How to Get Rid of Bad Bacteria in the Gut

We hear a lot about good and bad bacteria these days. Trying every new ‘friendly bacteria’ food and drink product on the market would be a full-time job. And what about the herbs, teas and plants we’re told get rid of bad bacteria? If we’re increasing our friendly bacteria with a yoghurt drink or sauerkraut, why would we then get rid of them by cooking with oregano—an anti-bacterial herb—for example?

It doesn’t really make sense, until you dig a bit deeper. Read on to find out why blaming bad bacteria for your symptoms is oversimplifying a very complex situation.


Bacteria are good or bad based on their environment
How to get rid of bad bacteria in the gut
How to get rid of bad bacteria in the gut naturally
What are the symptoms of bad bacteria in the stomach?
What foods kill bad bacteria in the gut?
How long does it take to kill bad bacteria in the gut?
Is it ever a good idea to try to kill bad bacteria in the gut?
Key takeaways

Bacteria are good or bad based on their environment

Our gut bacteria are a bit like children: their behaviour depends on who and what is around them. With no adults to supervise, class bullies soon become dictators.

Your gut is an ecosystem. Think of it like a huge national park: from plants and fungi at the bottom of the food chain to wolves and bears at the top, every species plays its part in maintaining the balance. Left to its own devices, it usually works perfectly.

But when something happens that takes out a part of the ecosystem—let’s say some humans decide wolves are enemies and almost eliminate them entirely—things go awry.

This actually happened in Yellowstone Park in the US, where wolves played a key role in keeping numbers of deer and elk down. When the wolves weren’t around to eat them, they multiplied and overate the willows and other vegetation important to soil and riverbank structure, leaving the landscape vulnerable to erosion. Without wolves, the entire ecosystem of the park suffered.

Initial research on gut bacteria has revealed that our large intestines could harbour key species too: peacekeepers that keep other species in check. Species that—like deer and elk—are usually benign or even beneficial, but left to run amok, could become problematic (Source: NCBI).

The difficult Clostridium

Some bacteria have a bad reputation: the severe, chronic diarrhoea-causing Clostridium difficile (C. difficile) is one example that springs to mind. But it’s hard to find evidence of a type of bacteria that always causes the same symptoms in everybody. Even C. difficile is found in the majority of guts—including up to 70 percent of all newborns—causing no symptoms at all (Source: NCBI).

In 2018, researchers identified a group of microbes that seem important for gut health and a balanced immune system. Belonging to the same family as C. difficile, these ‘clostridial clusters’ don’t wreak havoc like their power-hungry cousin. Quite the opposite—they keep the gut barrier tight and healthy, and soothe the immune system (Source: NCBI).

This initial research was so promising that scientists are now looking into how we could use these clostridial clusters to treat autoimmune, allergic and inflammatory disorders, including Crohn’s disease and obesity (Source: NCBI).

E.coli: friend and foe

E. coli has earned a bad name for itself. With good reason: E. coli is one of the most frequent causes of bacterial infections in humans. Enteritis, urinary tract infections, septicaemia and neonatal meningitis are just a few of this bacterium’s gifts to mankind (Source: NCBI).

But the E. coli family is huge, with hundreds of members at present count. Most E. coli strains do not cause disease and naturally live in the gut. E. coli normally colonises an infant’s gut shortly after birth (Source: NCBI), adhering to the mucus layer of the colon. It’s actually your most common ‘facultative anaerobe’ (meaning it can grow either with or without oxygen) (Source: NCBI). So if you get rid of E. coli, that leaves a big gap to fill.

Apart from opening up vast swathes of real estate in your gut and sending an open invitation to any microbe who might want to set up shop and proliferate, there are other reasons not to nuke E. coli. Commensal strains of the bacteria guard against potentially pathogenic invaders and significantly contribute to the development and ‘training’ of the immune system in your gut (Source: LINK SPRINGER).

E. coli also:

  • create metabolic ‘products’ that support the energy supply of the mucus layer in your colon
  • generate short-chain fatty acids (SCFAs)
  • stimulate motility
  • enhance blood circulation in the innermost layers of your colon walls (Source: NCBI).

E. coli Nissle 1917 is one of the most studied probiotic strains. Isolated by Professor Alfred Nissle in 1917 from the stool of a First World War soldier who, unlike all of his comrades, did not suffer from gut infections while fighting on the Balkan peninsula. Today, E. coli Nissle has been proven to help symptoms of ulcerative colitis (Source: NCBI), Crohn’s disease (Source: NCBI), and chronic constipation (Source: NCBI).
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How to get rid of bad bacteria in the gut

The best way to get rid of bad bacteria in the gut is by creating the right environment for a balanced and diverse microbiome to thrive.

