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Probiotics Side Effects & Adverse Reactions (List)

Probiotics are considered living microorganisms that, when ingested in sufficient quantities, are conducive to the health of their host.  The term probiotic is derived from the preposition “pro” (meaning “for”) and “biōtikos” (meaning “fit for life”), and is associated with the introduction of beneficial bacteria, contrasting with the term antibiotic (associated with the destruction of pathogenic bacteria).  Though fermented bacterial cultures have been referenced in literary works dating back to biblical times, Ukrainian immunologist Elie Metchnikoff (a recipient of the Nobel Prize in 1908 for his discovery of phagocytosis), is regarded as the founding father of probiotics.

Metchnikoff was first to formally document a connection between increased consumption of yogurt among Bulgarian peasants, enhanced health, and longevity.  At the time, Metchnikoff postulated that “Bulgarian bacillus” within yogurt replaced preexisting pathogenic gut bacteria, whereby it normalized bowel health and extended lifespan.  Despite Metchnikoff’s initial observation of probiotics in the early 1900s, probiotics weren’t formally acknowledged by mainstream science, health organizations, and mass media until the early 2000s.

Within the last decade, scientific research groups have made considerable advances in the identification of specific probiotic species and subspecies, as well as investigating the efficacy of probiotics for the treatment of medical condition.  That said, there’s currently insufficient quality evidence to suggest that probiotics effectively treat any medical condition.  Moreover, individuals supplementing with probiotics sometimes report unwanted side effects and/or adverse reactions.

Probiotics Side Effects & Adverse Reactions (List of Possibilities)

When many hear the term probiotics, they think of over-the-counter supplements used to maintain gut health and/or reverse dysbiosis.  Anytime a supplement is considered “natural” or available over-the-counter, a subset of individuals wrongfully conclude that it is somehow devoid of side effects or incapable of causing them.  Ardent supporters and/or marketers of probiotics promote the idea that ongoing probiotic supplementation will improve health while dismissing the possibility of side effects.

Although probiotics are generally regarded as safe, it’s important to underscore the fact that side effects and adverse reactions can occur as a result of supplementation.  Side effects are believed to result from bacteria-host interactions in which the probiotic supplement may be incompatible with the current habitat of the user’s microbiota, ultimately triggering a reaction.  Examples of common side effects from probiotics include: abnormal bowel movements, bloating, flatulence, gurgling, and stomach aches.

Understand that the number of side effects, specific side effects, and respective severities of each side effect – will be subject to significant individual variation.  One person might experience zero side effects from his/her supplementation with probiotics, yet another may report prominent adverse reactions.  Below is a comprehensive list of possible side effects that have been reported by users of probiotics.

Acne: A relatively uncommon side effect that some individuals report while supplementing with probiotics is acne.  It is possible that administration of probiotics may trigger a biological reaction that increases likelihood of acne breakouts.  Probiotics affect activity in the gastrointestinal tract, which is understood to modulate activation of the immune system, peripheral nervous system, and central nervous system.

Perhaps if unfavorable, this modulation might lead to an unexpected acne breakout.  It is also possible that acne breakouts after probiotics are nothing more than a transient, stress-response associated with the body attempting to adapt to the presence of new bacteria.  Furthermore, as the new bacteria are introduced, other pathogenic bacteria may get displaced and “die off,” which might also trigger a stress-reaction and/or detoxification phase in which acne breakouts occur frequently.

Some suspect that after the body adjusts to the probiotic supplement, acne outbreaks will diminish and/or cease altogether.  Nonetheless, if you’re experiencing acne flare-ups consistently after taking a probiotic, you may want to consider: switching to a different bacterial strain, manufacturer, or reducing the dose to determine whether your acne improves.  If the acne occurs regardless of the probiotic that you use, you may need to accept the fact that you don’t respond well to probiotic supplementation.

