SIBO, or small intestinal bacterial overgrowth, develops when too many bacteria grow in the small intestine, often due to disrupted digestion or slowed gut movement. Common causes include food poisoning, low stomach acid, impaired motility, certain medications, and previous abdominal surgery. Ageing, hormonal changes, and chronic stress can also play a part. These factors allow bacteria to linger where they shouldn’t, leading to bloating, discomfort, and nutrient absorption issues. Identifying and addressing the underlying cause with the help of a qualified nutritionist or functional medicine practitioner is key to long-term recovery.
If you’ve been struggling with bloating, discomfort, or digestive issues that never seem to go away, you may have come across the term SIBO, short for small intestinal bacterial overgrowth. It’s a condition that’s often misunderstood and, for many people, misdiagnosed. But understanding what actually causes SIBO can make all the difference when it comes to finding the right support and treatment, like our online course for support with SIBO at home.
Your gut is designed to keep bacteria in balance, with most of them living happily in the large intestine. When too many bacteria migrate up into the small intestine, however, they can interfere with digestion, trigger inflammation, and cause a wide range of symptoms from bloating and fatigue to food sensitivities and nutrient deficiencies.
There isn’t just one reason why this happens. SIBO can develop for many different reasons, and those reasons often overlap. From past food poisoning to slow gut motility, low stomach acid, or even certain medications, each factor plays its part in creating the right environment for bacterial overgrowth to take hold.
In this article, we’ll explore the most common causes of SIBO, how they affect your digestive system, and what you can do to address them. Whether you’re already managing gut symptoms or just starting to look for answers, understanding these causes is the first step towards improving your digestion and overall well being. For more information on the sort of timeline you can expect for healing, take a look at our article How Long Does SIBO Take to Heal?
What Is SIBO and Why Does It Develop?
Your digestive system relies on balance and timing. Each stage of digestion has a specific job: breaking food down, absorbing nutrients, and moving what’s left along efficiently. Most of your gut bacteria live in the large intestine, where they help finish the process. The small intestine, on the other hand, is designed mainly for absorption, with only small numbers of bacteria present.
SIBO, or small intestinal bacterial overgrowth, happens when too many bacteria begin to grow in the small intestine. These bacteria start fermenting food before digestion is complete, producing gas and irritation instead of a smooth digestive flow. The result can be bloating, discomfort, and changes in bowel habits. This can stem from things like reduced motility, low stomach acid, past infections, or certain medications.
SIBO doesn’t appear out of nowhere. It’s usually the result of several factors that disturb the normal rhythm of digestion. Understanding why it develops is the first step towards restoring balance and improving long-term digestive health.
How the Gut Normally Prevents Bacterial Overgrowth
Your gut has a number of clever built-in defences designed to keep bacteria in the right place and in the right amounts. These defences work together like a finely tuned system, maintaining balance and ensuring that digestion runs smoothly.
The first line of defence is stomach acid. Its strong acidity helps break down food and destroy unwanted bacteria before they can reach the small intestine. When stomach acid levels drop, which can happen naturally with age or through certain medications, more bacteria survive the journey and may begin to multiply where they shouldn’t.
Next are digestive enzymes and bile, which are released as food moves into the small intestine. They help break down carbohydrates, fats, and proteins while also creating an environment that’s less welcoming to excess bacteria.
Then there’s gut motility: the gentle wave-like contractions that move food through the digestive tract. This process, known as the migrating motor complex (MMC), acts a bit like a cleaning cycle between meals, sweeping away leftover food particles and bacteria. If this movement slows or becomes disrupted, bacteria have more opportunity to linger and grow.
When these systems are working properly, they keep the small intestine relatively clear and prevent bacterial build-up. But when one or more of them falter, it can open the door to small intestinal bacterial overgrowth, setting the stage for SIBO to develop.
Food Poisoning and Post-Infectious SIBO
Many people first develop SIBO after an episode of food poisoning. While the initial infection may pass within a few days, its effects on the gut can last much longer. During food poisoning, harmful bacteria release toxins that can inflame and damage the nerves controlling gut movement, particularly those involved in what’s known as the migrating motor complex (MMC).
The MMC acts like a housekeeping wave, sweeping food debris and bacteria through the small intestine between meals. When these nerves are disrupted by infection, the MMC slows down or stops working properly. This allows bacteria to remain in the small intestine longer than they should, giving them time to multiply and interfere with digestion [1].
Post-infectious SIBO can therefore develop weeks or even months after the original illness. People often don’t make the connection between the two, especially if their initial infection seemed mild or resolved quickly.