Of course, there are ways to directly kill bacteria, whether that’s by pharmaceutical antibiotics or antimicrobial herbs and supplements. But at this point in time nobody can be completely sure of everything you’re killing, or the knock-on effects of potentially wiping out whole communities of bacteria.

A lot of the latest research points towards encouraging the growth of ‘good’ bacteria in the hope of restoring balance to the microbiome, rather than getting rid of bad bacteria (Source: NCBI), (Source: NCBI). This is because—just like in Yellowstone Park—eliminating one or more species within an ecosystem has unpredictable effects.

However, there are some instances in which a Functional Medicine Practitioner or Registered Nutritional Therapist might recommend some gentle ‘weeding’ of your gut garden:

  • A positive SIBO test
  • Significant commensal bacterial overgrowth as shown on a stool test
  • The presence of one or more potentially pathogenic bacteria as shown on a stool test
  • High levels of yeast (usually Candida albicans but not always)

If you’d like professional support to help you figure out what your gut needs to stay healthy, join our three-month Gut Health Program where you’ll be joined by a community of like-minded health seekers and professionals to get your gut on track.

Candida albicans: the opportunistic yeast

When there’s a recently vacated space to fill in your gut, it appears that some bacteria and other microbes move in to fill it quicker than others (Source: NCBI). We don’t know enough about this to make concrete claims, but initial research suggests that candida (a type of yeast resident in nearly everyone’s guts) is one of the opportunistic species that rushes to pick up where others left off, creating an overgrowth that results in dysbiosis (Source: NCBI).

In one study in Nigeria, out of 208 children who had taken antibiotics within the last three weeks, 42.3% had candida overgrowth, compared to 20.8% of those with no recent history of antibiotic use (Source: NCBI).

Candida overgrowth is associated with:

It’s worth saying that association doesn’t mean causation: it could be that these conditions make it easier for candida to overgrow in the gut, rather than candida causing the conditions. We can’t be sure which yet.

And remember that candida seems to cause no problem at normal levels. It’s only when there’s a vacuum to fill that it starts to party. If you didn’t already know, candida is the yeast responsible for thrush, a vaginal infection that often happens after a round of antibiotics.

Most mainstream doctors don’t believe that candida causes gut issues, or disease anywhere else in the body, except in the case of people who already have weakened immune systems. A Functional Medicine Practitioner or Registered Nutritional Therapist may suspect a candida overgrowth based on your symptoms and the results of laboratory tests.


How to get rid of bad bacteria in the gut


Dysbiosis: too much, yet not enough

Dysbiosis is an imbalance of gut microbes. These researchers defined it as “a decrease in microbial diversity which promotes the expansion of specific bacterial taxa” (Source: NCBI)

That means that when the numbers of some bacterial families drop—or disappear completely—a few opportunistic families of bacteria (or other microbes, like candida) expand and grow in their place (Source: NCBI). So in this case, you lose some, you win some. But you might not like the prizes.

Researchers in one study (Source: NCBI) found dysbiosis to be associated with:

  • inflammatory bowel disease
  • irritable bowel syndrome (IBS)
  • coeliac disease
  • allergy
  • asthma
  • metabolic syndrome
  • cardiovascular disease
  • obesity

Many experts suggest modern Western living has a detrimental impact on the microflora of the gastrointestinal tract. Antibiotics are one aspect of that, but psychological and physical stress—and our diet—have been found to contribute to intestinal dysbiosis too (Source: NCBI).

Diversity, diversity, diversity

The science on the gut microbiome has taken massive strides forward since the turn of the century. One of the most important discoveries we’ve made is that bacterial diversity is key to a healthy gut. It’s something that research has uncovered time and time again: if you want a robust microbiome with a good chance of protecting you from disease, you need as many different species and strains of microbes down there as possible (Source: NCBI), (Source: NCBI), (Source: NCBI).

Dysbiosis happens when there’s an imbalance of the families of microbes in your gut (Source: NCBI). While we know that modern life takes its toll on our microbial diversity, there’s still no picture of an ‘ideal’ microbiome that we should be aiming towards. The only thing that seems certain is that diversity is key (Source: NCBI), (Source: BMC Microbiology).

Tim Spector, Professor of Epidemiology at King’s College, London, is author of The Diet Myth: the real science behind what we eat. After testing the gut bacteria of his son before and after a ten-day diet of nothing but McDonald’s food, he noted a 40 percent drop in diversity: 1,400 species of bacteria had disappeared from his stools. Loss of diversity is a “universal signal of ill health”, according to the professor.

