A Gross Tale: 9 Ways That Gut Bugs Cause Sickness and Pain

It’s a battle of good versus evil. Possibly a fight between the Rebel Alliance and the Empire. Think of it as a death match between the weak and the strong.

What on earth are we talking about? The battle going on inside the gut of every human being on the planet. This is no trivial matter… if the bad guys win, the person who’s health is affected will suffer.

Things like heartburn, bloating, gas, indigestion – all the way to psoriasis, joint pain, neck pain, cancer and even death.


The correct term to describe the inhabitants of the gut is the “microbiome”. It is a collection of about 10,000 different bacterial species that outnumber the cells in the human body by 10:1. All of the gut bacteria are estimated to weigh 3 pounds – almost the same as our brain.

The balance of the good guys to the bad guys determines if that person is healthy or chronically ill. One critical factor controls this balance… the strength of the immune system in the host.

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If the immune system is strong, it’s likely that there will be a balance. And… if the host is weak – look out below – a sickness spiral gets going like a snowball going downhill and it’s hard to stop. We call this “dysbiosis”.

A common way to get more good bacteria into the gut is to eat foods like sauerkraut, kombucha, kefir,  pickles and plain yogurt with active cultures.

Another route is the use of probiotics (the good guys). A good quality probiotic will contain prebiotics, which are sugars that feed the good guys in the capsule.

It is recommended to take the probiotic capsule on an empty stomach – about 30 minutes before a meal. Usually, one per day is enough. Here are some of the beneficial strains of bacteria to look for on the label:

  1. Lactobacillus paracasei
  2. Lactobacillus acidophilus
  3. Bifidobacterium bifidum
  4. Bifidobacterium lactis
  5. Lactobacillus rhamnosus
  6. Lactobacillus plantarum
  7. Saccharomyces boulardii
  8. Fructooligosaccharides (FOS)… the prebiotic that feeds the good bugs

These good guys strengthen the immune system – and the gut makes up about 80% of the immune system. The more good bugs there are leads to the less of the bad guys.

The result is better digestion, a more positive mental attitude (the gut bugs make serotonin – which is a “feel good” neurotransmitter for the brain), more energy and overall improved health.

A healthy gut leads to better sleep. Why? A little known fact is that melatonin, the primary sleep hormone, is made in the pineal gland of the brain – but 400 times more melatonin is made in the gut than in the noggin.

Healthy guts also lead to better moods, a more positive attitude and less brain fog.  Serotonin controls all of this. Guess where the majority of serotonin is made… in the gut.


The bad bugs can come from different sources. Many people that travel outside of the United States pick up bugs. They can come from contaminated food (usually exposed to feces), contaminated water, undercooked food and exchange of bodily fluids. This is another reason that safe sex is so important.

There are three main kinds of bad bugs:

  1. Parasites: these are definitely the nastiest of the bad bugs. They have arms and legs and actually crawl around inside the gut (really!). They go through a life cycle like this: EGG => LARVAE => CYST => ADULT. They lead to food sensitivities (like trouble digesting dairy), release toxic chemicals that form biofilms around the inside of the small intestine, put stress on the liver and tax the immune system. These critters cause tremendous damage to the little fingers that project from the lining of the small intestine, known as the villi. When these villi are damaged, nutrients are not absorbed properly.

(The villi toward the back of this photo are normal – those in the front are damaged.)

Some of the more common parasites include:

A) Cryptosporidium parvum: this is a highly invasive parasites that infects the entire GI tract. It is also sneaky and hides in the liver and gallbladder, which makes it difficult to eradicate. Some of the primary symptoms of this infection are: watery but non-bloody diarrhea, loose stools, anorexia, nausea, vomiting and abdominal pain. It does through a 7 day life cycle in the gut… which means that the number of these critters doubles every week in the gut if not treated.

B) Giardia lamblia: typically grows in the small intestine. It attaches to the lining of the small intestine and damages the villi – which leads to lactose intolerance, sucrose intolerance and reduces the ability to absorb fats. This often results in maldigestion, malabsorption and malnutrition.

