Living With Our Microbes: Rethinking the Fear of Parasites

What if our fear of parasites, and the cleanses it drives us to, is doing more harm than good? I believe it is. I believe the war we wage on the organisms inside us is stripping away the very microbes that protect us, and keeping our bodies in a state of fear that makes healing harder. This is a long article, because the argument deserves to be made in full. I want to take you through the science of the microbiome, what the soil taught me, what we have lost over the last few generations, and what Dr. Hamer showed us about microbes as part of healing. Then I want to give you a better way forward.

Parasites are the villain of the wellness world. Scroll for a few minutes and someone will tell you that worms are behind your bloating, your fatigue, your cravings, your grinding teeth and your poor sleep, and that a cleanse three or four times a year is the answer. NPR, the American public radio news network, reported in March 2026 that infectious disease doctors are now fielding more calls from people convinced they have parasites, with one popular influencer telling her audience she thinks 95% of us have them.

I see the other side of this in my practice. Clients come to me partway through a parasite protocol, or just finished one, often with loose stools, low energy and a gut that feels more unsettled than before. Many of them are frightened. They believe something is living inside them that has to be found and killed.

I want to offer a different way of looking at this. It comes from years of watching living blood, from studying the human microbiome, and from the work of Dr. Ryke Geerd Hamer and German New Medicine. It is a view of the body as an ecosystem, where microbes, including the ones we call parasites, are part of the living community that keeps us well.

How the Soil Changed My Mind

I did not start out thinking this way. For most of my life I have been a homesteader and an organic gardener. When something attacked my plants, I reached for a natural remedy to get rid of it. I was proud that everything I used came from nature.

Then I did the Soil Food Web Consultancy Microbiology program, Dr. Elaine Ingham, and I spent months looking at soil under the microscope. I watched bacteria, fungi, protozoa, nematodes and microarthropods all working together in the soil food web. Bacteria and fungi make the glues that hold soil into crumbs and give roots air and water. Protozoa and nematodes eat the bacteria and release nutrients right where the roots can take them up. And when that community is rich and diverse, the plant is protected. The beneficial microbes cover its leaves and roots, take up the space and the food, and leave nothing for a pathogen to settle on. A healthy plant in living soil can defend itself.

That was when it hit me. I had been following the same approach as big agriculture. They used chemicals and I used natural products, but the thinking was identical: find the pest and kill it. I was treating symptoms and ignoring the soil.

It was not long before I saw the same pattern inside us. Our gut is soil. Our microbes are the soil food web. When our colonies are full and diverse, they hold the space, feed the gut lining, train the immune system and leave very little room for an opportunist to take hold. When we strip them away, with antibiotics, processed food or a strong cleanse, we create bare ground. And bare ground is exactly where the weeds and pests move in.

We Are More Microbe Than We Realise

Your body is home to roughly 38 trillion bacteria, living alongside about 30 trillion of your own human cells. That is the most careful estimate we have, from researchers at the Weizmann Institute, who found the two numbers are so close that a single bowel movement can tip the balance one way or the other.

When we count genes, the picture changes completely. The European MetaHIT project catalogued 3.3 million microbial genes in the human gut, about 150 times more than the roughly 20,000 genes in our own genome. So we carry more microbial DNA than human DNA. Think about that. Most of the genetic information working inside us belongs to our microbes.

Those genes do real work. They break down fibres we cannot digest, make vitamins and short-chain fatty acids, train the immune system, help clear hormones and toxins, and protect the gut lining. And bacteria are only part of the community. Living with them are archaea, yeasts and fungi, viruses, protists and, in many people around the world, small worms. These are biomes within biomes, all shaping one another, much like the bacteria, fungi, nematodes and insects in living soil. Humans are a protrusion walk of microbes.

This matters for the parasite conversation. A body that is mostly microbial by genetic count is a body that has been in partnership with microbes for its whole evolutionary history. Health lives in the balance of that partnership.

What We Have Lost

If the gut is soil, how much of that soil have we already lost? Microbiologists Justin and Erica Sonnenburg at Stanford have spent years asking this question. I read there book a few years ago and it had a great impression on my and my approach the health.

