How to Starve Bad Gut Bacteria and Improve Gut Flora

If you have been influenced by all the media talk about taking probiotics and eating loads of yogurt to improve your gut flora, you are not alone. Gut flora and its massive role in our general health are relatively recent discoveries, but the evidence to support this is solid. 

In simple terms, flora/microbiome/microbiota refers to all the microorganisms that inhabit a certain part of the human body. These include bacteria, viruses, fungi, eukaryotes, and archaea. Out of these, bacteria are the most obvious microbial component.

Besides, when it comes to the gut, bacteria beat other microbes both in terms of number and variety. It is estimated that there around 1000 species of bacteria live in our gut and the total number of bacteria living in the gut is 100 trillion.

Yes, you read that right and this number is around 10 times the number of human cells in the gut.

We know bacteria for being bad for human health, but in their normal composition, gut bacteria have a mutualistic relationship with humans. They themselves survive on nutrients from humans but benefit the host by performing a number of important functions. 

However, the normal composition of the gut bacteria is susceptible to a number of factors including diet and the general well being of the host among others. Therefore, any disruption to these factors can give rise to an imbalance between the good and bad bacteria.

This then adversely affects the function gut bacteria perform and thus badly influences the general well being of the host.

In this piece here, we will go over all there is to know about gut bacteria and what you can do to keep them in an optimal balance and get the best out of them. So, let’s get started.

The Importance of a Healthy Gut and Gut Flora

As mentioned, our gut is host to a wide variety of bacteria. Out of these, a majority of the gut microbiome is found in the large intestine.

This community of bacteria lives in the intestine and is separated from the human cells by a thick layer of mucus. As long as this thick barrier of mucosal lining is intact, the bacteria don’t directly come into contact with our intestinal cells.

In fact, these bacteria along with immune cells in the gut fight against any pathogenic microorganisms. Other than this, they play an important role in digestion where they help digest any undigested food reaching the intestines.

the right foods can help you heal a leaky gut problem

Out of these good gut bacteria, lactobacillus species anaerobically respire and produce lactic acid as a waste product. Lactic acid plays an important role in keeping the pH of the gut acidic.

This level of pH means that pathogen bacteria can’t thrive in the gut. Lactobacillus species also prevent yeast growth in our gut, the overgrowth of which can hamper the digestive system. 

In addition to this, studies have found that these bacteria play their role in metabolism, immune system, and production of essential bio-compounds including vitamins and hormones.

However, if the normal composition of this bacterial community is disrupted by any means, the normal function of these bacteria gets disturbed.

This imbalance of good and bad bacteria is called dysbiosis and has been associated with diabetes, inflammatory bowel disease, obesity, and even some cardiovascular diseases.

Dysbiosis can happen due to a number of reasons including aging, use of antibiotics, eating a diet low in fibers because the gut microbiome thrives on complex carbohydrates, any chronic disease, and an unhealthy lifestyle.

So, the main question is how we can keep the gut microbiome in an optimal diversity and keep the bad bacteria at a minimum and improve the good bacteria. 

The role of the intestines in our overall health

Above, we discussed how good gut bacteria is crucial in keeping the pathogens at bay and maintaining the intestinal conditions optimal for bodily functions. Their importance becomes even more magnified if we consider the role intestines play in our overall health.

We know that well-working intestines break down our food into different micro and macro-nutrients. These are then absorbed and carried by the bloodstream to anywhere they are needed in the body. This main function of the intestines has been known for a long time.

However, different studies over the last few decades have linked gut health with the immune system, autoimmune diseases, mental health, skin conditions, and even cancer.

In addition to this, one of the biggest recent discoveries in medical science has been the gut-brain axis. This essentially refers to the biochemical signaling that occurs between the gut and the central nervous system.

In this, the gut bacteria directly and also by stimulating the gut’s immune cells secrete many chemicals including neurotransmitters and cytokines. Out of these, serotonin and leptin are the most important ones.

Serotonin is a hormone and has its role in stabilizing our mood, feelings of well-being, and happiness. And leptin works to regulate our body weight.