Anxiety: Certain individuals supplementing with probiotics have reported anxiety as a side effect.  It should be theorized that individuals most susceptible to experiencing anxiety after taking probiotics are persons with an underlying neuropsychiatric disorder.  Individuals with neuropsychiatric disorders are often highly sensitive to changes in peripheral and/or central nervous system functioning, each of which can be affected by probiotics through the gut-brain axis (GBA).

Probiotics can alter production and uptake of neuroactive peptides in the gut, which in turn could activate the sympathetic nervous system, alter vagal nerve activity, and/or generate neuroactive peptides that stimulate receptors in the PNS and CNS.  Another cause of increased anxiety in probiotics users is related to an increase in histamine.  Some strains of bacterial species including: L. bulgaricus, L. casei, L. reuteri, and L. helveticus – are capable of modulating and/or increasing histamine, which might provoke an anxiogenic response among persons with a histamine intolerance or sensitivity.

It is possible that feeling anxious, agitated, or nervous after supplementing with a probiotic is a temporary response associated with displacement of pathogenic bacteria.  Once these bacteria are eliminated from the GI tract, symptoms of anxiety may improve.  That said, if probiotics are exacerbating your anxiety, it is wise to switch up the dose, species, and/or cease administration for awhile.

Bloating: Among the most common side effects of probiotic supplementation is bloating.  Though not everyone will notice increased bloat after taking probiotics, many report feeling swollen and gassy with a stomach ache, especially if they recently began supplementing and/or tested a new probiotic strain.  In some cases, bloating may be attributed to increased water retention and/or digestive changes resulting from the billions of bacterial species attempting to colonize within the gastrointestinal tract.

Older bacterial inhabitants may die off, possibly leading to some sort of detoxification process in which bloating occurs until the gut has readjusted itself to accommodate new bacteria.  It is also possible that bloating is associated with administration of a supratherapeutic dose (containing an excessive number of colony-forming units or CFUs).  Additionally, histamine release by certain bacteria (among those with an intolerance or sensitivity) could also trigger bloating as a side effect.

To manage bloating, you might want to decrease your probiotic dose, switch to a different supplement, and/or take a break from supplementation for awhile.  Getting plenty of exercise, reducing intake of foods highest in histamine, and staying well-hydrated should prove helpful for bloating attenuation.  Although bloating is a fairly normal reaction to probiotics, if it becomes extreme, you may want to seek advice from a professional.

Brain fog: A problematic side effect that highly self-aware individuals may notice after taking probiotics is brain fog, or the inability to think clearly.  It appears as though bacterial species in the gut can influence vagal innervations and generation of neuroactive molecules, each of which is thought to alter activity in the brain.  The alteration of brain activity following the administration of probiotics could disrupt mental clarity and lead to a state of “foggy” thinking.

It is also possible that brain fog from probiotic administration is related to a detoxification process by which favorable bacteria displace other bacteria, and in the process of displacement, the older bacteria “die off” whereby they generate small quantities of neurotoxic metabolites.  Any neurotoxic metabolites crossing the blood-brain-barrier (BBB) might interfere with clarity of thought.  If you feel as though your thinking has become clouded as a result of probiotic supplementation, you may want to discontinue administration or modify your dose and wait for mental clarity to return.

Chills: An adverse reaction to probiotics reported by a small percentage of users is chills.  Those who claim to experience chills or feel chilled after taking probiotics typically experience other side effects such as: diarrhea, gastrointestinal distress, nausea, and/or sweating.  It is possible that, for some individuals, the chills are a byproduct of a probiotic-induced Herxheimer-like reaction in which the body is detoxifying itself from pathogenic bacteria.

If you’re experiencing a Herxheimer-like reaction, it could persist for a few days to several weeks before full recovery is made.  Some recommend continuing to administer the probiotic through this reaction, whereas others suggest discontinuing the probiotic temporarily and reintroducing it at a lower dose after the chills subside.  Assuming the chills are related to a Herxheimer-like response, you’ll want to stay sufficiently hydrated to flush out the dead bacteria.

