Treating SIBO Holistically Helps Patients Feel Better, New Study Finds

New findings reveal that popular treatments - especially antibiotics and low-carb diets - may quietly fuel a second wave of damage that's harder to detect and even harder to undo.

STORY AT-A-GLANCE

• New research shows over 70% of small intestinal bacterial overgrowth (SIBO) patients reported significant symptom improvement with holistic treatment, even when lab tests remained abnormal

• SIBO develops when digestive metabolism slows down and bacteria migrate where they don't belong, causing bloating, gas and food intolerances

• Antibiotics often worsen the condition by disrupting gut ecology and triggering candida overgrowth, creating a secondary fungal problem

• Restricting carbohydrates provides temporary relief but ultimately weakens metabolism; gradually reintroducing simple carbs helps rebuild gut health

• Addressing underlying causes like low thyroid function, hormone imbalances and poor motility is more effective than simply targeting bacterial overgrowth

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Small intestinal bacterial overgrowth, or SIBO, is more than just a gut imbalance — it's a sign your digestive system has lost its rhythm. While most people think of it as a bacterial problem, it's really a deeper issue with energy, motility and terrain. In other words, SIBO shows up when your gut slows down, your defenses weaken and bacteria migrate into areas they don't belong.

The symptoms, like bloating, gas, constipation or diarrhea, and even food intolerance, are frustrating enough. But what's worse is how often the condition gets misdiagnosed, mismanaged or misunderstood altogether.

Too often, the focus is on wiping out bacteria rather than asking why those bacteria took over in the first place. Antibiotics are handed out as first-line treatment, yet they often leave patients feeling worse — triggering yeast overgrowth and further disrupting the gut ecosystem.

What many practitioners miss is that SIBO tends to develop in people with low stomach acid, sluggish gut motility or thyroid-related slowdowns that let things stagnate. Add metabolic stress, iron overload or hormone imbalances to the mix, and you're dealing with a perfect storm, not just of bacteria but of terrain gone haywire. That's why short-term strategies don't work. They treat symptoms while the root causes remain.

A new real-world study out of Valencia, Spain, offers something different.¹ Instead of relying solely on lab markers, the researchers asked a better question: How do people actually feel after treatment? And that's where the answers start to get interesting.

Recognizing SIBO as a Real, Treatable Condition Improves Outcomes

A clinical study published in Nutrients examined how a comprehensive treatment approach improved the lives of people diagnosed with SIBO.² The researchers focused on whether patients felt better after 90 days, not just whether their lab tests changed.

They assessed both breath test results and self-reported health scores. Breath tests are commonly used to detect abnormal gas levels, like hydrogen and methane, that signal bacterial overgrowth in the small intestine. This was one of the largest studies of its kind, specifically analyzing real-life patient experiences.

• The study followed adults with confirmed SIBO — The 179 patients had a confirmed diagnosis of hydrogen- or methane-dominant SIBO. Most were middle-aged (average age 45.7) and 82.7% were women. All participants received tailored treatment involving medication, herbs, probiotics and a nutritionist-guided diet. The researchers wanted to see how this multi-layered approach impacted not just test outcomes, but people's day-to-day quality of life.

• Over 70% of patients felt better by the end of treatment — More than 7 in 10 patients — 72.6% — reported significant improvements in symptoms after three months. In contrast, only 41.3% had "normalized" breath test results. People felt relief from bloating, pain, stool issues and digestive distress even if gas levels remained elevated.

• Changes were seen quickly and continued to improve over time — Many patients started feeling better within 30 days, but the most consistent progress happened between 30 and 90 days. This suggests that healing your gut and rebalancing your microbiome takes time. It also reinforces the need for consistent follow-through. People who stuck with the protocol saw the greatest improvements by the three-month mark.

• SIBO with constipation showed slightly stronger symptom relief — People with methane-type SIBO, which is often associated with constipation, tended to respond slightly better than those with hydrogen-dominant SIBO, which usually causes diarrhea and gas.

  While both groups improved, 73.2% of methane SIBO patients saw relief, compared to 71.4% in the hydrogen group. The treatment's ability to restore more regular bowel patterns played a major role in this improvement.

Multi-Pronged Strategies Improved Digestion, Mood and Resilience

Patients reported better emotional balance, mental clarity, sleep quality and energy following treatment. Key gut symptoms, including bloating, constipation, diarrhea, urgency and post-meal fullness also improved, and better function in areas like mobility, self-care and participation in normal daily activities was reported. Stool quality improved as well. Many shifted from hard or loose stools to more normal stool consistency by day 90.

• Higher initial self-rated health predicted better outcomes — Patients who believed they were in better health at the start had a much higher chance of seeing significant symptom improvement. That finding speaks to the power of self-perception and mindset in recovery. When you trust your body and feel capable of getting better, your odds go up.