These chemicals are released in the blood and they affect brain function including cognitive function and limbic function. The brain, on the other hand, through the vagus nerve communicates with the gut and regulates its function.

So, any disturbance to this gut-brain axis not only disrupts our moods and mental functions but also can result in disturbance to gut function.

Simply put, any such disturbances can give rise to both brain and gut disorders including IBS, schizophrenia, Alzheimer’s disease, and depression.

In short, the intestines play a crucial role in our general health and wellbeing, and gut microbiota is at the forefront of the gut’s normal function.

good bacteria is essential to a healthy gut and gut heath improvements

What are the symptoms of bad bacteria in the stomach?

We hinted at what could happen if the optimal balance of gut microbiota is disturbed. In addition, we discussed how the right balance between good and bad gut bacteria is beneficial to our overall well being.

In this section, we will discuss how you can detect if you have an overgrowth of bad bacteria in your gut and will go over symptoms that indicate such a situation.

1. Digestive Disturbances

The gut flora has a major role in the proper functioning of our digestive system. Thus, if the bacterial balance is tilted in the wrong direction, digestive disturbances are the most common symptoms. These include frequent gas and bloating.

In essence, a person with bad gut bacteria will feel bloated most days of the week. Moreover, symptoms of diarrhea alternating with constipation, acidity, and constipation are also common.

If most of these symptoms occur simultaneously, they are now grouped under irritable bowel syndrome or IBS. If bad bacteria becomes a chronic problem, it can also lead to food sensitivities, food intolerances, and chronic bad breath. 

2. Psychological Symptoms

We talked about how gut flora has a central say in the workings of the gut-brain axis and the release of neurotransmitters. Thus, any disruption in the production of these neurotransmitters results in psychological symptoms.

These include hampered mood, difficulty to think and concentrate, anxiety, and even depression. 

3. Skin Symptoms

Because of the bacteria directly affecting immune cells, any disturbance can lead to local or central immune dysfunction. This results in altered immune responses with allergic and inflammatory skin conditions causing eczema, acne, and skin irritation.

Somewhat smaller studies have shown alterations in the gut microbiota also causing conditions such as psoriasis, rosacea, and impaired wound healing.

4. Autoimmune Conditions

Dysbiosis has also been linked to autoimmune conditions such as rheumatoid arthritis, type 1 diabetes, multiple sclerosis, and autoimmune liver disease. 

5. Sugar Cravings

The unhealthy dietary choices of a high-sugar, high-fat, and low-fiber diet can feed the bad bacteria. These bacteria thrive on sugar and can cause increased sugar cravings.

They do this by altering the taste receptors, affecting appetite hormones, and stimulating the vagus nerve which can lead to overeating.

It’s obvious that a bad gut can cause a variety of symptoms. However, before you blame any of your symptoms on a bad gut, it is advised to pay your doctor a visit to better establish the cause.

Nonetheless, efforts to keep your gut in optimal diversity is always going to help your health in general.

This post may contain affiliate links. My full disclosure policy is sort of boring, but you can find it here.

How to Get Rid of Bad Bacteria in the Gut?

Now that we have established how bad gut bacteria adversely affect our health, the next logical question to ask would be, “what we can do to keep bad bacteria in check”.

The best you can do in this regard is to improve your eating habits. Below, we will discuss the foods you need to avoid as well as the foods you need to consume to keep your gut microbiota in an optimal composition. This in essence means feeding good gut bacteria and starving bad gut bacteria.

fermented foods like sauerkraut are great for a healthy gut

What foods kill bad bacteria in the gut?

Foods that improve our gut flora as a whole and kill bad bacteria can be divided into two main categories of probiotics and prebiotics. We will talk about both of these in more detail.

1. Probiotics – Live Bacteria and Yeasts

One way of improving our gut flora or tilting the balance towards good bacteria is by eating probiotics. Probiotics are usually fermented foods cultured with live bacteria and/or yeasts.

However, not all fermented foods qualify as probiotics. To be considered a probiotic, food should have sufficient living bacteria that can survive food processing in our bodies. Two main species of live bacteria/yeast found in probiotics are:

Lactobacillus rhamnosus – occurs naturally in the gut and helps fight IBS symptoms, diarrhea and cavities,

Saccharomyces boulardii – is a type of yeast and helps with rotaviral diarrhea in children, Crohn’s disease, ulcerative colitis, and IBS.

