Dysbiosis (aka Parasites, Candida, Bacterial overgrowth etc.)

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Finding a good herbalist

Much of what's written in this article is entirely suitable for a person to work through themselves but, especially if things are quite bad, or you just know that you need further help, then there may be a great deal of benefit to you to go to whatever lengths necessary to find a good herbalist or truly holistic practitioner to guide you on to a safe and strong treatment program. There's a short write-up to suggest how you might go about finding such a person here

Dysbiosis; what is it?

Dysbiosis literally translates to 'bad life'; dys meaning wrong (as in dysfunctional) and bio meaning life (as in biography or biology)

An abundant stream of scientific research is showing that our well-being and a great many health conditions are far more affected by our 'microbiome', a word that encompasses our complex internal micro-biological life, than we ever could have imagined.

Dysbiosis is where the normal, healthy balance of that microbiome has been damaged by an infection of unhealthy organisms such as parasites, fungi or harmful bacteria.

Dysbiosis can damage our health in several characteristic ways:

1) substances such as entero-toxins, fungal spores and mycobacterial fragments get absorbed into the body from their overgrowth in the bowel causing toxic stress
2) the parasitic nature of dysbiotic organisms leaches away the nutrition from our food

3) the immune system is reacting against what it recognises as unwanted invaders. Many of the unpleasant symptoms of dysbiosis come from this immune response.


Symptoms & Diagnosis

Dysbiosis is immediately obvious when a person gets an acute infection in their gut. It typically causes a sudden and profound disruption in the form of vomiting, diarrhoea, fever etc.

However, in many cases, especially when the infection becomes chronic and the body gives up trying to violently expel the invader with vomiting or diarrhoea, the problem develops more widespread efffects.

The classic and most prevalent effect of dysbiosis is an uncomfortable feeling of pressure, swelling and bloating in the gut that doesn't only happen after eating certain foods or go away by itself.

Most people with dysbiosis also get some degree of disordered bowel function in the form of loose stools, increased frequency or urgency in going to the toilet. Many people also report suffering from significantly more gas than usual.

People with chronic dysbiosis also commonly feel fatigued and 'out-of-sorts', especially when their bloating is at its worst. They often report a much higher than usual level of aches and pains and it is now well proven that many chronic inflammatory conditions turn out to have dysbiosis as a primary contributor.

'Dysbiosis is a major cause of ill health, and its successful diagnosis and treatment has been seen to be the turning point in many people's health. However, our first major challenge in this area is that there are several other common health conditions that can give much the same kind of symptoms as those described above. Therefore, before focusing on dysbiosis as the certain issue you must first consider at least three other possible causes for your condition...


When it's gastritis

If you have the same classic symptoms of bloating etc. but you also get reflux in the form of discomfort and pain just under your ribcage, and a bad taste or feeling rising into your throat or mouth, then it is possible that your real issue is gastritis.

If this is the case, then you should know that there is a certain herbal formula that is extremely effective at rapidly alleviating, and often even curing, this common problem. It typically works so well that we can say that if you respond to treatment with these herbs then it is fairly a safe bet that this is what the problem was in the first place. The exact formula and other details are written up here.

When it's food allergy or intolerance

Food allergy & intolerance can look and feel like dysbiosis because of the same kind of inflammatory response of the immune system to something in the gut that it sees as unwanted.

However, in the case of allergy or intolerance, there is usually a history of digestive system problems going back much further, even into childhood, and there are usually other red flags for this such as a history of eczema, asthma, hay fever or migraine.

If this sounds like it could be you then consider the possibilitty that the best path to sort your health out may be to start with an elimination diet of gluten and/or dairy products, or by looking into some bona fide food allergy tests that use blood as the diagnostic medium. This important subject is written up in detail here.

When it's IBS

IBS or irritable bowel syndrome usually starts in the late teens or early twenties and, whilst bloating and disturbed bowel function etc. are also highly likely, there is usually a much stronger correlation to stress being the primary contributor.

IBS is a label that gets used way too often as a kind of catch-all when the real issue is something quite different that just hasn't been diagnosed properly. If you have that hallmark symptom of your gut problems starting in your late teens, early twenties, then consider IBS as a real possibility and carefully read the very detailed article about this complex condition found here.

shared symptoms of dysbiosis, food allergy, IBS etc.


Stool sample analysis

Mainstream medicine's approach to diagnosing dysbiosis is to analyse stool samples but this is only truly useful when there is a frank parasitic infection with one of the organisms that cause acute infections. In fact, many people with who do in fact have chronic dysbiosis have their problem go undiagnosed as a result of this method.

