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Probiotic side effects impact very few users. Only one in a million people get infections from Lactobacilli bacteria. These beneficial bacteria and yeasts help fight harmful microbes and boost immunity. Some users might feel temporary discomfort.
Probiotics are generally safe. Users may notice short-term digestive problems like bloating, gas and constipation. These symptoms usually go away within a few weeks. People with weakened immune systems or recent surgeries should be especially careful with probiotic use.
This piece gets into the side effects of probiotic supplements and foods. You’ll learn what these effects mean and how to reduce any discomfort they might cause.
People who start taking probiotics usually notice digestive changes first. These symptoms might feel uncomfortable but they’re usually mild and don’t last long. Knowing what reactions are normal helps you tell the difference between adjustment signs and serious issues.
New probiotic users often feel gassy and bloated during their original days or weeks. This happens because new bacterial strains change your gut microbiome and bacteria produce more gas than usual [1].
Your digestive system needs time to adjust to the new bacterial environment, which is perfectly normal. Studies show these side effects go away within a few days to weeks if you keep taking probiotics [1]. The symptoms that last longer might mean you need to change your probiotic strain or dose.
Bacterial fermentation causes this temporary discomfort. Probiotics that settle in your gut create short-chain fatty acids and gases as their metabolic byproducts[2]. You might feel bloated at first, but these same byproducts ended up helping your health.
Probiotics change bowel habits by a lot, sometimes in opposite ways. You might notice:
Softer stools and faster bowel movements [3]
Different stool consistency and frequency [4]
Sometimes, short-term diarrhoea [3]
Clinical studies showed probiotics help improve bowel function. Research found that people taking probiotics saw their stool consistency improve by 0.66 units (34%) on the Bristol Stool Scale after just one week compared to those taking placebo [5]. The same study found that complete spontaneous bowel movements almost doubled in the probiotic group [5].
These bowel changes often mean your probiotics are working. Your gastrointestinal microbiota is a vital part of gut motility. Research shows that probiotics increase beneficial bacteria like Ruminococcaceae [5]. More regular bowel movements usually follow these microbiome changes.
Some people report stomach discomfort or pain when they start probiotics, though less often than bloating or bowel changes. The pain feels mild rather than severe and should fade as your body adapts.
Scientists aren’t sure why this happens, but they think it’s part of your gut microbiome’s adjustment period. Studies that looked at children with functional abdominal pain disorders found mixed results about probiotics helping with pain relief. The evidence wasn’t consistent and had low certainty [3].
The connection between probiotics and abdominal pain gets more complex if you have irritable bowel syndrome (IBS). Even though you might feel uncomfortable at first, studies show probiotics can reduce IBS symptoms including abdominal pain over time [3]. Different bacterial strains and your unique gut microbiota affect how well they work.
Stomach pain rarely happens with probiotic use [3]. Persistent or severe stomach pain after starting probiotics might point to a deeper issue that needs medical attention.
Your chances of getting digestive side effects depend on several things:
Most people find these digestive symptoms are just temporary adjustments, not reasons to stop taking probiotics. All the same, you should talk to a healthcare professional if symptoms last more than a few weeks or become severe.
Digestive issues top the list of probiotic side effects, but these supplements can affect your body in other ways too. Anyone who plans to take probiotics should know about these non-digestive reactions, especially people with pre-existing conditions or sensitivities.
Foods rich in probiotics might give you headaches because they contain biogenic amines. These compounds—including histamine, tyramine, tryptamine, and phenylethylamine—naturally develop during fermentation and can affect your central nervous system [6].
Studies show these amines can stimulate the central nervous system, change blood flow, and trigger headaches in people who are sensitive to them. Research found that diets low in histamine helped reduce headaches in 75% of participants [6]. A review of 10 controlled studies, however, found no clear link between dietary amines and headaches, which suggests we need more research [6].
Probiotic supplements themselves, not just fermented foods, might cause neurological symptoms. Healthcare professionals have noticed that probiotics can sometimes create gut inflammation that affects the neuroendocrine system, which leads to:
Brain fog
Dizziness
Headaches [7]
The production of histamine in your digestive tract by certain bacterial strains in probiotics can add to these symptoms. One specialist puts it this way: “A probiotic should be used like a prescription because not everyone will respond the same way” [7].
Probiotics can sometimes show up as skin problems. These usually appear as rashes or itching that go away once you stop taking the probiotic [1]. These reactions happen either because of an allergic response to probiotic ingredients or an immune reaction to substances that probiotic organisms produce.
