How To Treat Bacterial Infections: A holistic Approach

how to treat bacterial infections naturally gut health specialist australia SIBO klebsiella blastocystis

Bacterial infections in the large bowel (also known as bacterial overgrowths or simply dysbiosis) come in many different shapes and sizes. Today we will be covering the multi-pronged approach to defining and treating bacterial infections or overgrowths in the large bowel.

Bacterial infections can take many shapes and sizes. First we have small intestinal bacterial overgrowth, or SIBO, which, as the name hints at, is an overgrowth of bacteria in the small intestine. Moving on to the large intestine we also have bacterial infections, or overgrowths known as dysbiosis (or an imbalanced gut). 

When I first started researching and writing articles here at Byron Herbalist I was very focused on the individual bugs. Things like Klebsiella, Escherichia coli, Citrobacter and others were all on my radar as possible issues that needed to be treated. I wasn’t alone in thinking that all of my gut symptoms could be caused by one particular bug or another. 

Since publishing these articles I have been contacted by dozens of people looking for more information on treating one bacterial infection or another. This article is my considered response. How do I look at treating bacterial infections of the gut, particularly in the large intestine (I’ll save SIBO, small intestinal bacterial overgrowth, for another day).  

But first a bit of the back story

One Infection, One treatment

For the most part the thinking outlined above, focusing on one particular infection or another, can be attributed to the different lab providers. Most gut tests, including the comprehensive stool analysis and the GI MAP, will flag overgrowths of individual bacterial infections. The issue here, that I have been slow on realising, is that these infections are only a symptom of a larger picture of gut dysregulation. 

Thinking along the lines of one bug one treatment you can easily fall into the trap of focusing too intently and missing the larger picture of an imbalanced gut. You may even treat, find that you have eliminated the bacterial infection (let’s say Klebsiella for example) and your symptoms haven’t improved. The important thing to remember here is that the gut is an incredibly complex and intricate ecosystem. True there are outright pathogens that need to be eradicated, but in the case of the more common bacterial infections that show up on lab findings we need to think more broadly. 

With this broader view we can recognise that many bacterial infections and overgrowths share one thing in common. Most are directly related to one another.

The More Common Bacterial Infections 

Introducing the Proteobacteria phylum of bacteria (and most notably the Enterobacteriaceae family within that phylum). 

Why are all of these fancy schmancy microbiology names important? Because this particular family is made up of a number of top offending bacterial infections including the following (1).

  • Escherichia coli
  • Klebsiella 
  • Enterobacter
  • Salmonella
  • Proteus
  • Yersinia 
  • Shigella
  • Citrobacter 
Image taken from: A Concise Manual of Pathogenic Microbiology

A few of these bacteria are normal residents of the human gut (Klebsiella and Escherichia coli) that can cause issue if allowed to overgrow. Others such as Salmonella, Yersinia and Shigella are invaders which can take up residence and cause symptoms. They are all gram-negative and most will cause symptoms if they are present in significant numbers.

The gram negative bacteria are implicated in a whole range of diseases. For example urinary tract infections are commonly caused by E. coli whereas Citrobacter can be found in off meat. Other common bacterial gut infections such as Klebsiella can commonly be picked up in the hospital setting.

A primer on gram-negative bacterial endotoxins. 
Gram negative bacteria contain, on their cell walls, a substance known as lipopolysaccharide, or LPS, also known as endotoxin. This substance is released when this particular class of bacteria multiply or die – a very important point here that we will circle back to with the treatment section. Some researchers are pointing to this particular substance as one of the key drivers of inflammation. Here the immune system responds to the presence of LPS and upregulates a number of different messenger molecules in attempts to respond to the invading bacteria (2).

This immune response may very well be the cause of many of the symptoms that you are experiencing.

Symptoms of bacterial infections and overgrowth

Symptoms from a bacterial infection or overgrowth in the large intestine could be any number of the following (3).

  • Recurring urinary tract infections 
  • Pneumonia
  • Gastroenteritis (abdominal cramps, vomiting, diarrhea) 

Less obvious symptoms may include 

  • Bloating after meals (especially 2-4 hours after for large intestine bacterial infections)
  • Diarrhea 
  • Constipation 
  • Stomach pains 
  • Headaches
  • Irritability

Here we can see some non-specific symptoms that may or may not be pointing towards bacterial gut infections. Some herbalists and naturopaths may decide to treat empirically – ie based on the presenting symptoms. 

I don’t have an issue with that approach but I would prefer to know what we are treating specifically. This is where some gut testing may be indicated. Here the decision is very much based on you, the patient and your presenting symptoms. Sometimes the GI MAP may be indicated to get specific information on gut infections ranging from bacteria to protozoa to viruses. Other times SIBO testing may be indicated (which is a topic for another day!). Ubiome testing is another option and will give a big picture view on the composition of bacterial communities in the large intestine.    

What Would constitute an overgrowth?

That’s a great question and it helps us circle back to looking the gut as an ecosystem. Below is an image of the more common phyla of bacteria. While Proteobacteria (the phylum that the less than friendly bugs listed above fall into) makes up over 35% of the bacteria found in the soil it only makes up approximately 4.5% of the bacteria within our digestive tract (4).

Within that estimated 4.5% of Proteobacteria in the healthy adult human gut the Enterobacteriaceae family may make up just 1% (5).