Because your microbiome—along with your genetic fingerprint and the environment you exist in—is highly individual, nobody can tell you for sure (yet) what will happen if you eradicate whole families of microbes from your gut.

Having said that, we do have some evidence that having certain types of bacteria in your gut is usually good news. These include:

Research so far has told us that having these in your gut at good levels means you’re less likely to suffer from chronic disease (Source: SCIENCE MAG), (Source: NCBI). They appear to have some kind of ‘gatekeeper’ effect: like the wolves in Yellowstone Park, they seem to keep the rest of the wildlife in check.

One group of researchers from the European Society for Neurogastroenterology and Motility (Source: Gut Microbiota for Health) say that along with Bacteroides, Prevotella, Oxalobacter and others,
these bacteria:

  • increase the protective function of intestinal microbiome overall
  • improve digestion
  • improve the function of immune system
  • improve elements of the nervous system

It’s important to remember that research on this is just beginning, though, and we still don’t have definite answers. If you’d like a professional to give you the latest research in plain English, and become part of a community of people all seeking better gut health, check out our Gut Health Program.

Liven up your Lactobacillus

Lactobacillus populations drop as we become unwell, and also as we age (Source: NCBI). Feed your Lacto friends with:

  • konjac root (also known as glucomannan or ‘shirataki’ noodles)
  • soy
  • apples
  • barley
  • wheat bran
  • walnuts
  • chicory root
  • artichokes
  • buckwheat

Boost your Bifido

One study found that taking a Bifidobacteria probiotic for 45 days reduced body mass index (BMI) and blood cholesterol in people with metabolic syndrome (Source: NCBI). You can make Bifido happy with a whole-food, high-fibre diet, which could include:

  • bananas
  • nuts
  • onions
  • garlic
  • oats
  • blueberries
  • apples

Encourage your E. coli

Other than for E. coli Nissle, research is lacking on the commensal (friendly) strains of E. coli. They seem to like a kind of plant sugar called fucose (Source: IAI ASM), found in:

  • Figs
  • Hazelnuts
  • Chickpeas

Speak to a gut health expert.


How to get rid of bad bacteria in the gut naturally

If you’re determined to get rid of bacteria in your gut, there are many antimicrobial plants and herbs that can do the job.

As we explained above, it’s usually a much better idea to encourage diversity and balance in your gut microbiome than it is to eliminate bacteria. If you have gut symptoms, you might think that you need to kill offending microbes to solve the problem. The reality is not that simple.

There are two main problems with thinking of dysbiosis in this way:

One: there are very few families of bacteria that are always ‘bad’

One person’s ‘bad’ bacteria can be another person’s good. Even traditional baddies have been found to have benefits in some people. For instance, H. pylori has been found to protect against autoimmune diseases in some populations (Source: NCBI), and some forms of the protozoa Blastocystis hominis cause no discernable ill effects at all in some hosts (Source: NCBI).

Two: you can’t wipe out individual strains

Antibiotics aren’t very selective when it comes to the bacteria they kill. Some have a narrower spectrum than others (they go after fewer, specific strains) but most of the ones people take today are broad spectrum. The problem is, when you take Amoxicillin for a bladder infection (for example) it’s not currently possible to only kill the particular type of bacteria causing the problem, and leave the rest alone.

Eighty to 90 percent of bladder infections are caused by certain strains of E. coli bacteria. The rest—if you’re interested—are usually caused by Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis or Streptococcus agalactiae (Source: NCBI). Whatever bacteria is responsible, you’ll most likely get a broad-spectrum antibiotic that kills almost all E. coli (there are hundreds of different types) in your gut as well as your bladder, leaving a swathe of space for opportunistic microbes to take over.

There are also herbs and supplements that in some cases, can be as effective as pharmaceutical antibiotics for killing bacteria (Source: NCBI). Research is uncovering more and more about how extracts from plants like oregano, thyme and garlic can help us in our quest for gut health, but right now, we have to tread carefully when we use them for this purpose. Read on for more on that in the next section.

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What are the symptoms of bad bacteria in the stomach?

There are very few bacteria that can survive in the harsh acidity of our stomachs, but one of those is H. pylori, which can cause symptoms like nausea, loss of appetite, bloating, belching and pain or burning in the upper abdomen.