In 2023 their team published the deepest look yet at the gut of the Hadza, one of the last hunter-gatherer peoples, who live in Tanzania without refrigeration, processed food or modern sanitation. The average Hadza adult carried about 730 species of gut microbes. The average Californian carried 277, fewer than half. The researchers recovered more than 91,000 microbial genomes, and 44% of them had never been recorded before. They also identified 124 gut species that are vanishing from people in industrialised countries.

The Yanomami of the Venezuelan Amazon, a village with no documented contact with the outside world, showed the same thing. In 2015 researchers found they carried the most diverse microbiome ever recorded in any human group, close to double the bacterial diversity of people in the United States. The team described a gradient: the more contact a group had with antibiotics and processed food, the less diversity it carried.

The Sonnenburgs also showed how this loss deepens over time. In a 2016 study in Nature, mice carrying human gut microbes were fed a low-fibre, Western-style diet. In one generation, most of the change could be reversed by bringing fibre back. Over four generations, more than two-thirds of the species disappeared, and adding fibre back could no longer restore them. The missing microbes had to be reintroduced along with the fibre to feed them.

So here is the question I keep coming back to. Over a few generations we have lost a large part of the microbial community our ancestors carried, through low-fibre diets, sterilisation and antibiotics. What were those microbes doing? How much of the protection we are missing today, against infections that now travel around the world in days, once lived in the colonies we no longer have?

Kill Is Kill: Why I Put Cleanses and Antibiotics in the Same Category

A parasite cleanse is usually a blend of strongly antimicrobial herbs: wormwood, black walnut hull, clove, oregano oil, berberine-rich plants and others, often with something to loosen the bowels. An antibiotic is a drug. They come from different places, and people often feel the herbal version must be gentler.

I put them in the same category, because the intention is the same and the approach is the same. Both are built on the idea that something inside us must be found and killed. Both act on a crowded, interconnected community where the target lives right beside the microbes that keep us well, and neither can ask the community who is friend and who is foe.

We know what this looks like with antibiotics. At Stanford, David Relman’s team gave healthy volunteers a standard five-day course of ciprofloxacin. It changed the abundance of about a third of their gut bacteria and reduced the diversity of the whole community, even though the volunteers felt completely normal. When they repeated the course months later, the gut settled into a new state that was different from where it started. Relman described it as if the beneficial bacteria remember what was done to them, and he noted that clinical symptoms may be the last thing to show up.

With herbs the research is much thinner. Some laboratory and animal studies suggest certain plants, such as oregano and berberine, can be more selective than drugs, and walnuts as a food actually feed butyrate-producing bacteria. But the herbal parasite blends people buy online have rarely been studied in humans at all, and they are usually taken at strong doses, for weeks, and repeated through the year. Even prescription dewormers shift the gut community: in a 2023 study in Ghana, people cured of hookworm with a single dose of albendazole showed a significant change in their gut microbiota.

In my book, Inner Garden: Cultivating Microbial Wholeness, I explain that wormwood, rosemary, black walnut and oregano have strong antimicrobial actions. In normal culinary amounts they are safe and even encouraged. Taken in concentrated supplement form, in large amounts, over long periods, they can unsettle the microbial harmony of the gut. Our ancestors used these plants whole, in food, teas, broths and salves, gently woven into daily life. The goal should never be to kill, but to restore balance. Whether chemical or natural, the approach has to shift.

When we wipe out everything, we create emptiness, and an empty terrain becomes the perfect ground for the next opportunist to move in. Each purge leaves the gut with less diversity and less ability to recover. This is why so many people find themselves repeating cleanses every few months, with symptoms that keep coming back.

There is also the effect on the gut itself. Many cleanses cause diarrhoea, and doctors interviewed by NPR warned this can lead to dehydration, poor absorption and mineral imbalance. They also explained that what people often see in the toilet after a cleanse, and take as proof of worms, is usually mucus, fibre or gut lining shed by an irritated bowel. The cleanse creates the very thing that seems to prove it worked.

Old Friends: The Organisms We Evolved With

Scientists have a name for the microbes and small creatures we evolved alongside: our “old friends.” The Old Friends Hypothesis, developed by Graham Rook, proposes that losing contact with these organisms in modern, very clean lives has left the immune system less well trained, which may help explain the rise of allergies, asthma and autoimmune disease. Worms are among those old friends.