It is also possible that the chills are a sign that you aren’t able to tolerate the specific strain of probiotic that you’re using.  If you constantly feel chilled after initiating probiotic supplementation, yet the chills haven’t improved for several weeks, you may want to discontinue the probiotics for awhile and/or switch to a different probiotic strain until you feel better.  Be sure to discuss the chills and other symptoms with a medical professional to rule out health conditions that might be contraindicated with your probiotic usage.

Cognitive impairment: Dysbiosis in the gut has been linked to cognitive deficits in animal models and humans, leading some to speculate that administering probiotics may ameliorate cognitive dysfunction.  That said, a side effect reported by a subset of individuals supplementing with probiotics is cognitive impairment.  If you suddenly notice that your ability to perform cognitively-demanding tasks has diminished and/or declined in days or weeks after you started taking a probiotic, the supplement might be to blame.

In some cases, the cognitive impairment resulting from probiotic supplementation is mild and eventually diminishes with continued administration.  On the other hand, some individuals report that the cognitive impairment worsens and/or fails to improve over time, possibly affecting work and/or academic performance.  Transient cognitive impairment is most likely a byproduct of the body adapting to the probiotic supplement and/or death of older, displaced bacteria.

Nevertheless, it is important to consider that too high of a probiotic dosage might be triggering excessive production of neuroactive peptides in the gut that modulate brain activity in such a way, that cognitive faculties become impaired.  Another reason for impaired cognitive function might be related to histamine sensitivity or intolerance as a result of increased histamine production.  To minimize probiotic-induced cognitive impairment, scale back on your dose, try a different supplement, and/or discontinue usage for awhile to determine whether your cognitive abilities return.

Constipation:  A common side effect of probiotics that many users experience is constipation or difficulty passing a bowel movement.  The constipation may be accompanied by a stomach ache from indigestion, and you might notice changes in the composition of your stool when you finally pass a bowel movement; constipation is associated with hardening of stools.  In some cases, the constipation will be a transient side effect that eventually subsides as the probiotics populate within your gastrointestinal tract and restore normative gut health.

It is also possible that the constipation you’re experiencing might be related to a Herxheimer-like reaction in which pathogenic bacteria die as a result of the newly-introduced healthy bacteria.  If you’re experiencing a “die off” of pathogenic bacteria, it might take several weeks before the constipation fully abates.  To minimize odds of dealing with constipation and/or reduce its intensity, you may want to scale back on your probiotic dosing.

Rather than taking a probiotic every day, you might want to try taking it every other day or even once every few days.  Sometimes users start with too large of a dose for their body to handle and constipation ensues as a result of excessive numbers of bacteria being introduced to the gut.  Other tips for coping with probiotic-induced constipation include: trying a different supplement, staying well-hydrated, eating fibrous foods, and engaging in physical activity every day.

Cramps: It is possible that you might experience cramping throughout your body as a side effect of probiotic supplements.  Those who report cramping tend to note that it most frequently occurs throughout their stomach region, and sometimes the upper chest area.  In rarer cases, some will notice that their entire body seems to feel achy and plagued with cramps that they never had prior to using a probiotic.

The cramps could be related to increased generation of histamine after introduction of the probiotics, but might also be related to the new bacteria modulating gastrointestinal activity.  A simple way to deal with the cramps that you’re experiencing is to decrease the dose of the probiotic you’re taking and increase consumption of water.  On the other hand, if you have a histamine sensitivity and are experiencing cramps, you may want to double-check and confirm that you’re not using a probiotic that modulates histamine.

Getting some extra rest and relaxation could also prove useful for individuals experiencing excessive cramping.  That said, if you cramp up each time you take a probiotic, you should listen to your body and interpret it as a sign that the probiotic may be intolerable.  If you continue to experience cramps as a side effect of the probiotic, discontinue it for awhile and rule out other medical conditions with your doctor.