Understanding this link helps explain why SIBO sometimes appears “out of the blue.” It isn’t a new infection, but a lingering consequence of one. Supporting gut motility and healing the intestinal lining are key steps in recovery after post-infectious SIBO.
Impaired Gut Motility and Digestive Slowdown
The movement of food through your digestive tract relies on a natural rhythm known as gut motility. Gentle, wave-like contractions move food and bacteria along the intestines, preventing stagnation. When this movement slows down, food and bacteria linger in the small intestine longer than they should, creating the perfect conditions for bacterial overgrowth.
Several conditions can interfere with gut motility. In irritable bowel syndrome (IBS), for example, nerve signalling and muscle contractions in the gut can become irregular, leading to alternating periods of sluggish and rapid movement. Diabetes can also affect motility by damaging the nerves that control digestive flow, a condition known as diabetic neuropathy.
Other issues, such as connective tissue disorders (like scleroderma or Ehlers-Danlos syndrome), can affect the muscles and tissues of the intestines, reducing their ability to contract effectively. Even long-term stress can slow digestion, as the body diverts energy away from non-essential processes when it’s under pressure.
When motility falters, the gut’s natural “clearing wave” (the migrating motor complex) can’t do its job properly. As a result, bacteria that should be moved out of the small intestine remain there, feed on undigested food, and multiply [2]. Supporting motility through diet, hydration, and targeted treatment is therefore an essential part of preventing and managing SIBO.
Low Stomach Acid (Hypochlorhydria)
If you often feel bloated or full after only a few bites, or notice undigested food in your stool, low stomach acid could be part of the picture. Although it’s rarely talked about, stomach acid is vital for healthy digestion. It helps break down food, signals the release of enzymes, and destroys unwanted bacteria before they reach the intestines.
When acid levels drop, that protective barrier weakens. Bacteria that would normally be neutralised in the stomach can slip through and begin to multiply in the small intestine [3]. This can trigger the same symptoms many people with SIBO recognise: bloating, discomfort, and changes in bowel habits.
Low stomach acid (or hypochlorhydria) becomes more common with age, long-term stress, or the use of heartburn medications such as proton pump inhibitors (PPIs). While these medicines can provide relief in the short term, they may also reduce the stomach’s natural defence over time.
You might think of high stomach acid as something to avoid, but the right amount actually supports comfort, not irritation. By helping food break down properly, it keeps digestion running smoothly and prevents bacteria from overgrowing where they shouldn’t. If you suspect low stomach acid might be affecting your digestion, a qualified nutritionist or functional medicine practitioner can help identify the cause and guide you toward gentle ways to restore balance.
Medications That May Contribute to SIBO
Many people are surprised to learn that some everyday medications can quietly disrupt gut balance. While these drugs often play an important role in managing other health issues, they can also change how your digestive system functions, sometimes setting the stage for SIBO.
Antibiotics are the most common example. They’re designed to kill harmful bacteria, but they also wipe out many of the beneficial microbes that help keep your gut ecosystem stable. After a course of antibiotics, the balance can take time to recover, leaving space for unwanted bacteria to grow in the small intestine.
Proton pump inhibitors (PPIs) and other acid-reducing medications can also have an impact. If you’ve taken them for reflux or heartburn, you might not realise that by reducing stomach acid, they make it easier for bacteria to survive the journey into the small intestine. Over time, this can encourage bacterial overgrowth [3].
Opioid painkillers and some antidepressants can slow gut motility, meaning food and bacteria move through the digestive tract more slowly. When things don’t move as they should, bacteria have more time to multiply, and that’s when symptoms like bloating, discomfort, or constipation often appear [2].
If you’re taking one or more of these medications and notice ongoing digestive problems, it’s worth discussing with your doctor or nutritionist. They can help review whether your treatment plan might be affecting your gut and explore ways to support healthy digestion while still managing your other health needs.
Surgical History and Structural Changes
If you’ve ever had abdominal surgery for the appendix, gallbladder, or another condition, it’s possible that physical changes in the gut could be playing a role in your digestion today [2]. Surgeries that involve the intestines can sometimes leave behind scar tissue (adhesions) or alter the natural shape and movement of the digestive tract. These changes may seem small, but they can have a big impact on how smoothly food and bacteria move through the small intestine.
When movement slows or a slight narrowing occurs, it creates pockets where bacteria can become trapped. Over time, these stagnant areas can encourage bacterial overgrowth, leading to bloating, discomfort, and other symptoms commonly associated with SIBO.