The research on them is surprising. A 2023 systematic review and meta-analysis of human studies found that helminth infection increases the diversity and richness of gut bacteria. Diversity is one of the strongest signs of a resilient gut. Researchers have even trialled small, controlled doses of hookworm and pig whipworm eggs for Crohn’s disease, ulcerative colitis, coeliac disease and asthma, because these worms calm an overactive immune response. The results so far are mixed, and this is still experimental, but the idea that a worm could help the gut would have seemed impossible a generation ago.

The story of Blastocystis is even clearer. It is the most common single-celled “parasite” found in human stool, and for decades a positive test meant a prescription to kill it. Then the research turned. A 2016 study found that people carrying Blastocystis had more diverse gut bacteria and fewer of the inflammatory Enterobacteriaceae. In 2024, a study in the journal Cell looked at 56,989 people from 32 countries. Blastocystis was linked to plant-rich diets, healthier weight and better cardiometabolic markers, and when 1,124 people improved their diets for six months, their Blastocystis went up.

So one of the organisms a cleanse is designed to remove turns out to be a sign of a well-fed, diverse gut. It is also fair to say that some parasites do cause real illness, such as Giardia from untreated water or worms in people living without clean sanitation. Those are specific infections with specific tests and treatments. They are a different thing from the idea that all of us are full of parasites that need regular clearing.

To me, words like pathogen, commensal and parasite work more like verbs than nouns. They describe what an organism is doing in a particular place and time, in a particular terrain. Helicobacter pylori is a good example. It is known for its link with stomach ulcers, yet a 2021 meta-analysis of 46 studies found that people carrying it had a lower risk of Barrett’s oesophagus, the condition that can lead to oesophageal cancer. The same organism can harm or protect, depending on the conditions around it.

An Immune System That Learns

Our immune system is not a fixed wall. It learns. Each time it meets a microbe, it studies it, works out how to respond, and keeps a memory, so the next meeting is faster and more precise. This is what immune memory means, and it is why we usually only catch certain illnesses once.

It also learns something just as important: what to leave alone. Most of what our immune system meets every day is harmless, from pollen and food to the trillions of microbes that live with us. Learning tolerance is as much a part of its education as learning to attack. Much of that teaching happens in the gut, where about 70% of our immune tissue sits right beside the microbiome.

This is where our old friends come back in. Contact with a wide range of microbes, and with worms, helps train the regulatory side of the immune system, the cells that calm a response and stop it from turning on harmless things or on our own tissues. Fewer teachers means a less experienced immune system, one that can overreact to pollen, to food or to itself. Many researchers see this as part of the reason allergies and autoimmune conditions have risen so quickly in industrialised countries.

Every time we wipe the gut clean, we also remove some of the immune system’s teachers. A body that is allowed to meet, learn and adapt builds wisdom over a lifetime. A body that is kept sterile, or cleansed again and again, is always starting over.

The Clean-Up Crew: Microbes in German New Medicine

Dr. Ryke Geerd Hamer looked at microbes in a way that changes the whole conversation. In German New Medicine, the body runs a two-phase program after an emotional shock: a stress phase while the conflict is active, then a healing phase once it resolves. His Fourth Biological Law, the ontogenetic system of microbes, describes the role microbes play in that second phase. Microbes are not the cause of disease. The body uses them, coordinated by the brain, to complete the healing phase, provided the right microbes are available when they are needed.

Hamer matched the microbes to the layers of tissue they work on. Fungi and mycobacteria break down tissue that grew during the stress phase. Bacteria work on tissues of the middle germ layer, such as bone and connective tissue, and help rebuild them. Each group arrives as a specialist for a particular job, and in his framework they work only in the healing phase. When we interfere with them, we can interrupt the repair itself.

This is the same thing microbes do in nature. In soil, in a forest or in a compost heap, microbes and small creatures are the decomposers. They move in where there is debris, break it down and return the nutrients to the living system. Nobody would call the worms in a compost heap an infection.

In my own understanding, the same logic reaches to the organisms we call parasites. When a body has been working hard to heal, there is debris to clear: old tissue, waste, mucus, the remains of past repair. Organisms that feed on that material are drawn to it, in the same way decomposers gather on a fallen log. Seen this way, finding a parasite tells us something about the terrain. It invites the question of what the body has been repairing, and what conditions have made that organism welcome.