Diarrhea: Another of the most common probiotic side effects is diarrhea.  Those who experience diarrhea after taking a probiotic report that its generally most extreme within the first few days and/or weeks of supplementation.  When you first start using a probiotic, billions of colony-forming units (CFUs) are being ingested and attempting to populate your gut, however, pathogenic and older bacterial strains are competing to stay alive with the newer bacteria.

As a result, the older bacteria may put up a fight prior to dying off, leading to irritation and/or inflammation of the gut lining, whereby you might experience diarrhea or loose stools.  The diarrhea may also be accompanied by chills, flu-like symptoms, and sweating.  Over time, it is thought that the diarrhea will subside as the body works its way through the “die off” phase and the new bacteria fully colonize.

Within 1 month of probiotic supplementation, users should no longer experience diarrhea as a side effect.  In the event that your diarrhea hasn’t subsided, it makes little sense to continue taking your probiotic.  Wait awhile and consider switching to a different probiotic manufacturer selling probiotics with different bacterial constituents and/or amounts.

Some individuals might notice transitions between bouts of constipation and diarrhea where they feel constipated most of the day, but then experience intermittent bouts of explosive diarrhea.  In this case, it’s probably a good idea to reduce the probiotic dose, continue drinking plenty of water, and replenish the body with electrolytes and nutrients by consuming nutrient-dense food.  Moreover, scale back on fibrous food and consider asking your doctor about taking an antidiarrheal (e.g. Imodium) to counteract the diarrhea side effect.

Dizziness:  Are you suddenly feeling dizzy or dizzier than usual after taking your probiotic?  Dizziness is another side effect that has been reported among a small percentage of users.  Those who experience dizziness after taking probiotics suggest that it occurs on an intermittent basis, and is generally of mild-to-moderate severity.  It is uncommon for the dizziness to be severe, long-lasting, and/or impair a person’s ability to function in school or work.

If you’re experiencing dizziness, you may want to first evaluate whether it’s actually related to your probiotic supplementation and not another factor.  Assuming you fully attribute your dizziness to the probiotic, it may be that you’re taking too high of a dose and/or a suboptimal strain of bacterial species for your body.  Cutting your dose in half or trying a different supplement may help attenuate the dizziness you’re experiencing.

It is also possible that the dizziness stems from another side effect induced by your probiotic (e.g. diarrhea) rather than the probiotic itself.  For example, if you experience ongoing diarrhea, the diarrhea may be causing you to feel lightheaded and dizzy.  In most cases, dizziness occurring early in treatment will diminish in time, but if it doesn’t, discontinuing your probiotic and consulting a medical professional is recommended.

Fatigue: A subset of individuals will become increasingly fatigued and/or lethargic when they start supplementing with probiotics.  If your energy significantly plummeted after you initiated probiotic supplementation, one possible cause for the fatigue is a Herxheimer-like reaction.  The probiotics might be waging war with pathogenic bacteria in your gut, and as the pathogenic bacteria “die off,” your body stays working hard to clear them from your system – ultimately causing you to feel tired or fatigued.

If your fatigue is caused by a Herxheimer-like reaction, it should diminish within 1 to 4 weeks after you began supplementing.  Should your fatigue persist for an extended duration (e.g. longer than 1 month), it’s probably not related to any sort of “die off,” but could be related to the specific bacterial strains within your supplement.  Bacteria in your probiotic may be generating biogenic amines within your gut that are sapping your mental and physical energy.

To combat the fatigue you’re experiencing, it makes logical sense to reduce your dose and/or test a completely different probiotic supplement (with different strains).  If the new probiotic induces the same effect, you may need to steer clear from probiotic supplementation altogether.  Also keep in mind that the time of day you’re taking the probiotic may exacerbate the fatigue in accordance with your circadian rhythm, so modify your dosing time to night if your probiotic makes you feel fatigued during the morning/afternoon.