Even procedures that don’t directly involve the intestines, such as certain gynaecological or bariatric surgeries, can affect motility or the position of nearby organs, subtly changing how the gut functions.
If your digestive symptoms began or worsened after surgery, it may not be a coincidence. Sharing your surgical history with a nutritionist or functional medicine practitioner can provide valuable clues about the underlying causes of SIBO and help shape a treatment plan that supports healthy movement and recovery.
Age-Related Factors in SIBO Development
As we get older, it’s normal for certain aspects of digestion to slow down or change. While these shifts are a natural part of ageing, they can make the gut more vulnerable to bacterial overgrowth.
One key change is a gradual decline in stomach acid production. Since stomach acid helps break down food and kill bacteria, lower levels mean more bacteria can survive the journey into the small intestine [3]. This can contribute to bloating, indigestion, and nutrient deficiencies, all of which are common in SIBO.
Gut motility also tends to slow with age. The wave-like contractions that move food through the digestive system can become less efficient, giving bacteria more time to linger and multiply where they shouldn’t. Medications that are more commonly used later in life, such as acid suppressants, painkillers, or antidepressants, can add to this effect.
Even subtle changes like eating less fibre, reduced physical activity, or slower metabolism, can influence how well the gut clears itself.
If you’ve noticed more frequent bloating or discomfort as you’ve grown older, it doesn’t necessarily mean it’s “just part of ageing.” Understanding how these changes affect digestion can open the door to simple, targeted adjustments that support gut motility, stomach acid levels, and overall digestive comfort.
Underlying Health Conditions and Hormonal Factors
Sometimes SIBO doesn’t develop in isolation; it’s linked to other health conditions that subtly influence how the gut works. Certain hormonal or metabolic imbalances can slow digestion, weaken gut defences, and make it easier for bacteria to overgrow in the small intestine.
Hypothyroidism, for example, can reduce gut motility. When thyroid hormone levels are low, everything in the body tends to slow down, including the movement of food through the digestive tract. This creates more time for bacteria to settle and multiply.
Similarly, diabetes can affect the nerves that control digestion, particularly when blood sugar levels remain high over long periods. This condition, known as diabetic neuropathy, can cause sluggish movement in the intestines [2] and increase the risk of bacterial build-up.
Chronic stress also plays a major role. When the body is under constant pressure, it prioritises “fight or flight” responses over digestion. This shift can reduce stomach acid, slow gut motility, and disturb the balance of gut bacteria. Such a combination can easily tip the system towards SIBO.
Recognising these underlying influences is important because treating SIBO successfully often means addressing what’s happening beyond the gut itself. Supporting hormone balance, managing stress, and stabilising blood sugar can all help restore digestive flow and prevent bacterial overgrowth from returning.
Lifestyle, Diet, and Emotional Stress
Your daily habits have a powerful effect on your gut. Even when the physical causes of SIBO are under control, the way you eat, sleep, and manage stress can either support recovery or make symptoms worse.
Stress is one of the biggest triggers. When you’re tense or anxious, your body moves into “fight or flight” mode, diverting blood flow away from the digestive system. Over time, this slows motility, reduces stomach acid, and disrupts the gut’s natural bacterial balance — all of which can encourage overgrowth [4].
Sleep is another key player. Poor or irregular sleep can alter hormone levels that affect digestion and immune function. Many people notice their bloating or bowel habits worsen when they’re tired or run down.
Diet also matters, but not in a one-size-fits-all way. Diets low in fibre or high in processed foods and sugars can deprive beneficial bacteria of nourishment while feeding those that produce gas and inflammation [1]. Skipping meals or eating erratically can add to the problem by throwing off the gut’s natural rhythm.
The good news is that these factors are within your control. Building calm into your routine, prioritising rest, and following a balanced diet tailored to your needs can make a real difference. Over time, these small, consistent changes can help restore digestive balance and reduce the likelihood of SIBO returning.
When to Seek Professional Support
If digestive symptoms such as bloating, pain, or irregular bowel habits are ongoing, it’s important not to ignore them. The first step should always be to speak with your GP, who can rule out other medical conditions that may cause similar symptoms, such as coeliac disease, inflammatory bowel disease, or thyroid disorders. Your GP can also arrange basic tests and ensure there’s nothing more serious underlying your discomfort.
However, once other conditions have been ruled out, many people find that NHS treatment options for SIBO are limited. While some GPs may be aware of SIBO, testing and treatment aren’t widely available, and management often focuses on symptom relief rather than identifying the underlying cause.