Images taken from: Proteobacteria: microbial signature of dysbiosis in gut microbiota 
Images taken from: Proteobacteria: microbial signature of dysbiosis in gut microbiota 

Conventional Treatments for bacterial Infections 

First off lets get the conventional treatment for bacterial infections out of the way.

It’s simple enough. Antibiotics.

If blood tests have narrowed down what particular bacterial infection is at play then possibly targeted antibiotics. Most likely we’re talking about broad spectrum antibiotics. 

To save us getting into antibiotic bashing I’ll keep it short and sweet. 

Unless antibiotics will save life or limb I prefer to stick to natural treatments for bacterial infections. A few reasons include.

Antibiotic resistance 

We’re talking about the alarming rise in the number of antibiotic resistant microorganisms. Now you might be thinking here that we can continue to develop bigger and better antibiotics – the so called arms race against nature – but antibiotic resistance among infectious microbes is currently winning. 

Let’s take Helicobacter pylori as an example. Back in the day single antibiotics were sufficient to treat this particular bacterial overgrowth. Over the span of the past 20 years we have had to turn to two and even three antibiotics used together along with an acid blocker (antibiotics are more effective in an alkaline environment and believe me the healthy human stomach is not alkaline!) (6). 

Helicobacter pylori’s antibiotic resistance appears to be worst in certain areas of the world. Africa tops the chart here with Asia coming in second. As with most things in this global culture it’s only a matter of time for this extreme antibiotic resistance to spread throughout the world (7).

Image taken from: Prevalence of antibiotic resistance in Helicobacter pylori : A recent literature review

If you are interested in the subject of antibiotic resistance then I would recommend the article The Antibiotic Resistance Crisis Part 1: Causes and Threats published in Pharmacy and Therapeutics.

Negative ‘side effects’ from Antibiotics.

The concept of side effects when talking about drugs is slightly amusing. Strictly speaking they are simply the effects of the drug.

Considering out gut microbiome, the multitude of microbes that live inside our intestinal tract, we can see a dramatic shift after antibiotic use. Originally we thought that the microbiome regained its balance after a short period of time (approximately 4-6 weeks post antibiotic use). As our detection techniques improved from physically culturing the bugs to DNA based technology we have been learning that antibiotic use may have a long term impact on the gut ecosystem. 

Let’s look at one particular paper to see what we currently think is happening in the gut after exposure to antibiotics.

One study – Long-term ecological impacts of antibiotic administration on the human intestinal microbiota – looked at the effects of a 7 day trial of clindamycin, an antibiotic used for bacterial infections. They used one particular genus that is found in high numbers in the human gut known as Bacteroides. After the 7 days of antibiotics they found that there was a reduction in diversity among this genus and a rise in just a few of the individual species which the researchers thought to have antibiotic-resistant genes – here we see the bacterial overgrowth issue that we are trying to treat in the first place! Even as long as 2 years post antibiotic use there was considerable changes possibly permanent. 

The authors conclude with an important statement that I think we all need to heed. 

“Currently, it is widely accepted that the indigenous intestinal microbiota stabilizes a few weeks after an antibiotic administration. However, when we analysed the bacterial flora in more detail, we found that this is not the case, and that a short-term antibiotic exposure can have persistent consequences for the individual treated. These results urge caution for a more restricted use of antimicrobial agents.”

This is big news. 

To summarise the thinking a paper published in the Frontiers in Microbiology spoke on the vicious circle that willy nilly antibiotic use has put us in 

“The dysbiosis brought about by antibiotics bear the added disadvantage of enriching the microbiota in resistant organisms. The human gut microbiota has been established as a significant reservoir of antibiotic resistance.” (10).

Basic translation. When antibiotics are used they create reservoirs of antibiotic resistance in certain bacteria within our gut. 

We could keep covering antibiotic overuse issues and the consequences for days but let’s move onto what we can do for bacterial gut infections. This time a more holistic, considered approach please. 

Natural Treatments for bacterial infections – A holistic approach 

Here again we can circle back to the gut as an ecosystem. Instead of looking at specifically treating the bacterial infections that a gut test like the CDSA or the GI MAP has flagged I prefer to see these flagged bugs as a sign of a broader gut imbalance. Tools that help to rebalance bacterial overgrowths include probiotics and prebiotic fibres and very select herbal medicines, starting with the more gentle and working up from there if needed.

Probiotics to treat bacterial infections

At first this may seem slightly counterintuitive. How can bacteria help to reduce bacterial overgrowths when the problem here too much bacteria?

Probiotics, and the beneficial bacteria that reside in your digestive tract have a number of different methods of helping to rebalance the gut and treat bacterial infections so let’s get into it.

When working with a gut savvy clinician we can start to get more targeted with the selections of probiotic strains. Let’s not forget that different probiotic strains have different actions! (11).

Lactobacillus plantarum

There are a few papers (cited in this review) showing that Lactobacillus plantarum can reduce the different members of the Enterobacteriaceae family. 

Lactobacillus plantarum binds to the intestine in a similar way as Shigella, Enterobacter, and Klebsiella. This may be a key point on how it helps to rebalance the gut. By competing with pathogenic bacteria for space this particular probiotic may help to reduce their numbers (13). 

Lactobacillus reuteri

Here again we see a probiotic that has shown benefit in reducing the numbers of different members of the Enterobacteriaceae family, effectively a natural treatment to bacterial infections of the gut. Particularly the strain DSM 17938 has shown some promise here. 

