Gut Infections - Viruses, Bacteria, Yeast and Worms - Aspire Natural Health

Gut Infections – Viruses, Bacteria, Yeast and Worms

The other day I  posted on the non-supplement, non-drug treatment of ‘traveler’s tummy’.

To help clarify things, I wanted to do a quick post on the things that can invade our guts and cause problems.

Our gut is a rainforest

We are colonized by microscopic life. Every square inch of our body outside (skin, hair, all our cracks and crevices) and in (our ears, nose, mouth and entire digestive tract from our mouth to our anus, and vagina, if you have one) are full of life.

And the truth is, we know relatively little about it and what it’s really doing.

The place we know the most, and it’s still just the tip of an iceberg, is the gut. We now know that ‘good’ bacteria living in our gut help us digest our food, make vitamins and other helpful and essential substances, protect us from invading microorganisms and talk to our immune system, helping to keep it running smoothly and prevent things like autoimmunity and allergies.

So much for the good guys (for now), let’s talk gut infections

The cast of villains:

  1. Viruses – Most gut infections, that cause diarrheas, are virus based. Viruses are still poorly understood little beasties. Most viral infections are temporary, sweeping in and then back out again. Antibiotics are completely ineffective against viruses, thus most gut infections do NOT need to be treated with antibiotics. Conventional medicine does have a few antivirals, and unfortunately they don’t work very well. Thankfully natural medicine has more. We suspect that in addition to our ‘good’ gut bacteria that we have a pool of viruses – our virome – as well. Are they good? Bad? How many of them are there? We have no idea.
  2. Bacteria – Most acute gut infections, that cause diarrheas, are NOT bacterial. However many chronic gut infections, the kind we’re going to treat in autoimmune disease and other chronic disease are going to be bacterial. Which is where antibiotics and antimicrobial herbal medicines come into play.
  3. Yeast – the role of yeast in the gut is poorly understood as well. We know they’re there, we just don’t really know what they’re doing. Are they normally good? Bad? We know most yeast infections come about NOT because of outside infection, but most often because the bacteria keeping them in check are destroyed. As an analogy: think about mice. Most often a population explosion occurs in mice because the animals that keep them in check – cats, foxes, hawks, owls and more – are destroyed by habitat loss or hunting. It’s not that a bunch of mice came in from outside (an external infection) but that the destruction of an ecosystem allowed them to get out of control. With yeast this most often occurs after a round of antibiotics (destroying good bacteria) when people get thrush (a yeast infection of the mouth or throat) or a vaginal yeast infection. Antibiotics don’t work against yeast, and anti-fungal medications such as nystatin and diflucan are needed. Good anti-fungal natural options exist as well.


Now for the gross stuff

So far we’ve been talking about microorganisms, stuff you can’t see unless you have a microscope. Now we start to get into stuff that you can (sometimes see), parasites. Parasites come in two broad categories.

  1. Protozoa – remember biology class when you looked at pond water under the microscope? You saw little critters with little helicopter blades (cilia) and amoebas (like the blob)? Those are protozoa, and they can cause gut infections. The most famous one here in the Western US is Giardia which you can get out of contaminated water and it causes a nasty diarrhea with a sulfurous smell to it. Giardia can be acute (meaning you get it, have it for a few days and then it goes away) but can pretty easily become chronic (meaning it doesn’t go away). Other protozoal infections I see popping up are Blastocystis Hominis / Fragilis and Entamoeba Histolytica. Most antibiotics are ineffective against protozoa and other drugs or combinations of drugs are needed. I tend not to use a purely natural treatment for protozoa as the protocols can be lengthy, mildly toxic, and long. I’ve seen people do ‘parasite’ purges for months only to retest and find that the parasites are still there. So I typically will use the prescription drugs, often with natural treatments added on for synergistic effect.
  2. Worms – the stuff of horror movies, and if you want to gross yourself out hit up Google pictures and you’ll get your fill. The truth is there are a lot of type of worms that can make themselves at home in our bodies. We can get them from contaminated foods, the environment (hookworms grow in the ground and can actually burrow through the bottom of your feet. Scary!) and pets (where I see it most often). There have been some impressive treatment of non-responsive IBD (inflammatory bowel disease; Crohn’s and Ulcerative colitis) with worm treatments. That is purposefully giving people worms to modulate their immune system. It has provided some dramatic help for some people. The worm that people are most familiar with are tapeworms. I use prescription drugs to treat worms, augmented with natural therapies.


If you suspect you have a gut infection, get tested

How do you know? If you come down with a diarrhea that doesn’t clear up in a reasonable amount of time, or that leaves you ‘never well since’, it’s worth getting tested. If you’re in a foreign country with a high risk of infection, get tested.

The standard testing that MD’s do can be effective if you are currently experiencing diarrhea, significant gas or bloating, or abdominal pain. It is capable of picking up protozoa, and worms as well as a few bacteria (if your MD selects to test for them). Many patients who have come to us have had this testing without finding anything, and we find much more use out of specialty labs.


At Aspire Natural Health we are experts at helping people suffering with digestive issues and autoimmunity.

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Email us at or call us at 425-202-7849.

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Photo attribution –

Another Interesting post:

Gut Bacteria Help us Detoxify and Maintain a “Non-Leaky” Gut