Your skin’s relationship with the gut microbiome is complex, as it’s your body’s largest organ and faces constant external challenges. Changes in gut bacteria from probiotic supplements can affect your skin [8].
Research suggests probiotics might actually help some skin conditions by modifying immune responses. Probiotic therapy looks promising to help manage eczema, atopic dermatitis, acne, and allergic inflammation [8]. The same mechanisms that let probiotics improve skin health can sometimes cause bad reactions.
Here’s what to do if you get a rash while taking probiotics:
Allergic reactions usually come from the ingredients in probiotic supplements rather than the actual microbes. Common allergens in probiotic formulas include: 
Dairy compounds (in lactobacillus-based products)
Soy derivatives
Egg proteins
Gluten [6]
People with yeast allergies should stay away from yeast-based probiotics like Saccharomyces boulardii and use bacteria-based options instead [6].
Very rarely, probiotics have been linked to eosinophilic syndrome, a serious allergic condition [9]. Some probiotics also contain inulin (a prebiotic fibre) that can trigger allergies in certain people [9].
People with histamine intolerance might feel worse with certain probiotic strains that produce histamine in the gut. Histamine is a molecule your immune system makes when it spots threats. This causes blood vessels to expand and become more permeable—leading to itching, watery eyes, runny nose, or breathing problems [6].
Allergic responses to probiotics typically show up as Type I hypersensitivity reactions. These happen when mast cells covered with allergen-specific IgE meet a cross-linking allergen [10]. This causes inflammation that shows up as hives, rhinitis, vomiting, and diarrhoea [10].
People with known allergies or intolerances should read product labels carefully and talk to a healthcare professional before starting any probiotic supplement. Anyone who notices signs of an allergic reaction should stop taking the probiotic right away and get medical help if symptoms become severe [1].
Most people handle probiotics just fine, but taking too much might lead to ongoing symptoms that tell you it’s time to adjust your intake. These warning signs help you tell the difference between normal adjustment and taking too many probiotics.
Your body needs time to adjust to probiotics, and temporary digestive issues are normal. Gas and bloating usually go away as your gut microbiome adapts. But if these symptoms don’t improve after a few weeks, you might be taking more than your body can handle.
Look out for these ongoing symptoms:
Bloating and abdominal distension that won’t go away
Gas that keeps coming back
Bowel movements that stay irregular
Stomach pain that persists
Studies show you should stop taking probiotics and talk to your doctor if bloating, gas, or other side effects last more than a few weeks. Taking more than 1 to 10 billion colony forming units (CFUs) might work against the benefits and cause uncomfortable digestive problems.
A prominent gastroenterologist explains it this way: “If the bacteria get to the food before us, they can turn it into gas.” This explains why taking extra probiotics doesn’t mean better results – it might just make you feel worse.
Digestive issues get more attention, but feeling thirstier than usual could mean you’re taking too many probiotics, especially with yeast-based supplements. Research shows people who take yeast probiotics often feel thirstier during their first week as their body’s microbial balance changes.
This symptom usually goes away on its own. If you stay thirsty, you might need to change your probiotic routine. Doctors suggest switching to bacterial probiotics instead of yeast-based ones if thirst becomes a problem.
Some people’s mouths feel dry too. Official side effect lists mention this symptom for certain probiotic strains, particularly acidophilus. Paying attention to how much water you need after starting probiotics tells you a lot about how your body handles these supplements.
Brain-related signs of probiotic overuse raise the most concern. Scientists at Augusta University found that probiotics can cause:
Brain fog and confusion
Poor concentration
Memory problems
Mental tiredness that lasts hours
Their study looked at 30 people with stomach problems. Twenty-two of them had brain fog, and every single one took probiotics – some used multiple kinds. The brain fog got so bad that some people couldn’t work anymore.
This happens because of Small Intestinal Bacterial Overgrowth (SIBO) and high D-lactic acid in the blood. People with brain fog were more likely to have SIBO, with much higher bacteria levels in their small intestine than healthy people. Three-quarters of them had high D-lactic acid – sometimes three times the normal amount.
Medical experts now say we should treat probiotics like medicine, not just food supplements, because they can affect your whole body. Taking probiotics without guidance or knowing which bacteria you need might create conditions that lead to brain fog by putting too many D-lactic acid-producing bacteria in your small intestine.
The Augusta University study showed something important: brain fog cleared up and stomach problems got better by a lot after antibiotic treatment and stopping probiotics. This tells us we need to take cognitive symptoms seriously as signs of taking too many probiotics.
Probiotics are safe for most people, but some groups face real risks when taking these supplements. The benefits need careful evaluation against known side effects for these groups. Knowing who should be careful could prevent serious problems.