It’s common for people to say ‘stomach’ when they actually mean the small and large intestine. Your stomach is separate—but connected to—your small and large intestine. The ‘gut’ is a friendlier name for your gastrointestinal tract: a group of organs that includes the mouth, oesophagus, stomach, pancreas, liver, gallbladder, small intestine, large intestine (or colon), and rectum.

When your food leaves your stomach, it travels through the small intestine, where there are more bacteria than in your stomach but about a hundred to a thousand times less than in your large intestine, the next destination (Source: NCBI).

H. pylori has been found to lead to stomach ulcers and stomach cancer, so it’s classed as a pathogen (Source: NCBI), but as we just mentioned, some researchers believe (controversially) that it can be commensal (neutral) or even friendly in certain people, preventing allergies and autoimmune disease.

SIBO: right bacteria, wrong place?

If there are too many bacteria in your small intestine, we call it SIBO (small intestinal bacterial overgrowth).

In the small intestine, the bacteria ferment the carbohydrates you eat and release gas as a by-product. They also eat some of the nutrients from your food. Together, these can lead to uncomfortable symptoms, including:

  • bloating
  • abdominal pain
  • belching
  • flatulence
  • nausea
  • fatigue
  • brain fog

Most experts believe that SIBO is an ‘overspill’ of bacteria from your large intestine into your small intestine: it’s not about the type of microbes present, it’s where they are and how many of them there are that causes the symptoms. However, some new findings point towards SIBO being an imbalance of the small microbiome we have in our small intestines, rather than an overgrowth (Source: NCBI).

You can only be sure you have SIBO if you take a test. If you’d like to talk to a professional about whether a SIBO test might be right for you, you can book a free 15-minute consultation with one of our practitioners.

The large intestine: meet your magical microbiome

Although there are microbes in your small intestine, your large intestine is the seat of your microbiome. It’s where your bacteria get to work on your food, producing all sorts of substances which, in an ideal world, keeps them happy and you healthy.

Today, very few of us live in an ideal world, so your large intestine is also where things can go wrong. It’s where the ecosystem we mentioned earlier can go awry, resulting in a lack of microbial diversity and dysbiosis. For you, that can mean gut symptoms like bloating, diarrhoea and constipation.

Dysbiosis can also result in:

  • bad breath
  • upset stomach
  • nausea
  • difficulty urinating
  • vaginal or rectal itching
  • chest pain
  • rash or redness
  • fatigue
  • having trouble thinking or concentrating
  • anxiety
  • depression

Because the science on our gut microbiomes is relatively new, there are few conditions that we can say are definitely a direct result of bad bacteria or dysbiosis. But, in recent years, the research has exploded to a point where few experts can deny the connection between the health of our gut and the rest of our body.

Here are some of the most common diseases linked to dysbiosis in the medical literature:

  • IBS
  • ulcerative colitis or Crohn’s disease
  • coeliac disease
  • diabetes
  • obesity
  • polycystic ovary syndrome
  • eczema
  • liver disease
  • heart disease
  • dementia
  • Parkinson’s disease
  • bowel cancer

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What foods kill bad bacteria in the gut?

There are many herbs and plant foods that kill bacteria in the gut. The problem is that they kill ‘good’ bacteria too.

We can’t say it enough: a happy microbiome is a diverse microbiome. Right now, we don’t know enough to say that any substance will only kill ‘bad’ bacteria in the gut. If you use any of the following, it’s likely your ‘good’ bacteria will take a hit too.


Raw garlic extract is full of allicin, a potent antimicrobial. Besides bacteria, allicin has been found to work against fungi, protozoa and viruses. Even Staphylococcus aureus (MRSA) has been shown to be susceptible to allicin (Source: NATURE).


Oregano oil is one of the most common substances used to treat SIBO. One study found it to be even more effective than pharmaceutical antibiotics for killing off wayward microbes in the small intestine (Source: NCBI).

Caraway seed oil, lavender flower oil and ajwain seed oil

Jason Hawrelak, a microbiologist, researcher and herbalist, found all these essential oils to be selective in activity, inhibiting the growth of potential pathogens like Candida albicans, the Clostridium family (which includes many beneficial strains) and Bacteroides fragilis. Interestingly, he found they had no effect on Lactobacilli or Bifidobacteria: the ones we almost always want to keep (Source: NCBI).

Green tea

The polyphenols in green tea inhibit the growth of Candida albicans and prevent E. coli, Staphylococcus and Streptococcus from setting up shop in your gut (Source: NCBI).

Pomegranate husk

The white part of the inside of this Middle-Eastern fruit is effective against E. coli (another family with beneficial strains), Campylobacter jejuni, Salmonella, Proteus, and many more. It also prevents these bacteria from sticking to teeth and causing dental cavities (Source: NCBI).
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How long does it take to kill bad bacteria in the gut?