Not only has Lactobacillus reuteri been shown to improve chronic constipation it has also been shown to reduce a number of different pathogenic and opportunistic bacterial gut infections (14).

In one study people with cystic fibrosis (a disease that has been characterised by significantly higher Proteobacteria, the genus that Enterobacteriaceae is in) took Lactobacillus reuteri for 6 months. There was a significant reduction in the Proteobacteria phylum – from 32.6% down to 10%!.

This is significant so I’ll repeat it. Taking one particular probiotic for 6 months reduced bacterial overgrowth in the large intestine by more than half.

The same study showed significant improvements in calprotectin (a marker of gut inflammation that you can read more about here) and the Gastrointestinal Quality of Life Index.

Image taken from: Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: A double blind prospective study  

Possibly the most exciting study compared infants who had received Lactobacillus reuteri for a month with those that did not. There was a reduction in a number of different pathogenic and opportunistic bacteria including 

  • Diarrheagenic E. coli
  • Salmonella spp.
  • Cronobacter sakazakii
  • Klebsiella pneumoniae
  • Enterobacter aerogenes
  • Enterobacter cloacae
  • Serratia odorifera
  • Hafnia alvei
  • Klebsiella oxytoca (17)
Image taken from: Probiotics and gut health in infants: A preliminary case-control observational study about early treatment with Lactobacillus reuteri DSM 17938.

And lastly, but not leastly, the same strain of Lactobacillus reuteri has been shown to significantly reduce methane levels in the gut. High methane levels is a hallmark of methane dominant small intestinal bacterial overgrowth. With just one month of taking Lactobacillus reuteri methane levels were consistently decreased and constipation was improved in 20 patients, again showing how important our bacterial composition is and how it can impact us on a day to day level (18).

Saccharomyces cerevisiae variety boulardii

We can’t go too far without referencing the star probiotic for gut health. Sometimes shortened to Saccharomyces boulardii or even SB this particular substrain/variety of baker yeast has some potent actions. Not only has S. boulardii been shown to greatly reduce parasite infection rates (which I covered here) it has also been shown to help with range of gut conditions plus it has a ton of science behind it.

  1. It has straight up antimicrobial activity. Not only does it directly inhibit the growth of bacterium it also reduces the spread of bacteria from the gut and neutralised bacterial toxins.
  2. S. boulardii stimulates the adaptive immune system (immunoglobulins) which target some pathogenic bacteria in the gut.
  3. Helps to soothe and repair the gut wall by reducing inflammation and cell damage 

There is good research showing that this particular probiotic is helpful in antibiotic-associated diarrhea, bacterial infections (Clostridium difficile, Helicobacter pylori), inflammatory bowel disease (Crohn’s disease and Ulcerative colitis) and parasitic infections as noted earlier (19).

Image taken from: Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders

Combination probiotics 

There are a whole range of combination probiotics that can help with bacterial infections in the gut. One that has an enormous amount of research behind is VSL#3.

Much of the research available for the use of VSL#3 involves the treatment of irritable bowel syndrome (IBS) (20, 21) and the treatment or maintenance of remission in different forms of inflammatory bowel disease (IBD) (22, 23).

Why are papers showing how the probiotic VSL#3 is helpful in IBS and IBD useful when talking about treating bacterial infections in the gut? While the jury is still out on what is actually causing these gastrointestinal disorders it has been shown that there is a very real and significant shift in the gut microbiome. 

The flora in the digestive tract of someone suffering from IBS and IBD is considerably different from the general population. This article is not the place to get into the nitty gritty of that particular subject but you can read more on that here and here for IBS and here for IBD if you want to delve further.

One interesting theory on the development of inflammatory bowel disease involves increased intestinal permeability (aka leaky gut). The theory goes, as outlined in a paper published in the American Journal of Physiology, that the leaky gut allows things across the gut wall, such as our resident gut microbes (beneficial and otherwise) that aren’t normally allowed across. This actives the immune system, which then becomes dysfunctional and begins to target the gut flora. Here we can see the benefits of VSL#3 probiotic use as it has shown, in animal studies, to seal up the leaky gut that may be driving the inflammatory bowel disease progression (24).

Not only does VSL#3 work by competing with the pathogenic bacteria (causing the infection/overgrowth) it also upregulates the bodies innate immunity by stimulating the production of defensins. These are antimicrobial peptides that are released by cells called paneth cells which are found in our small intestine (25).

These defensins are currently being avidly researched due to the ever increasing failure and damaging nature of our more conventional antibiotics (as we outlined above).More on that in this paper here.

Image taken from: Probiotic lactobacilli and VSL#3 induce enterocyte b-defensin 2 showing the increase of human-beta defensin 2 mRNA expression. It’s worth pointing out the time and dose dependence in the results. There was a peak around 6 hours and then a gradual drop off and the more probiotic taken the greater the effect (not to say that we should be megadosing on probiotics!)  

Prebiotics to Treat Bacterial Gut Infections

Here we come to one of my favourite subjects on gut health. Anyone that has been following along could have seen the subject of using prebiotics to treat bacterial infections and overgrowths coming for a mile away.

While I don’t want to rewrite the book and would send you off here to check out more about the ins and outs of prebiotics I think it is worth covering some key points on how prebiotics can help if you have a bacterial overgrowth in the large intestine. 