People with weak immune systems face high risks from taking probiotics. The World Gastroenterology Organisation suggests limiting probiotic use in immunocompromised patients to specific proven strains [11]. You should be extra careful with probiotics if you take immunosuppressive medications after organ transplants, receive chemotherapy, or use corticosteroids at doses above half a milligramme per kilogramme body weight [12].
Several case reports show serious infections in immunocompromised people who took probiotics:
Bacteremia (bacteria in the bloodstream)
Fungemia (fungi in the bloodstream)
Sepsis (life-threatening infection complications)
Patients with indwelling central venous catheters face extra risks because these medical devices can let probiotic organisms enter the bloodstream [13]. Some strains like Bifidobacterium have caused invasive infections and sepsis in patients with low immune function, so talking to your healthcare provider is vital before starting any probiotic regimen [14].
Beyond people with weak immune systems, those with certain serious medical conditions need to be careful with probiotics. Studies link probiotics to negative outcomes in specific patient groups.
Research shows that people with severe acute pancreatitis should avoid probiotics completely because they might increase death risk [6]. ICU patients have developed life-threatening infections after taking probiotics [15].
Other groups needing careful evaluation include:
Postoperative patients
Those with overwhelming infections
Elderly individuals with serious illnesses
Premature infants
Individuals with short bowel syndrome
Patients with dark blood in their stools (melaena)
Probiotic safety lacks complete study in these groups. Limited safety data has led the U.S. Food and Drug Administration to warn healthcare providers about risks to seriously ill patients [14]. Medical supervision becomes vital if you have severe health conditions and want to take probiotics.
Some probiotic strains can trigger or worsen symptoms in people with histamine intolerance by producing histamine in the digestive tract [6]. Histamine, a biogenic amine, can cause allergy-like symptoms including headaches, hives, digestive issues, and anxiety when overproduced.
Strains of Lactobacillus casei and Lactobacillus bulgaricus found in fermented foods produce high histamine levels [16]. However, specific strains like Lactobacillus rhamnosus, Bifidobacterium infantis, Bifidobacterium longum, and Lactobacillus plantarum help histamine-sensitive people by reducing biogenic amines [16].
The mechanism makes sense: histamine-producing bacteria have histidine decarboxylase enzyme that turns the amino acid histidine into histamine [16]. Strains without this enzyme works well for people with histamine intolerance.
Histamine intolerance often comes from unbalanced gut microbiota. Gramme-negative bacteria like Escherichia coli and Salmonella typhimurium can increase histamine release, adding to histamine overload [16]. Finding the right probiotic matters—one that helps gut health without increasing histamine production.
If you’re histamine-sensitive and thinking about probiotics, talk to a healthcare professional about specific low-histamine strains instead of avoiding probiotics completely [17].
The way you take probiotics can make a big difference in how well they work and what side effects you might experience. Each delivery method changes how these tiny organisms survive their trip through your digestive system and how your body reacts to them.
Probiotic supplements and food sources work differently in your body. You’ll find supplements in capsules, tablets, powders, and now even gummies. Natural sources include yoghurt, kefir, and sauerkraut. These options can lead to different side effects:
Survival rates: Commercial yoghurts contain probiotic strains like Lactobacillus bulgaricus and Streptococcus thermophilus that last well on the shelf. These strains often have trouble getting past stomach acid and bile salts, which limits how many reach your intestines alive [18]. Enteric-coated supplement capsules help more probiotics survive the trip [19].
Dosage precision: Most supplements pack 1-10 billion CFU (colony forming units) per dose, with some going up to 50 billion CFU or higher [11]. These concentrated doses might cause stronger side effects at first compared to foods, which naturally have fewer probiotics mixed with other nutrients.
Protection mechanisms: Tablet forms shield bacteria from harsh conditions, but the compression process can damage some cells [19]. Foods like chocolate naturally protect probiotics and feed them with prebiotics to help them grow [20].
Lab-tested probiotics go through more quality checks than food-based ones, which explains why yoghurt and fermented foods usually cause fewer side effects. Food sources also give you more bacterial variety plus prebiotics, though this mix might cause extra gas at first as the prebiotics break down [21].
If supplements give you too many side effects, switching to food-based probiotics might work better. Natural foods help control how bacteria enter and work in your gut.
Each probiotic strain can cause different side effects. Look for products with at least 1 billion CFU of Lactobacillus, Bifidobacterium, Bacillus or Saccharomyces boulardii strains [2]. Each group has many strains that affect your body differently.