Why I Keep Repeating Myself

I say this to almost every client, in almost every session. I explain the soil food web, the microbiome, the colonies we have lost, the clean-up crews. And I see it land. There is a look of recognition, a softening, an “aha.” Of course. We are part of nature. We are ecosystems.

Then a few weeks later the bloating comes back, or someone sees something strange in the toilet, or a friend posts about worms, and the same person is halfway through a parasite cleanse. The fear wins. The old story, that something is inside us and has to be killed, runs very deep. It is in our medicine, our advertising, our cleaning cupboards and our organic gardens. A single conversation does not undo it.

I understand why. A cleanse is fast and dramatic. It feels like doing something. Tending the terrain is slow. It asks for months of fibre, ferments and bitter foods, of rest and of patience, and the results come quietly. Most of us were never taught to trust anything that slow.

So I will keep repeating myself, because I believe this is the work that actually protects us. And I want to offer one more way of seeing it. What if the organisms we fear are not invaders at all? What if, as Dr. Hamer described, the body is allowing them in, as clean-up managers, because it has been on a healing track and there is debris to clear? If that is true, then a symptom that sends us running for a cleanse may be a sign that repair is already under way. Killing the crew does not finish the job. It stops it halfway, and the body has to begin again.

The question to ask is not “what do I need to kill?” It is “what has my body been healing, and what does my terrain need to finish?”

Fear Is Part of the Terrain

The fear itself deserves attention, because fear is not neutral to the gut. When we feel under threat, the nervous system shifts into stress mode. Stomach acid drops, digestion slows, the gut lining becomes more permeable and blood flow moves away from the belly. A 2023 systematic review of human studies found that psychological stress is associated with changes in the make-up of the gut microbiota. A review from the US military found the same pattern across psychological stress, poor sleep and other pressures, along with increased gut permeability and inflammation.

So picture someone who believes their body is infested. They feel watched from the inside. They check their stool, read every symptom as proof, and take strong herbs that loosen the bowels and unsettle the gut community. Each round of discomfort seems to confirm the fear, and the fear keeps the body in the very stress state that weakens digestion and the microbiome. It becomes a loop.

I live in Ecuador, where yearly deworming is a common habit. A three-pill course costs a few dollars at the pharmacy with no prescription and no test. When someone asked about it in a local online group, the answers ranged from “everyone does it” to “my doctor says it’s unnecessary unless you test positive.” One reply stayed with me: it is better to make your body a place where parasites don’t want to live than to take pills that kill everything. That is the heart of it. The deeper question is whether we are acting from fear or from understanding.

In German New Medicine terms, a fear like this can become its own conflict. In terrain terms, it is one more pressure on an ecosystem that is trying to find balance. Either way, the first step toward a healthier gut may be letting the fear go.

The Solution: Tending the Terrain

If microbes follow the condition of the terrain, then the most powerful thing we can do is tend the terrain. This is slower than a cleanse and far less dramatic, and it is what builds lasting resilience.

Restore your stomach acid. Strong stomach acid is the body’s first and best gatekeeper. It breaks down protein and kills many of the organisms we swallow before they ever reach the intestine. Bitter foods and digestive bitters before meals, fire cider, and eating slowly in a calm state all wake it up.
Support bile flow. Bile digests fats and also helps keep the small intestine clean. Bitter greens, dandelion, artichoke and beetroot support the liver and gallbladder.
Feed the community. Eat a wide variety of plants: vegetables, herbs, fruits, seeds and nuts. Fibre is food for your microbes, and plant-rich eating is exactly what was linked to a healthy Blastocystis population in the Cell study.
Add living foods. Fermented vegetables, cultured yogurt, kefir and ferments such as papaya and pineapple bring in microbes and enzymes and help the community diversify.
Repair the gut lining. Bone broth, gelatin and mucilaginous herbs such as slippery elm and marshmallow root soothe and rebuild the lining.
Get your hands in the soil. Gardening, walking barefoot and spending time in nature bring us back into contact with our old friends.
Calm the nervous system. Rest, slow breathing, sleep and time outdoors move the body out of stress mode so digestion can work again.

