If you’ve been struggling with symptoms that don’t make sense and won’t go away, you may be suffering from one of these two commonly under-diagnosed diseases:
Lyme disease or SIBO (small intestinal bacterial overgrowth)
And because the two conditions present very similarly symptomatically, it can be very tricky to determine exactly what’s going on.
To add an extra layer of complication, the answer to “is it SIBO or is it Lyme disease?” may be:
“It’s both.”
Some experts estimate that up to 70% of people infected with Lyme disease also have SIBO.
But knowing the correct particulars of your diagnosis will be a boon in sending your recovery in the right direction… so you can actually start feeling better ASAP.
What Is SIBO?
SIBO—small intestinal bacterial overgrowth—is precisely what it sounds like.[1] It’s a condition where there are far too many bacteria in the small intestine, an organ that usually contains very few (10,000 times fewer than the gut!).
Most of the time, these extra bacteria have traveled to the small intestine from the gut. And because the small intestine is where our food gets processed, those bacteria have a lot to snack on—especially not-yet-digested sugars and starchy carbs. That causes two big problems:
- It encourages bacteria to grow out of control in an area where they're not meant to be, to the point where even most beneficial bacteria (probiotics) can’t remedy the situation.
- Bacteria transform the undigested carbs into hydrogen or methane gas, which can cause gas attacks, painful bloating, and other uncomfortable GI issues.
And while SIBO starts in your GI system, its effects don’t stay there. In fact, SIBO symptoms can affect your entire body.
What Is Lyme Disease?
Lyme disease is a bacterial infection carried and transmitted by tick bites.[2] If an infected tick bites you, you’ll probably develop severe flu-like symptoms within a few days. Unfortunately, unless you realize you’ve been bitten—and most people don’t—you’ll probably just chalk it up to a nasty case of the flu.
Left untreated, Lyme bacteria hang out in the body until they sense the best time to attack. And they can attack anywhere in the body at any time. That usually starts with whole-body inflammation, including in the gut. Intestinal inflammation leads to leaky gut, which can easily set off a chain of disease-causing events.
Plus, most ticks carry multiple infectious bacteria. So if you have Lyme disease, there’s a good chance you have at least one co-infection as well. That can add layers of complexity to properly diagnosing the situation.
Overlapping Symptoms Make These Conditions Hard to Decipher
Both Lyme and SIBO can cause whole-body symptoms that seem unrelated to each other. That makes it much harder for most doctors to diagnose them properly. In fact, it can take years for some patients to get a correct diagnosis.
Lyme disease is especially sneaky.[3] It causes one set of symptoms when you’re first bitten, and different symptoms once the bacteria settle in for the long haul. The immediate symptoms can make you feel like you have the flu, and include fever, nausea, and abdominal pain. The longer-term symptoms stump most doctors, and they include anything from exhaustion to joint pain to chronic constipation and other GI symptoms.
The SIBO symptom list contains some identical issues including nausea, abdominal pain, constipation, exhaustion, and joint pain… along with many others.[4]
You can see why it’s so hard to figure out what’s going on. Both of these diseases can hit you with some hard-to-manage health challenges. So it’s crucial to get the right diagnosis… and begin the right treatment.
And here’s where things can get even more complicated…
Can Lyme disease cause SIBO?
It turns out that Lyme disease can cause three of the biggest risk factors for SIBO:
- Long-term or recurrent antibiotic use
- Dysmotility (slowed down movement in the small intestine)
- GI inflammation
First, there’s the antibiotic factor, which acts like a double-edged sword. During antibiotic treatment—used for both Lyme and SIBO—some of your symptoms may disappear. But both Lyme and SIBO are persistent infections, calling for long-term or recurring courses of antibiotics. And both, especially SIBO, can get worse quickly as soon as antibiotic treatment stops.