In addition to this, probiotics also aid digestion, ease vaginal infections and skin conditions and fight off urinary infections.

Besides fermented foods, probiotics are also found in dietary supplements.

They are also added to other foods and beverages such as Granola bars, protein shakes, and fruit juices. Some of the commonly known probiotics include:

  • Yogurt
  • Kefir
  • Kombucha
  • Sauerkraut
  • Pickles
  • Miso
  • Tempeh
  • Kimchi
  • Sourdough bread
  • Some cheeses

2. Prebiotics – Food for Good Bacteria

Prebiotics can be called food for bacteria as they help stimulate certain bacterial populations to multiply and survive in the gut. High-fiber foods are rich sources of prebiotics and human digestive enzymes are not able to break them down.

They make it to the large intestine where they are fermented by gut bacteria. Prebiotics are found in a variety of food items including but not limited to:

Food Sources for Prebiotics

foods best for gut health

In addition, some packaged foods contain ingredients like inulin and oligosaccharides which are also classified as prebiotics.

It must be noted that most people don’t eat enough fiber. It is estimated that an average American consumes about 15 grams of fiber per day, while the recommendation is 25 to 38 grams of fiber per day. 

When gut microbes consume prebiotics, they produce short-chain fatty acids (SCFAs) such as butyrate, acetate, and propionate, etc. SCFAs nourish the cells that line the gut and have been associated with reducing the risk of certain types of cancer.

ginger kombucha is excellent for a healthy gut

They also enhance calcium absorption and relieve constipation and diarrhea. SCFAs also enter the bloodstream and carry signals to the brain and regulate the immune system and inflammation. 

Foods That Are Terrible For Your Gut Health

In addition to eating gut-friendly foods, we also need to avoid foods that are bad for gut health. Below, we will talk about foods with the highest potential to cause damage to your gut health,

1. Processed Foods 

Processed foods being bad for our health is no secret now and their bad effect on gut health is a major contributor to that reputation. They not only contain added sugars, fats, and salts, which help bad bacteria thrive but they also lose many of their original nutrients during processing. 

Studies have shown that processed foods lack dietary fibers and affect good gut bacteria and their metabolism. With gut microbiota disturbed, which helps us regulate our weight, individuals eating processed foods frequently are more prone to conditions such as obesity, diabetes, and IBS.

2. Animal Proteins

It remains unclear whether the intake of red meat and other animal proteins directly affects gut bacteria, but they are considered bad for gut health. However, it is established that a strictly animal-based diet alters microbial composition within just 24 hours.

Increased intake of animal proteins such as meat, dairy, and eggs have been linked with a higher risk of conditions such as IBS and type-2 diabetes.

3. Genetically-Modified Organisms (GMOs)

The original idea behind GMOs was to cultivate crops that were resistant to pests and diseases. However, besides producing abundant crops, genetically modified foods have been shown to be detrimental to gut health.

For example, one of the herbicides used for GM purposes is glyphosate. Glyphosate gets absorbed in the food and unfortunately once inside the human gut, it acts as an antibiotic and kills only good bacteria

In the US, wheat, corn, and soybean are the most common GMOs, but these methods are used in a whole range of other crops. One way of avoiding GMO foods is to look for 100% organic foods.

This is because US law prohibits the use of genetic engineering in anything that is claimed to be 100% organic.

4. Gluten-Containing Foods

Gluten is a form of protein and is found in grains such as wheat, barley, rye, and spelt. Gluten has been linked to conditions such as celiac disease and dermatitis herpetiformis.

Celiac disease affects only 1% of the population and essentially refers to inflammation of the mucosa lining in the intestine. It has been presumed that people sensitive to gluten have a different gut flora composition and therefore show this different reaction to anything containing gluten.

5.  High FODMAP Foods

FODMAP refers to short-chain carbs and stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols.

These carbs are hard to digest and get used by gut bacteria in the intestine and result in a variety of digestive symptoms in sensitive individuals like gas, bloating, diarrhea/constipation, and stomach pain.