First off what is a prebiotic.  

This is an ongoing conversation and the concept of a prebiotic is constantly being updated. Here is a good outline of what a prebiotic is:

“The current prebiotic concept typically refers to nondigestible food ingredients or substances that pass undigested through the upper part of the gastrointestinal tract and stimulate the growth and/or activity of health-promoting bacteria that colonize the large bowel” (27).

And here you can see the updated thinking on prebiotic definitions since it was first proposed in 1995

Image taken from: Towards a more comprehensive concept for prebiotics

Prebiotics on a whole act to boost the good guys in the gut and in doing so decrease the bad guys. That’s exactly what we are looking to do when we are trying to address bacterial infections and overgrowths in the large intestine. Instead of going in and wiping out everything with broad spectrum antibiotics we can selectively boost the good and reduce the bad. Sounds great right?

How are Prebiotics acting?

If we take the idea that prebiotics boost beneficial bacteria in the gut ecosystem then the real question would be ‘how are the beneficial microbes helpful in reducing pathogenic infections?’

  1. They excrete beneficial metabolites – for example acids – which lowers the colonic pH. As we know some bacteria thrive in a higher (or more alkaline pH). These ones tend to be the less-than-friendly overgrowth types.
  2. Beneficial gut flora compete for space and nutrients – we call this competitive exclusion. We see this same concept in nature all the time. If a niche is occupied then it can be very hard for another organism to move in and make themselves at home. If the niche is unoccupied then anything can move in and set up shop!
  3. Beneficial bacteria in the gut can also directly antagonise the bacterial invaders. They can secrete antimicrobial peptides that actively deter the growth of the invading bacteria.
  4. Finally beneficial bacteria in the gut can enhance and modulate our immune system (28).

Below we can see a diagram on the benefits that our friend and constant ally Bifidobacteria contributes. Just brilliant stuff!

From: One of the first few papers that started it all – Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics

Different prebiotics include

  • Inulin
  • Fructooligosaccharides
  • Galactooligosaccharides
  • Lactulose
  • Select forms of resistant starch

A key point on taking prebiotics is to start low and slow and monitor your symptoms. If you suffer from bloating and distention then there may be a SIBO picture at play for you as well as colonic dysbiosis. 

Herbal Medicine To Treat Bacterial Gut Infections

Finally we come to herbal medicine. One of my favourite subjects! You might be asking yourself if herbs actually work why didn’t we just start here and be done with it? A good question worthy of a good answer. I’ll try to keep it brief. 

From my perspective (someone that battled chronic gut infections for years with all manner of herbs) I feel that we jump to antimicrobial herbs too quickly when trying to nudge the gut microbiota back into balance. There is even some (unfortunately unpublished data) showing that some antimicrobial herbs are almost as devastating on the gut microbiome as antibiotics. So here I think caution is advised. 

The perfect antimicrobial herb would knock back the bacterial infections and leave the beneficial bacteria alone. Unfortunately that may be too much to ask for. However, there are particular herbal medicines that are selectively antimicrobial. Almost as good. Let’s cover them now. 


Garlic has been shown to be a potent, but selective antimicrobial. It has been shown to be effective against a whole range of bacteria that are common in the overgrowth picture. I’ve included the table from the paper. True it is an in-vitro study but clinical evidence comes in handy here as well. People feel better after taking fresh garlic in therapeutic doses. 

Garlic has a long history of use as an antimicrobial agent. Probably longer than either of us could imagine. There have been studies dating back to the early 50’s looking into garlic as an antiprotozoal agent in the treatment of Giardia. As we continued to research the benefits of garlic we learned that it was effective against many of the top offenders including:

  • Pseudomonas
  • Proteus
  • Staphylococcus aureus
  • Escherichia coli
  • Salmonella
  • Micrococcus
  • Bacillus subtulis
  • Clostridium
  • Mycobacterium
  • Helicobacter

There is even some research showing that garlic is selectively antimicrobial (just what we are looking for). Garlic has been shown to be 10x as potent against E. coli compared to one of our beneficial gut bugs, Lactobacillus casei (30).

garlic antimicrobial herb gut health specialist byron bay naturopath herbal medicine parasite infection treatment

Pomegranate husk.

This is a herb that I have written about before, and one that I will keep exploring here at Byron Herbalist. Containing an abundance of tannins in the form of ellagitannins and phenolic acids pomegranate husk has been shown to be effective against a range of bacterial infections and overgrowths (31).

While we still haven’t quite worked out how pomegranate peel is antimicrobial the current thinking involves the ability of the tannins, found in abundance in pomegranate, to cut into the bacterial cell wall (32). 

Now what I can’t seem to work out is why this doesn’t appear to impact our beneficial microbes found in the gut too? Many of these tannin rich herbs have been consumed as food for eons. Perhaps, due to constant exposure, the microbes that make up our resident microbiome have learned to cope? 

That last little point brings me to another key herbal medicine when we are looking to improve our gut ecosystem and treat bacterial overgrowths.

Green tea. 

Green tea is widely thought to be very good for you. After digging through the research I might even go so far as to call it a superfood. You could spend the rest of your life researching green tea and only scratch the surface. 

This article is focusing on the treatment of bacterial infections in the gut so let’s keep the focus there.