• SIBO treatment linked to brain and mood improvements — People often report better mood and fewer symptoms of anxiety and depression after SIBO treatment. This is tied to the gut-brain axis, the communication highway between your gut and brain. Inflammation, poor motility and stress disrupt this pathway, so restoring gut health naturally supports mental clarity and emotional stability.

• Treatments likely worked by restoring gut barrier and microbial balance — Researchers believe that using glutamine, probiotics and prebiotics supported gut barrier integrity and reduced inflammation. Herbal antimicrobials (like berberine, peppermint and oregano oil) targeted overgrowth without destroying beneficial species. These mechanisms help reshape the ecosystem of your small intestine, allowing good bacteria to thrive and limiting the survival of problematic ones.

• The gut's healing process took time and multiple strategies — This wasn't a one-size-fits-all or quick-fix model. Each patient received guidance from a nutritionist, along with clinical supervision. Diet was customized, herbs were chosen based on gas type and reintroduction phases were paced gradually. This multi-layered approach allowed for better tolerance and more lasting results.

Why Cutting Carbs and Using Antibiotics Often Make SIBO Worse

If you've been told to cut carbs to control bacterial overgrowth, it's time to rethink that approach. Starving your gut reduces symptoms for a while, but it won't fix the problem — and in the long run, it will slow your metabolism, impair gut motility and shrink your food tolerance. That's not healing. That's trading one form of dysfunction for another.

• SIBO isn't caused by eating carbs — It's a metabolic breakdown. When your digestive system is underpowered — when your thyroid is sluggish, your stomach acid is low or your gut motility is compromised — bacteria that should stay in your colon creep into your small intestine and multiply. That's when symptoms like bloating, discomfort, gas and constipation take over.

• Antibiotics aren't the solution — If you've already been through a round of antibiotics like rifaximin for SIBO, you could be dealing with something else, too — candida overgrowth. Western medicine often overlooks the fact that antibiotics don't just kill bacteria. They disrupt your entire gut ecosystem.

  Yeast like Candida albicans are left behind, untouched and ready to spread. They move fast. And when you've cut carbs in the hopes of "starving" the bad bacteria, candida doesn't die. It adapts. It transforms into an invasive, aggressive form that damages your gut lining and creates a second layer of dysfunction — fungal overgrowth layered on top of bacterial imbalance.

How to Fix SIBO Naturally

To truly recover, you need to address both problems — SIBO and candida overgrowth — at the same time, and you need to start by rebuilding your metabolism and immune defenses. Here's where I would start:

1. Avoid fiber and complex carbs until your symptoms ease — If you have SIBO, your gut is often overwhelmed by bacteria that have migrated into your small intestine, where they don't belong. Many healthy foods — especially those rich in fiber or starch — become problematic in this state. That's because they ferment too quickly or aren't broken down properly, which feeds the overgrowth and leads to gas, bloating, discomfort and inflammation.

   Different types of carbs affect your gut differently. Soluble fibers, for instance, are typically tolerated better than insoluble ones. Soluble fiber ferments more slowly, giving your digestive system more time to process it. But if you're dealing with active symptoms, even these make things worse. Insoluble fibers are often especially irritating — they bulk up stool and speed up digestion, which exacerbates symptoms like diarrhea, urgency or cramping.

   Your best strategy early on is to limit trigger foods. Focus on those that are easiest to digest and least likely to fuel bacterial overgrowth. This includes soft fruits without skins and well-cooked white rice.

   Avoid beans, raw greens, whole grains and fibrous fruits or vegetables until your system stabilizes. As your digestion improves, you'll gradually regain tolerance. The key is listening to your body and expanding your diet slowly. Move from simple, low-fiber carbs to more fibrous whole foods once your gut is calm.

2. Feed your gut cells without feeding harmful bacteria — Your small intestine is designed for absorption — not fermentation. But when bacteria overgrow in this area, even nutritious carbs become fuel for the wrong microbes. That's why choosing the right carbohydrates is essential, especially during early recovery.

   Simple carbs that are rapidly absorbed in your upper intestine tend to be better tolerated by those with SIBO. These carbs don't reach your colon, so they're less likely to feed harmful oxygen-tolerant bacteria that produce toxins like endotoxin. In fact, by avoiding fermentation, they help lower endotoxin exposure and reduce inflammation throughout your gut lining.

   At the same time, this approach gives your cells a clean source of energy to repair tissue and improve motility. Start with carbs like white rice, fruit juices with pulp or whole fruits. Once your symptoms improve and your digestion stabilizes, begin introducing gentle complex carbs like well-cooked squash or peeled potatoes. From there, gradually reintroduce more fibrous options like root vegetables, and finally beans and whole grains.