Fibre deserves a special mention. When our gut bacteria ferment the fibre in plants, they make short-chain fatty acids such as butyrate, propionate and acetate. Butyrate is the main fuel for the cells lining the colon, and a strong, well-fed colon wall is our first defence against parasites, pathogens and inflammation. In my book I call short-chain fatty acids nature’s parasite protectors.

The Parasite Out Protocol

In my book, Inner Garden: Cultivating Microbial Wholeness, I share a step-by-step protocol for people who are worried about parasites or have finished a cleanse and feel worse. It has six phases, and each one builds on the one before. Go slowly, add one phase at a time, and let your body tell you when it is ready for the next.

Starve the problem, feed the solution. Take one full month without sugar, including sweet fruits such as bananas, mangoes and dried fruit. Sugar feeds yeast and opportunists, fuels inflammation and slows the immune system. Eat leafy greens, root vegetables, nuts, seeds, good proteins, herbs, spices and good fats, with a few berries. If you slip, return gently. This is practice, not punishment.
Rebuild the terrain with fermented foods. Have 4 to 6 small servings a day, used like seeds scattered through your meals, and match them to your gut.
- If your gut feels bloated or sluggish: 1 tablespoon of raw sauerkraut brine before meals, 1 teaspoon of fire cider in warm water once a day, or 2 tablespoons of ginger kraut with a meal.
- If your symptoms are body-wide, such as fatigue, brain fog or skin issues, and your gut feels fragile: 1 to 3 tablespoons of homemade yogurt or kefir in the morning, 1 to 2 ounces of beet kvass before a meal, or 1 teaspoon of miso stirred into warm water.
- If your digestion is strong: kefir, live yogurt, kimchi or fermented garlic, rotated for variety.
- If you react easily to histamine-rich foods: start with ½ teaspoon of fermented garlic honey in warm water, or 1 tablespoon of lightly fermented pickles, and build slowly.
Replant with probiotics. Choose a multi-strain probiotic with 75 to 100 billion CFUs that includes Lactobacillus acidophilus, L. rhamnosus, L. plantarum, Bifidobacterium longum, B. breve and the beneficial yeast Saccharomyces boulardii. Better still, open a capsule into yogurt, live kraut brine or cooled fire cider and let the microbes multiply in your kitchen.
Feed the microbes you want. Aim for 10 to 15 grams of prebiotic fibre a day, mostly from food: roasted chicory root tea, Jerusalem artichokes, dandelion greens, green banana flour or plantain, and cooked and cooled root vegetables. Start small. A little gas is your inner soil adjusting.
Build resilience with polyphenols. Choose two a day: green tea or teas of turmeric, rosemary or oregano; turmeric in your cooking; dark chocolate of 85% cacao or more; dark berries; and garlic, ginger, thyme, rosemary and oregano in your food. Used as whole plants, these gently discourage unwanted microbes, including parasites, while feeding the beneficial ones. They strengthen without stripping.
Sweep and soothe, only if needed. If symptoms linger once the first five phases are in place, short courses of gentle binders taken away from food can help carry waste out: activated charcoal, food-grade diatomaceous earth and inner-leaf aloe gel. Soothing herbs such as marshmallow root and DGL licorice help repair the gut lining. These are helpers. They never replace the foundations.

This is not a war. It is a return: to your body’s own wisdom, to microbial relationship and to the terrain. When your beneficial microbes are strong, they crowd out what does not belong. Killing makes you weaker. Cultivating makes you resilient.

If you have real symptoms that worry you, such as blood in your stool, weight loss, or diarrhoea after drinking untreated water, a proper stool test through a clinic can tell you what is actually there. A specific organism can then be addressed specifically, while the rest of your ecosystem is left to do its work.

Living With Our Microbes

We are ecosystems. Most of the genes at work inside us are microbial, and the organisms we have been taught to fear include some of our oldest partners. When we see the body this way, the question shifts from “what do I need to kill?” to “what is my terrain asking for?”

A parasite, a yeast or a stubborn bacterium is a messenger about the conditions inside us. When we restore digestion, feed our microbes, repair the gut lining and let the nervous system rest, the community rebalances on its own. That is the work I do with my clients, and it is the same work a gardener does with the soil. Health is not about killing everything. It is about learning to live well in relationship.

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