First off what is in green tea that makes it so special. 

Green tea is composed of amino acids and proteins, carbohydrates and trace elements. Focusing in on the gut we come to polyphenols, which makes up to 30% of green tea’s dry weight. Polyphenols is an incredible class of compounds that I find myself slightly obsessing over lately. In green tea we can find flavanols, flavandiols, flavonoids, and phenolic acids. Then within the flavonols of the green tea find epicatechin, epigallocatechin, epicatechin-3-gallate, and  epigallocatechin-3-gallate (EGCG) (33).

Too much info? I told you I’ve started to obsess over this!

With broad strokes in mind let’s take it back to the bigger picture. 

These catechins, particularly the EGCGs, are thought to be the main movers and shakers in regards to the health benefits of green tea. Including being potent antioxidants and helping to regulate cholesterol and blood sugar. There is even some evidence to show that these particular compounds found in green tea have anti-cancer properties too (34).

When we focus in on the gut flora, we can see that they help to modulate the gut bacteria in good ways. 

What the research is showing us 

  • Green tea improves gut barrier function and increases the production of antimicrobial peptides (animal study) (35).

  • Green tea, particularly EGCGs, have anti-biofilm properties against a range of bacterial infections possibly by interacting with bacterial cell to cell communication (quorum sensing) and interfering with the production of virulence factors that some pathogenic bacteria like enterohemorrhagic E. coli secrete (36).
  • One human study (there aren’t many with green tea and the microbiome so this is exciting!) found that 400ml of green tea consumed daily favourably altered the gut  microbiome. It shifted the gut community away the gram negative community of bacteria possibly by increasing the butyrate producing bugs (here we see increases in Lachnospiraceae, Ruminococcaceae, and Bifidobacteriaceae). The study also commented on the decrease in inflammation and bacterial translocation too! By increasing butyrate producing bacteria (the good guys like Bifidobacteria) and the suppression of the endotoxin producing bacteria (the bad guys) helps to decrease the background inflammation commonly seen in gut imbalances (37). 
  • Just to be thorough (and not to be called out for cherry picking research papers to prove a point) I wanted to include a human trial in which green tea supplementation did not alter the gut flora (38). I found this study’s results slightly puzzling as it contradicts the massive amount of animal and in vitro studies and the few human studies that I could dig up. 

Other Herbal Antimicrobials

Honestly we could go on and on listing all of the incredible and potent herbal antimicrobials and we would only be scratching the surface.

Herbs high in essential oils can play a big part in treating bacterial infections. These include 

  • Oregano 
  • Thyme
  • Rosemary 
  • Nigella sativa (black seed)  

There seems to be a trend towards using the essential oil of these herbal medicines and leaving out all of the other helpful constituents that you would get in a whole plant extract. Oregano oil is a top seller when it comes to herbs for gut infections but have we considered that it may be too strong? If we are using broad spectrum, heavy hitting herbal antimicrobials are we doing a similar type of damage to the gut microbiome as pharmaceutical antibiotics? Possibly…

gut health specialist byron bay digestive health herbalist australia

The big guns. Herbs for systemic infections

Another class of antimicrobial herbs that are commonly used to treat gut infections are the berberine containing herbs. One of my mentors Dr. Jason Hawrelak recommends to avoid long term use of herbs high in berberine unless they are absolutely needed. Things like systemic infections and tooth abscesses may call for high berberine herbs and certain parasite infections that can be treated quickly may call for berberine containing herbs too.

Herbs with a decent amount of berberine include

  • Coptis chinensis
  • Philodendron 
  • Goldenseal
  • Barberry

One thing to keep in mind with these high berberine herbs is that they may knock your beneficial bacteria around. Taking them high dose long term would be best avoided unless absolutely needed. For me I look at these herbs like these (in particular Coptis chinensis) as close to antibiotics that we can get with plants. Sometimes they are absolutely needed. Other times we can use less heavy hitting herbs to do the same job and minimise the damage to beneficial bacteria in our gut.

The Full Workup and Treatment Plan. Bringing it all together

As always the disclaimer (this should probably be at the top of the article…thanks for sticking it out!). It is best to work with a skilled gut clinical when undertaking any serious gut protocol. Here is the reason. 

Just picking one of the natural approaches to treating bacterial gut infections listed above could help. It might make you feel better than you have in awhile. In some it may help to completely resolve their gut symptoms. For most, especially if you have been struggling with gut issues for quite some time, it will take a considered approach and the combination of a range of the natural treatment options available. 

In some we might do some preliminary gut testing to rule in or rule out small intestinal bacterial overgrowth, parasite infections or bacterial infections and overgrowths in the large bowel. If you have been struggling with gut health issues for years then we almost definitely will test. 

Some grass roots herbalists and naturopaths decide to treat empirically. They will take a considered history from the patient and then treat according to symptoms and suspected imbalances. While I do think this is a valuable approach it does have its limitations. 

When there is a long term gut imbalance at play I feel that it is important to have a solid idea on what is being treated. The approach for SIBO is different compared to the approach for a large bowel bacterial overgrowth, which is different again when we are treating parasitic or even fungal overgrowths. Heck the treatment approach between methane dominant SIBO and hydrogen dominant SIBO is different! 