Some antibiotics and antimicrobial herbs kill bacteria instantly (Source: NCBI), but using them won’t necessarily help your symptoms.


Bacteria can develop resistance quickly

Bacteria might not have brains, but they’re clever. They evolve in a similar way to humans, except their lifespans are much, much shorter, so they can ‘learn’ how to survive through an antibiotic attack over generations (Source: NCBI).

Antibiotics and antimicrobials can kill the most susceptible bacteria first, leaving behind the stronger strains to multiply and take their place, reducing diversity (Source: NCBI).

You might not be killing the bacteria you think you are

Because we probably don’t know what type of bacteria is causing our symptoms—or whether our symptoms are happening because of a general dysbiosis rather than an attack by one rogue family of bacteria—we end up using a ‘scattergun’ approach with any antimicrobial we find. The problem with this is that we have just as much chance of eradicating the bacteria we need as the ones we don’t (Source: NCBI).

Bacteria can ‘hide’ in biofilms

Another smart tactic bacteria use to evade antibiotics and antimicrobials is to club together to form a polysaccharide matrix—a kind of shell—that shields them from harm. There’s some evidence to show that they do this when under threat i.e. when we try to get rid of them (Source: NCBI).

You may cause further dysbiosis

By definition, antibiotics and antimicrobials kill bacteria and reduce the diversity that is key to a healthy microbiome (Source: NCBI).

If you’re a bit flummoxed by the science, why not join our Gut Health Program—with access to a Registered Nutritional Therapist for the three-month duration—to get the fundamentals of good gut health?

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Is it ever a good idea to try to kill bad bacteria in the gut?

Here are two instances in which you should seek advice from a professional on how to gently and systematically weed unwanted microbes from your gut:

After a stool test has identified a potentially problematic overgrowth

A comprehensive stool test reveals the levels of key bacterial species in your lower intestine (colon), as well as the presence of candida and other yeasts. Our most advanced test also checks for parasites and levels of inflammation in the lower gut, along with many other intestinal health biomarkers. For this test, you provide a small sample of your stool (poo) that you send to a lab for analysis.

Because a stool test can tell us which specific bacteria and yeasts are present at higher levels than normal, it’s possible to use specific antimicrobial herbs that have some evidence behind their ability to eradicate particular types of bacteria and yeasts (Source: NCBI). The science isn’t perfect on this yet, but it does give practitioners a better chance of getting rid of problematic overgrowths without causing too much collateral damage.

After a breath test has confirmed SIBO

SIBO stands for small intestinal bacterial overgrowth, which, like it sounds, is the presence of too many bacteria in your small intestine, which should harbour very low levels of bacteria compared to the large intestine (Source: NCBI). If you have the symptoms of SIBO, a health practitioner may recommend a SIBO test. Symptoms include:

    • bloating
    • abdominal pain
    • belching
    • flatulence
    • nausea
    • fatigue
    • brain fog
    • fatty stools

It’s estimated that up to 15% of people have SIBO, and it’s now believed to be the leading cause of IBS (Source: NCBI).

A medical doctor usually prescribes antibiotics if a patient tests positive for SIBO. A Functional Medicine Practitioner or Registered Nutritional Therapist would recommend a course of herbal or plant-based antimicrobials, such as an emulsified form of oregano oil, berberine or lauric acid (derived from coconut oil). Studies have found herbal treatments for SIBO to be just as, or even more effective than antibiotics (Source: NCBI).
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Key takeaways

  • It’s easy to blame ‘bad’ bacteria for your symptoms but it’s unlikely that one particular kind of bacteria is responsible for your issues.
  • Your gut is a complex and delicate ecosystem with over 1,000 bacterial families. Like a rainforest or national park, knocking one species out can have drastic effects on the whole environment.
  • Research suggests that when it comes to gut health, we should aim to have as many different species of bacteria as possible. Trying to get rid of bad bacteria usually affects the good ones too and reduces diversity.
  • Reduced diversity can result in dysbiosis: an imbalance in the communities of bacteria and microbes that make up your microbiome. Dysbiosis is associated with many conditions both inside and outside the gut.
  • There are a few instances where a health professional may recommend trying to get rid of bad bacteria. Otherwise, supporting and encouraging diversity within your microbiome is a better idea.

For expert advice from our practitioners on how to heal your gut, fix leaky gut, the best foods for gut health and lots more, check out our blog.

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Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.

Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.
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