CONDITION
Small Intestinal Bacterial Overgrowth
Small intestinal bacterial overgrowth describes a situation in which the population of bacteria in the small intestine becomes unusually large. The small intestine normally holds relatively few bacteria compared to the large bowel, and when that balance shifts, digestion and nutrient absorption can be disrupted. The result is often chronic diarrhoea, sometimes with weight loss, changes in appetite, or intermittent vomiting. The condition can emerge at any age and for different reasons. In some dogs—particularly young to middle-aged, large-breed animals such as German Shepherds—bacterial overgrowth appears without an obvious underlying cause, sometimes linked to a relative deficiency in a type of antibody called IgA that ordinarily helps keep the intestinal environment in check. In other cases, bacterial overgrowth develops secondary to another condition, such as exocrine pancreatic insufficiency or a problem with intestinal movement, and this secondary form can occur at any age, including in older dogs. This page explores what an owner may observe, what processes underneath may be contributing, how the condition is investigated, and what approaches exist to address it.
Why this matters now
Small intestinal bacterial overgrowth can emerge at any age, but the idiopathic, breed-associated form is typically a disease of young to middle-aged dogs, with a median age at diagnosis of around two years. Certain breeds, particularly German Shepherds (linked to a relative deficiency in intestinal IgA) and other large breeds, may be more prone to the condition. Bacterial overgrowth secondary to other underlying disease, such as exocrine pancreatic insufficiency or motility disorders, can occur at any age, including in older dogs. The condition is less commonly recognised in cats, though it may occur in association with chronic enteropathy or anatomical abnormalities.
The pattern often begins with intermittent soft stools or mild digestive upset that may seem to come and go over weeks or months. Over time, the diarrhoea may become more persistent, and weight loss can develop gradually despite a maintained or increased appetite. The severity and speed of progression vary considerably between individuals, and some animals remain relatively stable for extended periods whilst others deteriorate more noticeably. In cases where bacterial overgrowth is secondary to another condition, the progression may reflect the underlying disease as much as the overgrowth itself.
Signals & patterns
Early signals
Intermittent soft or loose stools
The stools may be softer than usual or occasionally loose, often without a clear pattern at first. Some days may appear normal, and the change can be subtle enough that it takes time to recognise a trend.
Increased frequency of defaecation
An animal may begin passing stools more often than usual, sometimes with smaller volumes each time. This can occur alongside the softening of the stool or independently of it.
Excessive gas or bloating
Flatulence may become more noticeable, and the abdomen can appear mildly distended or uncomfortable, particularly after meals. The gas often has a particularly unpleasant odour.
Rumbling or gurgling gut sounds
Owners may hear loud borborygmi, the audible churning and gurgling of the intestines, which can be more pronounced than usual. This reflects increased fermentation and movement of gas and fluid through the gut.
Subtle changes in appetite or eating speed
Some animals eat more quickly or appear hungrier than before, whilst others may show mild hesitation or discomfort around mealtimes. The overall appetite often remains present, but the pattern can shift.
Later signals
Persistent watery or greasy diarrhoea
The stools may become consistently loose, watery, or have a greasy appearance, sometimes with an oily sheen. The odour is often markedly foul, and the volume can be large.
Progressive weight loss despite eating
The animal may lose body condition steadily over weeks to months, even when appetite remains normal or increases. Muscle mass can diminish, and the ribs or spine may become more prominent.
Dull coat or poor skin condition
The coat may lose its shine and become dry or brittle, and the skin can appear flaky or less elastic. These changes often reflect chronic malabsorption of fats and fat-soluble vitamins.
Reduced energy or general malaise
Some animals become less active or seem generally less comfortable, though the change can be gradual and easy to attribute to other factors. The overall sense is of an animal not thriving as it once did.
Click to read about the biological mechanisms
How this is usually investigated
Investigation of suspected small intestinal bacterial overgrowth typically begins with a careful history of the pattern of digestive signs and any prior treatments, alongside physical examination to assess body condition and detect any underlying structural or systemic concerns. Because bacterial overgrowth is often secondary to another process, the approach tends to involve tests that look for those underlying causes first, followed by measures that may suggest overgrowth itself. The picture often sharpens gradually as results accumulate and as the response to initial management is observed.
Cobalamin (B12) and folate
Trypsin-like immunoreactivity (TLI)
Faecal analysis
Abdominal ultrasound
Histopathology
Options & trade-offs
Management of small intestinal bacterial overgrowth usually involves a combination of approaches tailored to the individual animal and the suspected underlying cause. Some animals respond well to a single intervention, whilst others require adjustments over time as the picture becomes clearer. The approach that suits one household or one dog may be less practical or less effective in another, and there is often a period of observation to see what combination works.
Antibiotic therapy
Antibiotics that act on gut bacteria, such as metronidazole or tylosin, are often used to reduce the bacterial population in the small intestine. The course may last several weeks, and some animals are given repeated or rotating courses if signs recur. In some cases a longer, lower-dose maintenance regimen is used to keep the bacterial population in check.
Trade-offs: Antibiotics can be effective in resolving signs relatively quickly, but they do not address any underlying cause and signs may return when the course is stopped. Prolonged or repeated use raises questions about antibiotic resistance and effects on the wider gut microbiome, and some animals experience side effects such as nausea or further loosening of stools.
