positive effects on obesity and the F/B ratio in a different study35.
For an abnormally low F/B ratio, certain strains of Lactobacillus and Bifidobacterium bacteria can help regulate it. Lactobacillus plantarum boosted Firmicutes bacteria, suppressed Bacteroidetes bacteria, and reduced inflammation by releasing nitrogen oxide36. Bifidobacterium bifidum had similar effects and promoted antioxidant production. These two strains are commonly combined for many patients with inflammatory bowel disease (IBD)37.
Key Takeaways
- Pathogenic bacteria release toxins, displace beneficial bacteria, and cause infections, leading to health issues.
- Bacteria have specific dietary needs; deprivation can cause discomfort or cravings by releasing toxins or producing dopamine.
- Incorporating probiotics and prebiotics can help you introduce beneficial bacteria and maintain balance in the gut.
- A diverse microbiome is crucial for preventing chronic illnesses linked to gut dysbiosis.
- High levels of Firmicutes can lead to fat storage and weight gain. A Western diet increases the Firmicutes/Bacteroidetes (F/B) ratio.
- A plant-based, fiber-rich diet helps maintain a healthy gut microbiome.
- Probiotics like Lactobacillus, Bacillus, and Bifidobacterium support gut health and prevent dysbiosis.