A key difficulty with diagnosing dysbiosis from stool samples alone is that everyone has enormous numbers of bugs in their gut even when they are in good health! The average person has 400-500 different kinds of bacteria and fungi growing in their digestive tracts at any one time. In fact, most adults have at least one kilogram and hundreds of billions of microbes living in their guts when they are perfectly well! Yes, at least some of those organisms will be unhealthy and parasitic but this only becomes an issue when they overgrow and spread out past a point of normal containment. It is their ratio to the whole of the microbiome in its ecological 'rainforest' of the gut lining that matters far more than finding them present in trace amounts in the stools.

To further complicate matters you can get a very skewed version of the situatuon from any one-off sample because we will get a wide variation in the relative numbers of micro-organisms in the stools according to a host of day to day fluctuations in things such as food intake, immune activity and the life-cycles of the various bugs themselves!


Clues in the history

One of the most useful ways to understand the cause of any chronic health problem is to closely question what was happening in a person's life when their problems first began. Many people who turn out to truly have dysbiosis were relatively healthy right up until the time they contracted a gut infection, often from eating out, or travelling, or moving into a new environment, and then everything started from there...

Another common origin story for dysbiosis is when a person has had to take a course of antibiotics or antifungal drugs for some other reason whereupon all the good bacterial flora in their guts has been wiped out and an infection of bad bugs has taken over the newly available space, and never left since...

In my own practice, I use a hydrogen breath sensor, pictured below, to help narrow the field of enquiry down, because high levels of bad bugs in the gut typically produce higher levels of hydrogen in the breath. However, even this is not a definitive test, rather it is a helpful guide within the bigger picture of the person, their symptoms and their history...


Empirical Medicine

If you have good reason to think that dysbiosis may be your key issue, then the next thing to do is to practice empirical medicine. This is where you form a working theory of what you think is the cause of a problem and then proceed with a treatment that you trust will be strong enough to effectively deal with that problem.

If the person then gets better then you were right, if they don't get better then, so long as you were confident in your treatment, you must consider your theory to have been wrong. If any of that sounds clumsy, or unscientific to you, then you're right about that but you should know that the approach of emperical medicine continues to underly an enomous amount of how all forms of medicine are practiced to this very day, people are complicated, and everything is a theory until it can be proven.

The following treatment steps are what we can be confident will either cure, or at the very least significantly improve, dysbiosis. At least enough to be certain whether it is or isn't the core issue,

Step One - 'Weeding the Lawn' - Anti-microbials

If you were to spread out all the tiny folds in your digestive tract it would cover an area that was larger than two entire tennis courts. This happens because of tiny projections in the gut called 'villi' that are there precisely to increase that surface area enough that the essential process of absorbing nutrients can take place in an optimal environment.

A good way to understand dysbiosis is to think of this space as being like a large lawn which has been over-run by unhealthy weeds, insects, fungi etc. In this case the first thing you must do is kill off the weeds, fungi etc. and then after that you can successfully plant new seeds to help regrow a healthy lawn.


Dysbiosis can be a difficult problem to cure; whatever kind of 'bad-life' is in there you can be sure it won't want to leave so you must be prepared to give it a big push to get out. Fortunately, there are two substances that no bacteria, parasite or fungi has yet learned how to resist despite thousands of years of their continual use in humans; Garlic and Wormwood.


Dosage is crucial in herbal medicine; the right dosage of any herb is essential to getting good results with it. Regular amounts of fresh garlic in the diet will help prevent dysbiosis to a good extent but to kill off a well-established dysbiosis in the gut you need a lot more than the regular amounts normally found in food, plus it needs to be raw!

For most people a therapeutic dose to weed out dysbiosis is 4-6 medium sized cloves at a time. This amount of Garlic is best taken with food at either lunch or dinner time and it is best to do the garlic onslaught at least two times a week or not more than three times a week,

The length of time to properly do this treatment with Garlic is 2 or 3 times a week for 6 weeks but be prepared to do extra weeks if you obviously improve on the treatment but start getting worse again when you stop. Parasites, in whatever form they come, are true survivors; you have to be prepared to keep making their home a most uncomfortable place to be until they finally give up and go for good.

Do note that, according to the method of empirical medicine as described above, if you are not clearly responding to the treatment within 3 or 4 weeks then you should stop and pause for thought.; because it may well be that the root of the problem is actually not dysbiosis but rather something quite different as discussed earlier...