At this stage, it can be very helpful to work with a nutritionist or functional medicine practitioner who specialises in gut health. These practitioners can arrange comprehensive SIBO testing, review your diet and lifestyle in detail, and create a personalised plan that supports your digestion and overall well being. They take the time to understand what’s driving your symptoms (whether that’s low stomach acid, poor motility, medication use, or previous infection) and build a plan that addresses these root causes.
In short, see your GP first to rule out anything serious, then consider a gut health specialist for more focused, long-term support. With the right guidance, SIBO can be effectively managed, helping you regain comfort, confidence, and control over your digestion.
Taking Steps Towards Better Digestive Health
Recovering from SIBO takes time and commitment, but it’s absolutely achievable with the right support. At IBS Clinics, we take a holistic, evidence-based approach to treatment, looking at your whole health, not just your symptoms.
After a short initial consultation to discuss next steps, your journey begins with a comprehensive consultation, where we take the time to understand your full health history, current symptoms, and lifestyle. From there, we may recommend you take a SIBO test to confirm bacterial overgrowth and identify the type that’s causing your symptoms. This allows us to create a clear, personalised plan that addresses both the cause and the effect.
Your tailored programme might include a nutritional plan designed to rebalance gut bacteria, restore motility, and support nutrient absorption. You’ll also receive lifestyle guidance to help manage stress, improve sleep, and strengthen your digestive defences. For many people, combining nutrition, supplements, and lifestyle support provides long-lasting relief and a real sense of control over their well being.
We also offer a new SIBO recovery course, created to guide you step by step through understanding, testing, and restoring gut balance, so you can get support with SIBO at home. This is ideal if you want structured support with expert oversight.
You’ll need to be open to small but meaningful changes: adjusting your diet, following a supplement plan, and tuning in to how your body responds. Our team will guide you through every stage, helping you understand what’s working and what to expect along the way.
If you’re ready to move forward, our practitioners are here to help. You can book an initial consultation to discuss next steps, or contact us at IBS Clinics on 01296 612202 or e-mail customerservice@ibsclinics.co.uk to find out more about SIBO testing, nutrition programmes, and our holistic approach to gut health. With the right plan and professional guidance, lasting digestive comfort and improved well being are within reach.
Conclusion
SIBO can be frustrating and confusing, especially when symptoms seem to come and go without clear reason. But with the right understanding and support, recovery is entirely possible. By identifying the underlying causes (low stomach acid, past infection, slow motility, or lifestyle factors) you can take meaningful steps towards restoring balance in your gut.
At IBS Clinics, we believe in supporting the whole person, not just resolving the symptoms. Through expert guidance, personalised nutrition plans, and specialist SIBO testing, our team can help you uncover what’s driving your digestive issues and support you on the path to lasting relief.
If you’re ready to take control of your gut health, get in touch with IBS Clinics today to arrange a consultation or learn more about our SIBO testing and recovery course. With a structured plan and ongoing support, you can move towards better digestion, renewed energy, and long-term well being.
References
- Knez et al (2024), The Importance of Food Quality, Gut Motility, and Microbiome in SIBO Development and Treatment, Science Direct. https://www.sciencedirect.com/science/article/abs/pii/S089990072400114X
- Mayo Clinic (2025) Small Intestinal Bacterial Overgrowth (SIBO) Symptoms and Causes. https://www.mayoclinic.org/diseases-conditions/small-intestinal-bacterial-overgrowth/symptoms-causes/syc-20370168
- Cleveland Clinic (2025) Hypochlorhdria (Low Stomach Acid: Symptoms, tests, Treatment. https://my.clevelandclinic.org/health/diseases/23392-hypochlorhydria
- The Chartwell Hospital (2022) The 5 Top Causes of Small Intestinal Bacteria Overgrowth (SIBO) https://www.gut.thechartwellhospital.co.uk/the-5-top-causes-of-small-intestinal-bacteria-overgrowth-sibo
Author – Tracey Randell
At IBS Clinics, Tracey Randell, a renowned Nutritional Therapist and one of the few IFM Certified Practitioners in the UK, extends her specialised knowledge and unique approach to managing and treating IBS and other gut-related conditions effectively.
Tracey’s profound understanding of Functional Medicine allows her to connect the dots for complex health conditions, identifying and addressing the root causes to curate personalised and comprehensive health plans for her patients. Her holistic approach focuses on resolving underlying imbalances and optimising gut health, enabling the body to correct other issues and attain overall well-being.
At IBS Clinics, we are dedicated to being your partner in navigating your gut-related health concerns, offering expert care and individualised treatment plans to alleviate your IBS symptoms and enhance your quality of life.
You can read more about Tracey on our About page here.
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