A working diagnosis (in my humble opinion based on personal history) is necessary to track your progression. The longer the gut has been imbalanced the longer it will take to shift it back into a healthy, stable place. When we have established what is causing the imbalance in your gut we can focus on a combination of the different approaches outlined in this article, always working towards rebalancing and nourishing your healthy gut flora to eliminate symptoms and get you back on track towards health.

Work With me

Currently I am months away (December is rapidly approaching!) from finishing my health science degree. As of yet I am unlicensed and unable to work with you on your gut health problems. I have been contacted by handfuls of people looking for help getting their gut health back on track so I have started putting together a waiting list for when I am licensed to practice. If you would like to be included on the list please get in touch on and we can go from there.

If you’ve read this far, chances are you have some experience with poor gut health. Take the time to leave a comment and share your thoughts so others can learn too! 

References and Resources

  1. A Concise Manual of Pathogenic Microbiology
  2. Initial responses to endotoxins and Gram-negative bacteria
  3. Resistance in gram-negative bacteria: Enterobacteriaceae
  4. Proteobacteria: microbial signature of dysbiosis in gut microbiota 
  5. Diversity of the Human Intestinal Microbial Flora
  6. The challenge of Helicobacter pylori resistance to antibiotics: the comeback of bismuth-based quadruple therapy 
  7. Prevalence of antibiotic resistance in Helicobacter pylori : A recent literature review
  8. The Antibiotic Resistance Crisis Part 1: Causes and Threats
  9. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
  10. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances 
  11. Probiotics: Choosing The Right One For Your Needs
  12. Colonic Food: Pre- and Probiotics
  13. A mannose-specific adherence mechanism in Lactobacillus plantarum conferring binding to the human colonic cell line HT-29.
  14. Lactobacillus reuteri (DSM 17938) in Infants with Functional Chronic Constipation: A Double-Blind, Randomized, Placebo-Controlled Study
  15. Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: A double blind prospective study 
  16. Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: A double blind prospective study
  17. Probiotics and gut health in infants: A preliminary case-control observational study about early treatment with Lactobacillus reuteri DSM 17938.
  18. Effect of Lactobacillus reuteri (DSM 17938) on methane production in patients affected by functional constipation: a retrospective study
  19. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders
  20. VSL#3 Improves Symptoms in Children With Irritable Bowel Syndrome: A Multicenter, Randomized, Placebo-Controlled, Double-Blind, Crossover Study
  21. A randomized controlled trial of a probiotic, VSL#3, on gut transit and symptoms in diarrhoea-predominant irritable bowel syndrome
  22. Probiotic Preparation VSL#3 Induces Remission in Children with Mild to Moderate Acute Ulcerative Colitis: A Pilot Study
  23. Effect of a Probiotic Preparation (VSL#3) on Induction and Maintenance of Remission in Children With Ulcerative Colitis
  24. Probiotic mixture VSL#3 protects the epithelial barrier by maintaining tight junction protein expression and preventing apoptosis in a murine model of colitis
  25. Probiotic lactobacilli and VSL#3 induce enterocyte b-defensin 2 
  26. Guardians of the Gut: Enteric Defensins
  27. Towards a more comprehensive concept for prebiotics
  28. Prebiotics and resistance to gastrointestinal infections
  29. Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics
  30. Antimicrobial properties of Allium sativum (garlic)
  31. Antioxidant and antibacterial potential of pomegranate peel extracts 
  32. Antibacterial, antioxidant and tyrosinase-inhibition activities of pomegranate fruit peel methanolic extract
  33. Beneficial effects of green tea: A literature review
  34. Diet, the Gut Microbiome, and Epigenetics  
  35. Green tea polyphenol epigallocatechin‐3‐gallate improves epithelial barrier function by inducing the production of antimicrobial peptide pBD‐1 and pBD‐2 in monolayers of porcine intestinal epithelial IPEC‐J2 cells
  36. Targeting Bacterial Biofilms by the Green Tea Polyphenol EGCG
  37. Green Tea Liquid Consumption Alters the Human Intestinal and Oral Microbiome  
  38. Long-Term Green Tea Supplementation Does Not Change the Human Gut Microbiota
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  1. Hi – you kindly responded to me on another page about B.Wadsworthia. Is it possible to have an overgrowth of that and Klebsiella? The reason I ask is because I cannot tolerate starch at all. If I eat wheat or potatoes or rice or pastry or pasta or porridge, I get a little wheezy within hours of eating it, often sneeze, always have blocked ears, and the next day, I get breathless easily on the slightest amount of exertion. My lip/leg will get itchy in the regular places and I often find I get post nasal drip when I lay down to sleep along with a racing heart and insomnia. My guess is, my immune system is ramped up so minor things like dust in the bedroom might be triggering a response. I’ve just started taking a prebiotic with the yeast that fights Klebsiella (I cant think of the name its something like saccharides) and it does not seem to be helping on its own. Maybe I need to look into treating the biofilm issue as suggested.

    The thing is, I have barely had any of the foods that I know will trigger a response for about two years. I am not rigorous because cutting down on most common problem food types (fodmaps, gluten, lectins, histamine intolerance, etc) has never solved the problem, so I do have something starchy about once a week and live with the symptoms because I know I have not gotten to the root of the problem. That means my diet is mostly meat and dairy with the veg I can tolerate. I have suspected a reaction to sugar but when I used artificial sweeteners or fruit, I still respond. What I realised recently is that a lot of the starches I eat would be combined with dairy – butter on the spuds/bread, cheese on the pasta, etc – so I wondered if it was also the fat I was eating causing probs, which lead me to ask you about B.Wadsworthia.