Lactobacillus handles stomach acid better than Bifidobacterium [5], which means less stomach discomfort. When you’re on antibiotics, yeast strains like, Saccharomyces boulardii work well because antibiotics don’t kill them like they do bacterial probiotics [4].
Some bacterial strains make substances called biogenic amines – histamine, tyramine, and phenylethylamine – that can cause headaches and upset stomachs [22]. Lactobacillus casei and Lactobacillus bulgaricus make more histamine, so they might not suit people sensitive to it.
The amount you take matters with specific strains. Children’s diarrhoea improved faster with Lactobacilli doses of 10^10 CFU or more, but lower doses made it last longer [22]. This shows that taking too little can sometimes make things worse.
How probiotics are packaged affects how well they work. Regular probiotics don’t last in moist environments like gummies, but spore-forming bacteria do better[19]. These spore-based probiotics survive stomach acid and only become active in your intestines where there’s no oxygen [20].
Finding the right combination of strain and delivery method reduces side effects and boosts benefits. Research shows that probiotics work like medicine – everyone responds differently to various strains and formats.
Managing probiotic side effects requires smart consumption strategies. The right dose, timing and expert guidance will give a better experience with these beneficial microorganisms.
Your body needs time to adapt to probiotics, especially when you have sensitivity to supplements. Taking half the contents from capsules or using probiotics every other day gives your body a gentler start. Research shows this method helps reduce digestive discomfort and lets your microbiome adapt at its own pace [23].
“Starting at a lower dose also helps you find your minimal effective dose” [23]. This helps you identify the smallest amount that works without causing discomfort. You can gradually increase the dose to find your personal tolerance level without overwhelming your system.
The benefits and side effects of probiotics change by a lot based on their consumption timing. Taking probiotics with breakfast works best because stomach acid levels are lowest during this time [24]. Your digestive system might handle probiotics better with food instead of an empty stomach if you have sensitivity issues [24].
Timing becomes even more significant if you take antibiotics. You can take certain probiotic strains like Saccharomyces boulardii and Lactobacillus rhamnosus with antibiotics. Other Lactobacillus and bacillus strains work better an hour or two before or after the antibiotic [3]. Your gut needs probiotics for at least two weeks after finishing antibiotics to recolonize properly [3].
Get medical help right away if:
Medical consultation before starting probiotics is vital if you have a compromised immune system, serious illnesses or other health conditions [26]. Note that probiotics might not suit everyone, particularly people with severe illnesses, immunosuppression or those recovering from major surgery [24].
Treating probiotics like medications instead of casual supplements ended up being safer. Most people get the best results from regular, consistent intake rather than occasional use [3].
Probiotics can do wonders for your health, but you need to know what it all means to use them safely and effectively. Your body might need some time to adjust, which can lead to mild digestive changes. People with weak immune systems or serious health conditions need to be extra careful.
The right way to use probiotics starts with picking the correct strains that work for you. You should think over your health and how you’ll take them. Start with small doses, time them right, and pay attention to how your body reacts. Of course, if you notice any severe or lasting symptoms, you should see your doctor right away.
Getting your gut health on track with probiotics takes time and attention. Don’t worry if you notice some side effects – they usually go away within weeks as your body gets used to them. You’ll get the best results when you find the sweet spot between benefits and what your body can handle. Choose your products wisely and keep your doctor in the loop about what you’re taking.
Q1. What are the most common side effects of taking probiotics?
The most common side effects are temporary digestive issues such as bloating, gas, and changes in bowel movements. These typically resolve within a few weeks as your body adjusts to the new bacteria in your gut.
Q2. Are probiotics safe for everyone to take?
While probiotics are generally safe, certain groups should be cautious. People with weakened immune systems, serious illnesses, or those recovering from surgery should consult a healthcare professional before taking probiotics. Pregnant women and infants may also need to avoid certain probiotic strains.
Q3. How can I minimise potential side effects when starting probiotics?
Start with a lower dose and gradually increase it over time. Taking probiotics with food, particularly at breakfast when stomach acid levels are lower, can also help reduce irritation. If side effects persist, consult your healthcare provider.
Q4. Can taking probiotics daily have long-term effects?
For most healthy individuals, taking probiotics daily is safe and can provide ongoing benefits for gut health. However, it’s important to choose the right strains and maintain consistent intake for optimal results. Always monitor your body’s response and consult a healthcare professional if you have concerns.
Q5. Do probiotics interact with medications?
Probiotics can interact with certain medications, particularly antibiotics. If you’re taking antibiotics, it’s best to space out your probiotic intake, taking them at least two hours before or after your antibiotic dose. Always inform your doctor about any supplements you’re taking, including probiotics, to avoid potential interactions.
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