Next, Lyme disease can affect the nerves in the digestive tract, which can cause dysmotility.[5] The slowed-down process leaves food lingering longer in the small intestine. The longer the bacteria have access to food, the more they can flourish. That’s why SIBO patients are around 600% more likely to suffer with dysmotility.[6]
Finally, Lyme disease can cause long-term systemic inflammation.[7] Intestinal inflammation can throw the gut microbiome out of healthy balance, allowing pathogenic bacteria to grow out of control. Those pathogens attack the protective gut barrier, leading to leaky gut—meaning the pathogens escape into the bloodstream. From there, they can sneak into the small intestine and create or worsen SIBO.
The Right Probiotics for Lyme & SIBO Support
If you have Lyme disease, your gut microbiome is almost certainly out of balance—a condition called dysbiosis where harmful bacteria outnumber beneficial bacteria in the gut (the large intestine).
And if you have SIBO, you’re definitely dealing with a bacterial imbalance in your small intestine.
To support your gut and encourage a healthy bacterial balance in both the small and large intestines, one of your greatest allies can be probiotics. But there’s a problem…
When you already have SIBO, a problem of bacterial overgrowth, you don’t want to fuel it by adding more bacteria—even probiotic bacteria—into the mix.[8] Unfortunately, that’s what happens with most commercial probiotics, which can make you feel much worse. And that’s why a lot of doctors will tell you to avoid probiotics when you have SIBO.
But avoiding probiotics altogether solves nothing; both Lyme disease and SIBO call for probiotic support to fully address the problem. The trick is to use the right probiotics…
Spore Probiotics to the Rescue
In order to NOT encourage the intestinal challenges that come from Lyme disease and SIBO, a probiotic must have the following characteristics.
- It can’t go to work in the small intestine.
- It must survive stomach acid and digestive enzymes to reach the gut intact and alive.
- It has to kill off pathogens in the large intestine.
- It must support and encourage many different types of beneficial bacteria to flourish.
There’s only one type of probiotic that meets all of those qualifications:
Spore Probiotics.
Spore probiotics have tough protective shells that allow them to stay alive in harsh environments. Unlike other probiotics, they can withstand extreme temperatures and easily survive digestion to make it all the way to your gut alive and ready to go to work.
When they reach your large intestine, spore probiotics shed their endospore shells and begin their trek—traveling from the top of your large intestines to the bottom, wiping out bad bacteria, and encourage your beneficial bacteria to thrive along the way. This helps to support a healthy balance in your gut microbiome.
And a healthy gut microbiome can help bring balance to your immune system as well, so you can tackle health challenges head on...
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Sources
- Achufusi TGO, Sharma A, Zamora EA, Manocha D. Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods. Cureus. 2020;12(6):e8860. Published 2020 Jun 27. doi:10.7759/cureus.8860
- Canadian Lyme Disease Foundation (CanLyme). Symptoms. Accessed June 13, 2025. https://canlyme.com/symptoms/
- Zaidi SA, Singer C. Gastrointestinal and hepatic manifestations of tickborne diseases in the United States. Clin Infect Dis. 2002;34(9):1206–1212. doi:10.1086/339871
- Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterol Hepatol (N Y). 2007;3(2):112-122.
- Schefte DF, Nordentoft T. Intestinal Pseudoobstruction Caused by Chronic Lyme Neuroborreliosis. A Case Report. J Neurogastroenterol Motil. 2015;21(3):440-442. doi:10.5056/jnm14118
- Roland BC, Ciarleglio MM, Clarke JO, et al. Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth. J Clin Gastroenterol. 2015;49(7):571-576. doi:10.1097/MCG.0000000000000257
- Halperin JJ. Chronic Lyme disease: misconceptions and challenges for patient management. Infect Drug Resist. 2015;8:119-128. Published 2015 May 15. doi:10.2147/IDR.S66739
- Rao SSC, Rehman A, Yu S, Andino NM. Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clin Transl Gastroenterol. 2018;9(6):162. Published 2018 Jun 19. doi:10.1038/s41424-018-0030-7