    What has convinced me even more that I am dealing with more than one overgrowth is a) I took a probiotic with inulin for a short while, and it made me feel AWFUL and b) since I started the new prebiotic that targets Klebsiella, I have been really strict with starches and would say I had almost none. I made myself a trifle the other day, with ingredients that included a tiny bit of maize starch in the custard, topped with whipped cream. I had to use it up so had two portions during the course of the day. The next afternoon, I had the worst episode of breathlessness I have ever experienced after walking only a few yards up a slight incline, and I am not sure I did not pass out for a split second as I sat in my car gasping for breath (please do not worry – these symptoms have been looked at by a team of specialists over the space of a couple of years and the very fact they come and go has confounded us all. Point is, I have been very thoroughly checked out). This episode happened against a background of having less starch than I would usually have and more dairy/meat (if I cant eat legumes, grains, pots, wheat or anything starchy, there is not much left).

    I’ve read a few of your articles about this and appreciate that you have pointed out inulin might cause problems with Klebsiella so other prebiotic fibres would be your recommendation. I just wanted to be sure it is possible to have an overgrowth of both before I try to make a plan for myself based on your wonderful articles. Please remember, I do not have the funds for private tests so I am having to treat myself based on my responses.

    In short, I am thinking reduce the fat, stay off the starches for the time being, continue with the new prebiotics, take something to treat the biofilm and then look at herbal meds? Not sure what I can take instead of inulin but I will try to find out. If my reply is too long winded please feel free to ignore all of the background info.

    1. Hi Rose,

      Happy to help where I can.

      Your case sounds quite complex and chronic (I assume this has been more of a long term issue?). There are a number of key things/red flags to rule out that would present in a history (coeliac disease, SIBO, gut infections and the probable dysbiosis that you suspect). It is almost impossible to tease out the details without a consultation.

      One thing I can say is that partially hydrolysed guar gum is one of the better tolerated prebiotics and would help in cases of bacterial overgrowths. I am working on an article and can post the link here when it is done.

      Sorry that wasn’t much help!


  2. I’m treating a large intestine dysbiosis from cdiff, and From taking antibiotics. I don’t have Sibo, but a GI map test showed dysbiosis. I’m treating with PHGG and trying to increase my intake of fiber as tolerated. My question is about the PHGG. I’m up to 1/2 teaspoon per day ( going slowly to avoid too many symptoms) but i find even at that amount I get gassy and slightly uncomfortable. Nothing I can’t deal with, but is this normal? Will these side effects eventually go away? Thank you!

    1. Hi Bernadette.

      Very hard to speak to without knowing your case. That said I haven’t had a patient yet who has not tolerated the PHGG if we introduce it low and slow. Some need to work it up at a slower rate. Extra gas is common. I interpret this as the microbiome shifting. There will be some fermentation happening. A lowering of the gut pH is the goal!


  3. Thanks for sharing such useful information. I too have an overgrowth of Klebsiella in my colon (GI Map). My main symptoms are IBS-M (constipation alternating with Diarrhea). I have been taking 1 SB tablet a day, combined with 1 broad probiotic. I have read that starch nurtures the growth of Klebsiella and has a role in Ankolising Spondylitis as well. I must I do love bread and pasta. I am happy to reduce my intake of starch but was interested in your opinion and experience in relation to what extend the reduction of starch can impact the reduction of Klebsiella. Keep up your wonderful site.

    1. Hi Maria,

      Thanks for your comment!

      I don’t focus specifically on reducing starch unless absolutely necessary. Klebsiella (generally) is quite easy to treat by reducing the pH of your gut and targeting it with appropriate herbal medicines as well as probiotics.

      If you are experiencing any bloating (or worsening of other symptoms post meals) I would explore the small bowel as well – more here –

      Hope that helps.



  4. Hi Todd happy to see your articles. I did a comprehensive stool analysis which showed Klebsiella ++++ and proteobacter. Could you please tell me what herbs to take? I have lots of food sensitivities and histamine issues that I can hardly eat anything. Shall I take garlic and green tea? I put garlic cloves in the microwave for a few seconds. Not sure what prebiotic is good for me as I tolerate low fodmap better. Thank you Todd and waiting for your reply.

    1. Hi Valsa,

      There are a few low FODMAP prebiotics like PHGG and acacia fibre that are helpful here. If you need to go even slower then sometimes I start off with ground psyllium seed (the husk is not quite as good but useable in a pinch) and then move up as tolerated.



  5. Todd’s expertise with all the facets of SIBO (leaky gut, constant bacterial infections, reflux, diarrhea…) is quite awesome. This article shows just how much he has thoroughly studied and gotten inside the subject. I had done a lot of research on the topic due to my own SIBO condition, but he keeps surprising me with information and knowledge that l had not heard of. His approach is gentle and self-experimental, so the patient is constantly learning about his own condition and how to manage (and work towards curing) it. I have only been in his contact for about 6 months, but my awareness and ability to manage the SIBO has dramatically increased digestive power, and in so doing, the quality of life. Anyone with chronic SIBO will know what l mean. Thanks Todd. This article is so informative, and answers so many SIBO-related questions.

