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  • Writer's pictureMartha Lewis

What’s living in your gut can cause insomnia: H. pylori, candida and parasites

Updated: Oct 27, 2022

This may gross you out but if you can’t sleep, you most likely have pathogens in your gut that are keeping you awake at night. I’m talking about bacteria like H. pylori, yeast like candida and parasites like giardia.

These lovely creatures are nocturnal and so they're eating, excreting, releasing toxins and causing lots of inflammation in the middle of the night. Since cortisol is an anti-inflammatory hormone, your body will release cortisol to deal with that inflammation. Cortisol suppresses melatonin and wakes you up, causing your heart to beat faster and your mind to race when you want to be sleeping. These pathogens are a common reason my clients wake up at 3 and 4am and have a hard time going back to sleep.

H. pylori

H pylori is a type of bacteria in the stomach lining that many of my clients have. You can get this bacteria through uncooked food and it also spreads through saliva which means it can easily spread among family members.

H. pylori thrives by raising the pH of the stomach. Your stomach needs to be acidic to break down protein. If you have H. pylori you probably aren’t digesting food very well, especially meat and other proteins. When your stomach is less acidic, it also impairs pancreatic enzymes that digest food, leads to other bacterial overgrowth and reduces absorption of nutrients like vitamin B12, zinc, iron and amino acids.

Betaine HCL supplements can make H. pylori worse. HCL stimulates it, then it produces more urease which increases the pH of the stomach so it can thrive. I recommend avoiding HCL until you know for sure that you don’t have H. pylori. Biopsies commonly miss finding H. pylori because they sample a specific area and may test an area where H. pylori happens not to be there.

Many doctors don’t treat H. pylori unless you have digestive symptoms. As a functional health coach, I always want to deal with H. pylori because it causes ulcers and an increased risk of gastric cancer and lymphoma. Also, many of my clients start sleeping better once we take care of it!


Candida is a normal part of your gut flora but it can easily take over when your gut isn’t healthy. Maybe you’ve heard about this yeast and you know that candida thrives on sugar. What you may not know is that candida also eats the waste products of other bacteria and parasites. Many people continuously struggle with candida because they aren’t dealing with the primary infection that’s feeding it.

Some signs that you might have candida are:

  • headaches

  • fatigue

  • brain fog

  • weight loss

  • allergies

  • fungus in your nails

  • a really white coating on your tongue

  • vaginal yeast infections

I test for candida in 2 ways with my clients. The GI Map which is a stool test looks for it. But you have to have a serious overgrowth for it to show up there. So I also add candida to the IgG food sensitivity test that I run.

You can also do a “spit test” yourself to see if you might have candida. You spit into a glass of water and watch what happens. If your spit starts to grow “legs” and snake to the bottom of the glass, if your spit is cloudy and sinks quickly to the bottom or if cloudy specks stay suspended in the water, there’s a good chance you have a candida infection.

You get rid of candida by first taking care of the primary infection like parasites or bacteria overgrowth. Eliminating sugar is key, too. Taking supplements like Candidastat and Mega Mycobalance is the third step.


You’ve probably heard of giardia but there are many other parasites that could be keeping you awake at night. I had Blastocystis hominis. Yikes!

These pathogens can cause digestive symptoms like diarrhea, abdominal pain, gas and joint pain. But many times people are “asymptomatic” and so their doctor won’t treat it. Parasites can cause other symptoms, though, such as insomnia so I always suggest addressing them.

You can take anti-parasitic herbs if you have a parasite. I like Raintree’s Amazon AP. But you also want to take a biofilm buster. These organisms form a protective shield called a biofilm around themselves so they can thrive. So you need to break down that biofilm so the herbs can do their work. I use Biocidin for this.

We usually get parasites through contaminated food and water. If you’re travelled out of the country, you likely have a parasitic infection, although you can pick them up in first world countries, too. I suspect I got my parasite when I travelled in Nepal and India 12 years ago. That’s when I started getting my other symptoms, too, like hypothyroidism and not being able to lose weight.

How to get rid of pathogens to sleep better

The only way to truly get over insomnia is to find out what’s causing it. There’s something going on in your body that is causing it and I can help you find out what it is.

The best way to find out if you have any of these pathogens is to do a GI Map. This stool test shows what’s living in your gut, both good and bad. The lab has recently made the test more sensitive to H. pylori so it’s less likely to miss it. Knowing what's in your gut is especially important since it determines what supplements are right for you. How you deal with H. pylori is drastically different than what you do about a parasite.

Since I’m a functional health coach and not a doctor, if your test results show that you have H. pylori, candida or parasites, I am required to give you a letter to give to your doctor. You have 3 options for what to do about it.

  1. Take an antibiotic. There are 3 issues with this approach. First of all, you take an antibiotic for 10 days. The life cycle of h pylori is at least 30 days. Secondly, pathogens form a biofilm or protective shield around themselves. It’s hard for antibiotics and herbs to get through the biofilm. That’s why I recommend a biofilm buster to break down the biofilm so that the supplements or antibiotics can get through and do their job. Lastly, antibiotics kill both good and bad bacteria and damages the gut wall which is exactly what we’re trying to heal.

  2. Self-treat with an herbal protocol and a biofilm buster.

  3. Take antibiotics AND do the herbal protocol.

Many of my clients choose to self-treat instead of taking antibiotics. My goal is to give my clients all the information they need to make the best decision for themselves.

These pathogens also keep your gut from being able to heal. If you have a parasite that's continuously damaging your gut wall and feeding bad bacteria, all the probiotics in the world aren't going to help. (In fact, if you have bacterial overgrowth, probiotics can make things worse.) Dealing with pathogens is the step that most practitioners overlook when they work on healing the gut. Here are the 5 steps you need to take to truly heal your gut.

Your sleep is not going to miraculously get better. In fact, the longer you've been struggling, the less likely it is to magically improve without working on rebuilding your health.

I know how easy it is to keep waiting and hoping because you don't want to take a risk, you don't want to make changes, you don't want to spend more money trying to figure this out.

You know the saying about the definition of insanity: doing the same thing over and over again and expecting different results.

You have 3 choices:

  1. do nothing and keep being miserable because you aren't sleeping

  2. keep trying this supplement and that pill and this doctor and that gadget, crossing your fingers and praying that this will be the one that actually works

  3. commit to the only program that looks at how both your body and your mind are causing your insomnia and dedicate yourself to making the necessary changes to solve this problem once and for all

Most insomnia is caused by something physically going on in your body. It could be hormones, your gut, your liver, your digestion, and more. Lab testing will tell us exactly what's causing it.

How you handle stress and your thoughts about sleep also play a role in your sleeplessness. I give my clients valuable tools to help with anxiety about sleep and stress in general.

The only way to start sleeping better is to address both the body and the mind. It's not a quick fix because there is no quick fix. if you think about it, it’s taken you years to get to this point. Even if your insomnia started recently, your body has been slowly breaking down for a while or a stressful event put you over the edge. Once you stop sleeping well, diet, exercise and a supplement aren't enough to get your body healthy and sleeping again.

If you're ready to figure out your sleep and tired of trying things that don't work, let's chat. On our call, you'll finally understand what's causing your insomnia so you don't have to spend any more tortured nights lying awake frustrated because you don't know how to fix this. If you're ready to figure out your sleep, the first step is to schedule your call here.

Or get the What's Causing Your Insomnia? assessment to find out what could be keeping you awake at night. The assessment will tell you if your gut, liver, blood sugar, hormones and more are sabotaging your sleep so you know what to address.

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