C) Blastocystis hominis: typically found in humans, farm animals, birds, fish and even cockroaches. Most significant is that it affects the synovial fluid in joints – causing neck and joint pain. Other symptoms include watery diarrhea, gas and abdominal pain.

2. Bacteria: a group of single cell organisms (no arms or legs on these guys).

Some of the most common bacteria are:

A) Clostridium difficile: causes watery diarrhea 3 – 15 times daily in mild infections. More severe infections can cause bloody stools, fever, swollen abdomen and kidney failure. Most people have some in their gut… but it isn’t a problem as long as the host’s immune system is healthy enough to keep them in check.

B) Helicobacter pylori (H. Pylori): probably the most well-known bacterium. It causes heartburn/reflux, duodenal/peptic ulcers, migraine headaches, and can lead to stomach cancer. THIS IS A HIGHLY CONTAGIOUS BACTERIUM. If the spouse or significant other has it, the other partner is likely to have it too. It also is easily transmitted from adults to children. The moral of the story is that if one family member tests positive, the rest of the family needs to be tested too. See the information on testing and treatment below.

C) Citrobacter: responsible for respiratory tract infections, urinary tract infections, sepsis (bacteria in the blood), and rheumatoid arthritis which may cause neck/joint pain.

3. Yeasts, fungi and Candida albicans: these organisms are normally found in small amounts. They have a predilection for mucous membranes… such as the eye, mouth and lining of the digestive tract. People with healthy immune systems often have no symptoms. Compromised individuals may have skin lesions, sinus problems, white coating on the tongue, digestion issues, athlete’s foot, brain fog and joint/neck pain.


Stool testing is the best way to see if there is a gut infection. Samples are collected over three consecutive days and sent to the lab in a refrigerated container for immediate analysis. The reason for 3 days of sampling is to improve the chance of detecting the bad bugs since some have a 7 day life cycle.

The client must properly prepare for the test by taking a “biofilm buster” for two weeks prior to the test. This biofilm is like sludge that forms on the lining of the small intestine and can obscure the results.

The lab tests the samples in different ways:

  1. Microscopy: looking for Ova/Parasites and Yeasts under a microscope
  2. Microscopy with Trichrome stain: using staining techniques to further identify Ova/Parasites and Yeasts.
  3. Antigen testing: looking for chemical traces of gut bugs that cause the immune system to produce antibodies to protect the host. Most useful to identify Crypto, Giardia, H Pylori
  4. Cultures: growing bugs in a Petri dish. It identifies bacteria, yeasts and fungi.


First of all, the test results must be interpreted by a qualified physician or Functional Medicine clinician. If a FM clinician finds a positive tests, by law they must refer the patient to their doctor for treatment.

After that, the physician’s treatment may vary. Some doctors will see a positive test but the patient has no symptoms. Often, in these cases, the doctor will decide not to treat the bugs. Other physicians will prescribe strong antibiotics… which will kill the bad bugs – but kill a lot of good bugs too. Oftentimes, this will leave the person worse off than if they were left alone.

A second option is for the person to self-treat. By this, we mean that the treatment is done at home under the supervision of a Functional Medicine Practitioner. Botanical treatments are used – which kill off the pathogens but are less destructive to the good bugs in the gut. This is often the best route to go to minimize long-term issues after treatment.

Here’s the moral of the story: the bugs in the gut are often overlooked as a source of health issues. When there are more bad than good gut inhabitants, mysterious health issues oftentimes appear.

A Functional Medicine Practitioner is trained to test, treat and follow up with any gut issues and is probably the best clinician to consult if the patient has long-term health issues that will not go away.

PS: I’m offering a free 30 minute no-obligation consultation to discuss issues like this. Just go to www.stopneckpainnaturally.com and click on “Get One-On-One Help”.

See ya on the other side!

    — Howard

Here Are 5 Natural Ways to Relieve Your Neck Pain Right Now...

(Especially If You Can’t Sleep At Night Or You’re Facing Dangerous Surgery)

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