  6. Thank you for this comprehensive study and report. You and your work are providing light for those needing help and answers in confronting this difficult illness.

    I’ve been diagnosed with high levels of intestinal candida (stool test) along with high levels of SIBO (for hydrogen and combined hydrogen/methane)through a lactulose breath test.

    Specfically, the stool report indicates:

    3+bacteroides fragilis; 4+bifidobacterium spp; no growth escherichia coli; 1+lactobacillus spp; 3+ enterococcus spp; 4+clostridium spp;

    2+klebisella pneumoniae/variicola; 1+streptococcus anginosus.

    I suffer daily from such intense muscle pain in the upper legs (as well as early morning stomach pain, depression/anxiety and tinnitus). Are these symptoms related to my SIBO/candida, in particular the intense leg thigh pain? Are there remedies you can suggest? Any insight and advice you can provide are so very much appreciated.

    Stay well and safe.

  7. Hello
    My son has 4+ citrobacter frendii complex and 3+ citrobacter frendii isolate 2

    1+ Bacteria licheniformis
    I have started him on a probiotic, will that be enough to get rid of it? Thank you

  8. Hi!
    Just wanted to say thank you for your articles!
    Reading them one by one is more addictive that watching soap operas 🙂
    And yet. Helping people can be hard and demotivating, but please let it be known to you that even people from the other side of the world like me are reading you.

  9. Hi, I prefer holistic healing and I’ve known of many oils for removing infections. Is there yet a product of combined oils or herbs to remove teeth infections. There are oils for use in the mouth but I am wanting a product to remove infections in teeth besides rinses. Or just internal infections in general. 🤔🤗

  10. Thank you for this great piece of knowledge. I had a blood test that showed high levels of streptococcus. What are you herb recommendations please

  11. “Twenty years ago while living in LA at sea level a lung specialist told me ” you have the worst scarred lungs I have seen in my 17 years of practice. I since retired and moved up here to Jackson WY elevation 6,200 feet I experienced shortness of breath and dry cough till i started on Pulmonary fibrosis herbal formula, It has really helped me become more relaxed, breathe better, easier and more from my diaphragm, just as you they it would. Many thanks for this great product.

  12. I’m living proof that you can live comfortably with COPD. I have emphysema, but emphysema doesn’t have me. After years of living with chronic obstructive pulmonary disease (COPD) with a bronchodilator medication approach, I didn’t have much improvement till I started using World Rehabilitate Clinic Herbs Formula which has made a tremendous difference With a period of 2 months. They specialize in internal and pulmonary medicine, all my symptoms have declined completely, I feel normal again, but I have a few weeks left completing the treatment. I can now go about my daily activities. It’s also crucial to learn as much as you can about your diagnosis. Seek options visit ( worldrehabilitateclinic. com).  

  13. Hi Todd,

    Do you recommend sanitising living spaces and personal use items while treating/clearing bacterial overgrowths in order to avoid re-infections? And also protect other peeople sharing the same living space from contracting the bugs? Especially if symtoms are systemic like oral, nasal, uro-genital and can easily spread through touch? Thanks much.

  14. Hi! I was wondering what you thought about Microcidin AF and Biocidin? Would you recommend one or the other or a combination of both? Thanks so much for your answer!

  15. Hi Todd, just to say how much I enjoyed your article, and how much I love your easy/personal writing style. I love the confession of obsession about polyphenols too. I am a naturopathic nutritional therapist working in England and felt I must reach out and thank you for your amazing work here and your references. I do not specialise in any particular health area, partly because every client presenting with x will also have y and z things that need addressing first. But gut health is way up there so I do try to keep abreast. I just did a stool test on myself (no GI symptoms) but just wanted to see where on the scale someone who ought to have a healthy gut given their knowledge and crucially healthy diet and lifestyle habits, has. I found I was in the top 11% for microbiome diversity. I think that this can serve as hope for those who are struggling. As a teenager I was taking back to back antibiotics for tonsilitus, so many that I lost forever the thick lustrous hair I once had. But it shows that despite that, we can recover. My diet makes a point of increasing biodiversity and so it gives me increased confidence on what I recommend to my clients. But your point about seeing the big picture when a stool test comes back really resonates with me. Rather than rolling out the big guns (herbs) straight away, using other beneficial bacteria to competitively inhibit etc seems so very sensible, and fits in with my thinking very much. So, a big thank you again. I shall look out for more articles. Nicki

  16. I have been suffering with cdiff recurring for 6 months now. Originally caused by taking 1 Dr. prescribed antibiotic for bladder infection. I am also unable to fully clear up the UTI. Currently taking goldenseal but since it interferes with blood pressure pills I’m afraid. Would appreciate ANY help.

  17. This sounds quite promising – someone who thinks like I do. I’ll look forward to seeing other information from you.
    I did want to point out something that is unknown except among some of those who are dealing with it. A diagnosis of FQAD is becoming more and more common as more and more people realize what has happened to them after taking a fluoroquinolone antibiotic. They become fluoride-poisoned, and it is a devastating condition that is extremely difficult to recover from. FQ abx destroy the microbiome in a big way, in addition to the permanent deposition of fluoride into receptors for ++ and + valence minerals.
    So, green tea? Green and black tea are plants that take up fluoride from the soil they are grown in, and those of us with FQAD must avoid them.
    Just a nota bene to those who might benefit from knowing this.

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