   The goal isn't to restrict carbohydrates forever. It's to give your gut time to rebuild and your mitochondria the energy they need to repair digestive tissues. As your gut health improves, your ability to digest and benefit from more complex carbs will return — without flaring symptoms or fueling overgrowth. Ultimately, instead of restricting carbs, focus on eating 250 grams of the right types daily.

3. Address the terrain that allowed overgrowth in the first place — SIBO and candida don't happen in a vacuum. They show up when your body becomes a safe haven for them. Candida, for instance, thrives in estrogen-dominant environments. It also feeds on excess iron.

   Balancing hormones, avoiding xenoestrogens in microplastics and keeping your iron levels in check are all part of this healing equation. And if your thyroid is underactive, everything — from motility to immune defense — slows down. That's why I often recommend checking thyroid function if you've been stuck in the SIBO-candida loop.

4. Monitor your body temperature to keep candida in check — Low body temperature gives candida exactly what it wants — a cooler, more hospitable environment where it can spread. Fungal pathogens like candida thrive when your temperature dips below normal while higher body temperatures help suppress fungal growth and keep your internal defenses strong. If your daytime temp consistently falls below 98.6 degrees F, you're giving candida room to take hold and multiply.

5. Stop treating symptoms in isolation and start rebuilding your inner environment — You don't need a low-carb protocol or a long course of antibiotics. You need a metabolic foundation strong enough to resist bacterial and fungal overgrowth in the first place.

   That means fueling consistently with the right healthy carbs, avoiding environmental chemicals, lowering stress and giving your body the raw materials it needs to keep your gut ecosystem stable. Once your terrain improves, the bad bacteria stop thriving — without you needing to attack them head-on with antibiotics.

This approach is slow, steady and rooted in repair, not restriction. If you've been caught in the cycle of antibiotics, antimicrobials and elimination diets, it's time to shift your strategy. You're not broken; you're just under-fueled and over-stressed. Start by fixing your metabolism, and your gut will follow.

If you're dealing with both SIBO and candida, the solution isn't to pick one to battle — it's to shift the terrain they're living in. A well-fed, high-functioning gut doesn't allow overgrowth to take hold. That's the real goal here. And it's absolutely within your reach.

FAQs About SIBO

Q: What is SIBO and why is it often misdiagnosed?

A: SIBO happens when bacteria that belong in your colon migrate into your small intestine. This leads to bloating, gas, abdominal pain and irregular bowel habits like constipation or diarrhea. It's frequently misdiagnosed because many of its symptoms mimic other digestive disorders, and standard breath tests often give inconsistent results.

Many doctors treat it as a simple bacterial problem, when in reality, it's a sign of metabolic and digestive dysfunction that allows overgrowth to happen in the first place.

Q: What makes this study's findings so important for people with SIBO?

A: The Nutrients study redefines what success looks like in SIBO treatment. Instead of chasing perfect lab results, it focused on whether people actually felt better after individualized treatment, including diet changes, herbs, probiotics and medication. And they did — more than 70% of participants experienced relief from bloating, stool issues, fatigue and digestive distress, even if their breath tests still showed elevated gas.

Q: Why do antibiotics and low-carb diets often make SIBO worse?

A: Antibiotics like rifaximin temporarily reduce bacterial overgrowth but often cause collateral damage by disrupting your gut's microbial balance. This opens the door for fungal pathogens like candida to take over. Meanwhile, cutting carbs in an effort to "starve" bacteria weakens your metabolism, slows gut motility and stresses your immune defenses — conditions that make both SIBO and candida worse, not better.

Q: What's the link between SIBO and candida overgrowth?

A: When antibiotics knock out bacteria, yeast like Candida albicans thrive in the disrupted environment. Candida becomes more aggressive under stress, especially when carbs are restricted. It shifts into an invasive form that damages your gut lining and worsens inflammation. Many people unknowingly end up with both SIBO and candida — two overlapping imbalances that require a dual approach to resolve.

Q: What's the best way to heal from SIBO and candida overgrowth long-term?

A: Lasting recovery starts by restoring your metabolic health and internal terrain. The goal isn't to fight microbes — it's to make your gut a place where overgrowth can't take hold. That includes:

• Supporting gut repair with simple carbs like whole fruit and white rice before gradually reintroducing more fiber

• Avoiding hormone, low body temperature and iron imbalances that feed candida

• Ditching elimination diets in favor of nutrient-dense, metabolism-supporting foods

• Improving thyroid function to activate gut defenses

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1. Nutrients April 3, 2025, 17(7), 1251

2. Nutrients April 3, 2025, 17(7), 1251