So, any food rich in FODMAP can be terrible for gut health and these include but are not limited to:

  • Milk
  • Wheat
  • Rye
  • Barley
  • Garlic
  • Onion
  • Apples
  • Apricots
  • Peaches
  • Legumes and pulses
  • Dessert wine and rum

It must be noted that high-FODMAP foods badly affect only a small percentage of the total population and are not otherwise detrimental to gut health.

Supplements that help keep your gut balanced

The good news is that nowadays there are a number of health supplements readily available that can optimize your gut health. 

1. Zenwise Health Digestive Supplement – Contains a combination of probiotics, prebiotics, and digestive enzymes that promote healthy digestion. Its natural ingredients like turmeric (which has loads of benefits – some even believe turmeric is good for your hair), ginger, apple pectin, and bladderwrack among others help relieve any digestive symptoms like bloating and gut discomfort.

Zenwise Health Digestive Bliss Bundle - Digestive Enzymes, NO BLØAT, and Travel Size Tin

2. Nutrition Essentials Probiotic Supplement – This certified organic probiotic powder claims to contain 900 billion colony-forming units of probiotics. It fights off any bad bacteria and aids gut function on the whole. Moreover, it is gluten and dairy-free, so people with sensitive guts can benefit from it. On top of it, it comes with a money-back guarantee where you can return it no questions asked.

Probiotics for Women and Men - with Natural Lactase Enzyme and Prebiotic Fiber for Digestive Health - 80%+ More Potent Supplement for Gut Health Support - Vegan Raw Probiotic Formula Made in The USA

3. Doctor Danielle Leaky Gut Repair Supplement – This supplement powder contains nutrients like  L-Glutamine which helps repair any damage to the gut lining and basically starves bad bacteria. It fights off any inflammation and helps symptoms such as bloating, constipation, diarrhea, gas, and cramps.

Doctor Danielle Gut Assist - Leaky Gut Repair Supplement Powder - Glutamine, Arabinogalactan, Licorice Root - Supports IBS, Heartburn, Bloating, Gas, Constipation, SIBO from

4. Florastor Daily Probiotic Supplement – With Saccharomyces boulardii strain in its composition, this probiotic supplement improves your gut flora and restores natural bacterial balance in the gut. 

Florastor Daily Probiotic Supplement for Men and Women – Saccharomyces Boulardii lyo CNCM I-745 (500 mg; 100 Capsules)

How long does it take to kill bad bacteria in the gut?

Our gut is constantly exposed to a variety of elements ranging from toxins to pathogens. On top of that, it has a continuous battle going on between good and bad bacteria in itself. Therefore, any efforts to optimize gut health should be sustained.

We pointed out that the gut microbiome alters within 24 hours if you switch to a strictly plant-based diet or animal-based diet. Therefore, you can expect the results of your efforts in as short as a couple of days.

But, bacteria have a tendency to become dormant if they don’t find favorable conditions. In this, they may find shelter in a biofilm which is a slime layer embedded in the GI matrix and is difficult to penetrate even for strong antibiotics.

So, it takes a sustained effort to establish a healthy gut environment that would gradually starve dormant bad bacteria. Some say this can take up to six months.

Therefore, don’t lose heart if you are not seeing the results of your efforts and just continue healthy habits of eating gut-friendly foods and avoiding gut-damaging foods.

The Takeaway:  You Can Improve Your Gut Flora

Medical science finds it hard to cover the whole scope of gut health and its effects on our overall well being. With the gut-brain axis at the core, it has implications not only on how our food is processed but also affects our mental health.

Gut flora has a mutualistic relationship with our body. They depend on us for providing a favorable living environment and in return play their part in some important functions for us.

However, the normal composition of gut flora is susceptible to a number of factors and keeps on changing. The overall balance between good and bad bacteria determines the state of our gut health.

By better understanding our dietary choices, and their effects on our gut, we can turn our gut flora balance in our favor. But, it is a constant battle and the key is to make sustained dietary and lifestyle changes and never give up.

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If you have a fussy gut, here are some ways to starve out the bad bacteria and encourage good bacteria and good gut health.