How to best take the Garlic is entirely up to you. So long as you get it into you 2 or 3 times a week it will do its work in making your gut an extremely inhospitable place to be a bad bug. Some people simply peel the cloves of garlic then chop them into small pieces and swallow them like little pills with plenty of water. Mixing the freshly peeled and cut garlic into something like a Guacamole or Salsa can make it a more pleasant experience but remember that you must not heat the garlic before eating it. The page on Garlic in the herbal A-Z has a lot more detail about this great friend of our health and a recipe called 'dynamite on toast' that might take your fancy - all that is found here.

Allium sativum (Garlic)



The main herb that I reach for in the treatment of my own patients with dysbiosis is Wormwood. This herb is exceptionally helpful at clearing out stubborn gut infections and even the worst of the worst cases, e.g. patients with medically diagnosed drug-resistant gut infections, are almost always seen to eventually respond to Wormwood.

The down-side to Wormwood is that it is an incredibly hard herb to take in tea or tincture form because of its remarkably bitter taste. In our clinic, we get organic Wormwood, as a raw herb, that we then send to a local company to put into capsules. The typical dose of this product is 4 capsules each night for at least 4-6 weeks.

Note that we do not sell this online and, as mentioned at the beginning, consider finding a good herbalist to be sure to be getting the right stuff yourself. More about weird and wonderful Wormwood here.

Artemisia absinthium (Wormwood)


Die-Off Reactions

You must be aware that, after a few days of either Garlic or Wormwood or both that, assuming you really do have dysbiosis then you are likely to get a die-off reaction.

This process, called a 'Herxheimer reaction', can make you feel quite seedy for a few days. How much it happens varies a lot between different people and likewise exactly how they feel is variable but people typically talk about having felt super tired, or how they felt like they had a flu with random aches and pains, or how their bowel got even more upset for a time.

Note that if any of this happens the first one or two times you take Garlic or Wormwood then it may be that these medicines are too strong for your system at those doses and you either need to reduce the dose or consider another approach.

However, if you are ok for the first few days but then you suddenly start getting die-off reactions, then be encouraged that this probably simply means you are on the right track and that you should just hang in there! Things usually do get better after a short while, i.e. a few days, and then it is usually noticeable that the person's health starts to significantly improve after this point, especially because their immune system registers that it is finally winning against a foe that it could just not get on top of hitherto.

Two white blood cells amongst red cells under the microscope


Drugs for Dysbiosis

You will see if you look into the literature on this subject that there are many Doctors who advocate for the long-term use of antibiotic or antifungal drugs to treat chronic dysbiosis.

It may be that this will be the right approach for some people but I can truthfully report from my own clinical experience that drugs have not appeared to be anywhere near as helpful as the herbal approach and it can clearly be seen that these chemicals are rather hard on people's general health...

That said, some drugs are good at killing things and if a person has actual, literal worms in their digestive tract then they should certainly take a single dose of one of the pharmaceutical worming drugs such as Vermox.

These drugs both paralyse the parasite as well as interfere with its metabolism to the point it can be easily passed out. If in doubt, take a dose of something like Vermox, it will not harm you or your microbiome. If your condition resolves itself, then great! If not, and you do truly have dysbiosis, then you need to treat it over a much longer time frame with the kind of approach discussed here.


Are sugars and yeasts a problem?

I want to say something about a massive misconception in this area that has caused a great deal of grief to people. It is the idea that came about in the 1980s when anyone with the symptoms of dysbiosis was thought to have an overgrowth of the fungal organism Candida albicans. Early writers in this subject were convinced that a diet that contained sugars and yeasts was much to blame for the problem and so strongly advocated extremely restrictive diet programs as part of the cure.

I say this caused grief because, unless you have tried cutting out sugar and yeast containing foods from your diet, you won't know just how painfully limited your life can become. People would report improvements so long as they strictly followed the regimen but as soon as they relented from the program their symptoms would come straight back and I met a lot of people who lost a lot of strength and vitality from this approach.

Organisms in the bowel will feed on whatever waste products are available to them. Avoiding refined sugars will help your immune system be healthier, which certainly is a big deal to getting better from dysbiosis, but such sugars are absorbed much higher up the digestive tract than the bowel.
Dietary yeasts have nothing to do with anything unless you have an actual allergy to one of the ingredients in the yeast-containing food.