Dietary modification
Changing to a highly digestible diet, often one with moderate fat and easily absorbed protein and carbohydrate, may reduce the substrates available for bacterial fermentation and ease the workload on the digestive system. Some diets are formulated with specific fibre types or prebiotics intended to favour a healthier bacterial population. In other cases a novel or hydrolysed protein diet is tried, particularly if food sensitivity is also suspected.
Trade-offs: Dietary change can be helpful and is generally well tolerated, but the response varies and it may take several weeks to see whether a particular diet is making a difference. Some animals are reluctant to accept a new food, and the cost of prescription or specialised diets can be a consideration for some households.
Cobalamin supplementation
When serum cobalamin is low, supplementation by injection (and sometimes oral forms, though absorption may be unpredictable) is often given to restore normal levels. Cobalamin is needed for cellular metabolism and gut health, and correcting deficiency may improve the animal's overall condition and support healing of the intestinal lining.
Trade-offs: Supplementation is straightforward and carries little risk, but it addresses a consequence of the overgrowth rather than the overgrowth itself. The frequency and duration of treatment depend on how quickly levels normalise and whether the underlying problem is being managed.
Treatment of underlying conditions
When bacterial overgrowth is secondary to another disorder—such as exocrine pancreatic insufficiency, partial obstruction, or a motility problem—management focuses on addressing that primary condition. Enzyme replacement for pancreatic insufficiency, for example, can restore more normal digestion and reduce the circumstances that favour bacterial overgrowth.
Trade-offs: Treating the underlying cause can be highly effective in resolving bacterial overgrowth, but it requires identifying that cause in the first place, which is not always straightforward. Some underlying conditions require long-term or lifelong management, and the response may take time to become apparent.
Probiotics and prebiotics
Probiotic supplements containing specific strains of beneficial bacteria, or prebiotics that provide substrates intended to support a healthier microbial community, are sometimes used alongside other treatments. The aim is to help restore a more balanced gut environment, though the evidence for their effectiveness in bacterial overgrowth is still developing.
Trade-offs: Probiotics are generally safe and may be helpful in some individuals, but the range of products is wide and the strains, doses, and formulations vary considerably. Not all animals respond, and it can be difficult to predict which product, if any, will make a noticeable difference.
Common misconceptions
"A stool test can diagnose small intestinal bacterial overgrowth directly."
Faecal tests examine the bacteria present in the large intestine and the stool, which may not reflect what is happening higher up in the small intestine where overgrowth occurs. Whilst faecal analysis is useful for ruling out parasites and some infections, bacterial overgrowth in the small intestine is usually inferred from clinical signs, blood tests such as cobalamin and folate, and the response to treatment rather than from stool culture.
"Once treated with antibiotics, bacterial overgrowth will not come back."
Antibiotics can reduce the bacterial population and resolve signs in the short term, but if the underlying cause—such as a motility disorder, structural abnormality, or immune deficiency—remains, the overgrowth may recur when the antibiotic course ends. Some animals require repeated courses, dietary management, or treatment of an underlying condition to keep the problem in check over the longer term.
"All dogs with chronic diarrhoea have bacterial overgrowth."
Chronic diarrhoea has many possible causes, including inflammatory bowel disease, food sensitivity, parasites, pancreatic insufficiency, and others. Bacterial overgrowth is one pattern among several, and it may occur as a primary problem or secondary to another condition. The investigation is usually a process of narrowing down the possibilities rather than assuming one explanation from the outset.
Related conditions
Exocrine Pancreatic Insufficiency (EPI)
Exocrine pancreatic insufficiency can present with similar signs—persistent diarrhoea, weight loss despite good appetite, and poor nutrient absorption—because both conditions disrupt the normal digestive process, though the underlying mechanisms differ. Distinguishing between the two often requires specific testing of pancreatic enzyme levels.
Inflammatory Bowel Disease in Cats
Inflammatory bowel disease in cats can alter the normal intestinal environment in ways that may predispose to bacterial overgrowth, and both conditions can produce overlapping signs of chronic diarrhoea, weight loss, and digestive upset. In some cases, the two may occur together, complicating the clinical picture.
Inflammatory Bowel Disease in Dogs
Inflammatory bowel disease in dogs can disrupt the normal structure and function of the small intestine, creating conditions that may allow bacterial populations to increase beyond their usual numbers. The two can share similar signs, and chronic intestinal inflammation may predispose to bacterial overgrowth in some individuals.
Megaoesophagus
Megaoesophagus can lead to small intestinal bacterial overgrowth when delayed gastric emptying or changes in gut motility allow bacteria to multiply in the small intestine. Both conditions can contribute to malabsorption and weight loss, though they affect different parts of the digestive tract.
Gastroenteritis in Cats
Gastroenteritis in cats may present with acute signs that can resemble a flare of bacterial overgrowth, and recurrent or persistent gastroenteritis may sometimes create intestinal changes that predispose to bacterial population shifts. Distinguishing between transient inflammation and an underlying overgrowth pattern often depends on the duration and response to initial measures.
If your dog or cat has had persistent digestive signs, it may be worth reflecting on the pattern you have observed—how long it has been present, whether it comes and goes, and how it has responded to any changes in diet or treatment so far. The wider context of metabolic health, including how the gut, pancreas, and liver work together, can offer useful background for understanding why these signs develop and what may influence the course. This is the sort of detail that can inform conversations at the next appointment and help shape the approach going forward.
Last reviewed: 1 July 2026 · Dr Alastair Greenway MRCVS