The short answer to the question 'do sugars and yeasts cause dysbiosis?' is no. It is chronic infections of unhealthy organisms in the gut that cause dysbiosis and it is a certain fact that you may limit the food supply to these organisms by restricting your diet but that doing so will no more kill them off than it caused them to get there in the first place.


Step Two - 'Re-seeding the Lawn' - Repopulation

Once you have started effectively 'weeding' out the dysbiosis you need to get and keep healthy bacteria inside your body for a very long time i.e. the rest of your life!

Fermented foods

In the long-term, there is also a lot to be said for eating fermented foods to encourage good bacteria in the gut and to prevent a reinfection of dysbiosis. You will find a wealth of practical information on the internet about how to use and enjoy fermented foods, they are all good so really it is a matter of trying things out and finding whatever suits your personal tastes to keep using regularly - a short list includes: yoghurt, sauerkraut, kefir, miso soup, kombucha, tempeh and pickles.


There are many other probiotic supplements in the world of health supplements these days and it's highly likely you will be able to find good products if you have a look around.

You don’t need large quantities of probiotics but you do need to ingest them regularly. Living, healthy bacteria can very quickly make more of themselves in the 'Garden of Eden' they consider your gut to be.

The marketers of probiotics will try to convince you to buy their product above the others because it contains 'so many billion' more good bugs than the competition. Ignore them, it is not the numbers going in that count, it is the quality - and to be sure of quality, you may need proof!

Proving your probiotic

~ Ingredients

  • 1 small tsp of your probiotic powder or 2 probiotic capsules that have been opened and the powder sprinkled on to a spoon
  • 1 cup of milk (cow's milk is best for this but you can use Soy if you don’t have any)
  • 2 small trays or containers (no lids are necessary) that have been sterilised by pouring boiling water over them. 

~ Instructions

  • Pour the milk in equal portions into the two containers.
  • Stir the probiotic powder into the milk in just one of the containers.
  • Place both containers in a cupboard and leave overnight
  • In the morning pour both containers out into the sink and watch what happens.

The container that just had the half cup of milk in it should pour out as expected.
The container that had the probiotic stirred into it should be obviously thicker and hopefully it will have started to curdle. Good, viable, living and healthy probiotic bugs do not take long to rapidly repopulate themselves when they have a good source of food, such as the milk, to eat from so approximately 8 hours should be ample for them to start eating, digesting and curdling the milk.



Not everyone needs to think about this side of things but, especially if you have a history of poor bowel elimination, or some specific areas of bowel pain, then it may be wise to use either Plantago husks, more about them here, or Slippery elm powder, more here.

I use plenty of both of these in my practice but there are no set rules about who to give them to or even how much of them to take. Again, in line with empirical medicine, we may choose to simply 'try and see'.

Does the general condition and bowel health significantly improve on either herb? Does it worsen when they are stopped and again improve when they are re-introduced?

If we come back to the analogy of the lawn, the 'prebiotic' place in this scheme of things, can sometimes be necessary to help prepare the ground for sewing the good seeds of healthy bacteria.

Plantago is particularly helpful as a bulking fiber, it is much used in herbal medicine for both constipation and diarrhoea as a balancing, steadying substance to regularly move through the bowel.

Slippery elm has no equal as a herb to help internally bandage a wounded gut and it can be especially valuable when the person can point to there being a quite specific pain in one or other part of their bowel where we might reasonably expect there was some grazing or other damage to the gut lining in that part of their body. Detailed instructions on how to use either of these herbs are found on their respective pages linked above.

Ulmus fulva (Slippery Elm)

Staying Well

Many people can cure their dysbiosis and prevent it coming back by occasionally having some raw Garlic in their diet and by having a reasonable amount of fermented foods or perhaps a supplement containing good bacteria to keep the gut healthy.

One last point is that if you find that you do get much better with using this approach but then get worse soon after you ease off the treatment then it may well be that your core problem is an immune system that is not healthy enough to keep the bad bugs in check by itself. In that case have a close look at your immune health, more here

Constitutional Health Note:

Finally, there are many other old ways of healing from Nature that you might like to learn more about and if so, then a good place to start would be to learn about your constitution to help better understand how dysbiosis became an issue in your health as well as what kinds of foods, herbs etc. may best help you in other ways.

There is a brief introduction to this subject here and a more detailed section on working out which constitution you are here.

Please understand that I cannot personally advise you without seeing you in my clinic.
This living 'book' is my labour of love so, wherever you are, I wish you peace & good health!



© 2011 R.J.Whelan Ltd