Flu-like symptoms: A rare adverse reaction to probiotics that some report is experiencing flu-like symptoms.  If you experience flu-like symptoms after supplementing with a probiotic, most would suspect that this is a byproduct of a Herxheimer reaction.  Some theorize that the bacteria within probiotics eliminate a considerable number of other bacterial inhabitants within your gut by displacing and killing them.

As some bacteria “die off” in the process of supplementing with probiotics, they may release toxins that activate the immune system and lead your body to suspect an infection.  The upregulated immune response may make you feel nauseous, fatigued, chilled, sweaty, and/or as though you have the flu.  Couple this with possible diarrhea, constipation, and severe stomach aches – and it’s easy to see how some might report flu-like symptoms after starting probiotics.

Still, it is important to avoid assuming that flu-like symptoms are definitively a result of your probiotic supplement – they could be a sign of another medical condition.  Report all flu-like symptoms to your doctor and ensure that probiotic supplementation isn’t contraindicated with your current medical status.  The most obvious way to reverse flu-like symptoms (if they were a result of probiotics) is to quit using probiotics for awhile.

Gas: An extremely popular side effect of probiotics is gas or gassiness.  You may notice that you pass more gas than usual, some of which might be exceptionally malodorous.  Many consider the increased gas production and generation to be a sign that your body is responding well to the probiotic supplement and that bacteria are successfully colonizing within your gut.

Some individuals might not pass more gas than usual, however, they may feel as if there’s an increase in gas production and/or gas staying trapped throughout the stomach region.  The increased gas production may lead to bloating and/or stomach aches.  To cope with the emergence of gas as a side effect, it is recommended to avoid holding in your gas and stay physically active.

You may also want to try modifying your dietary intake and/or altering the dose of the probiotic you’re using.  In most cases, increased gas production diminishes with continued supplementation.  In fact, some individuals report significantly less gas and fewer smelly farts after they’ve consistently used a probiotic for several months.

Gurgling: An extremely common side effect that you’re likely to notice when taking a probiotic is an increase in stomach gurgling, growling, and/or rumbling sounds.  The noises coming from your stomach after taking your probiotic might make certain individuals concerned as to whether their supplement is causing some sort of sickness.  Some people might even freak out at the idea that there are billions of little bacteria that proliferate in the gut after supplementing with a probiotic.

Experts consider the gurgling noise side effect as indicating that the probiotics are improving your gastrointestinal function.  Individuals with silent stomachs that are devoid of gurgling noises tend to experience an increase in constipation and/or bowel irregularities.  The gurgling is a result of the stomach lining contracting more frequently than usual and modulating the flow rate of food throughout your gastrointestinal tract.

Headaches: Among the most frequently-occurring side effects of any supplement or drug is headache.  If you experience headaches after taking probiotics, there are likely a couple potential culprits to consider including: a mini Herxheimer-like reaction (in which the immune system is activated), the release of biogenic amines (e.g. histamine), or other probiotic-induced side effects.  Those experiencing a Herxheimer-like reaction as a result of probiotic-induced death of older bacteria within the GI tract can experience a headache due to proinflammatory cytokines, oxidative stress, endotoxin release, etc.

Should you suspect that bacterial die off is causing your headache, staying hydrated and getting sufficient rest is critical.  A headache might also be caused by release of biogenic amines within the gut as induced by the new bacterial species.  These biogenic amines may cause excessive vasoconstriction (leading to a standard headache) or possibly vasodilation (provoking a migraine).

Individuals with a history of headaches and/or migraines may be most prone to experiencing various forms of headaches as a side effect.  Also consider that unmanaged side effects such as diarrhea can lead to headaches by depleting the body of electrolytes and inducing dehydration.  Getting plenty of sleep, altering your probiotic dose, drinking adequate water, and strategically using headache relief medication may prove helpful for counteracting this side effect.

Increased thirst: Though fairly uncommon, increased thirst has been reported as a side effect of probiotic supplementation.  If you recently started taking a probiotic and feel thirstier than usual and/or as though you can never seem quench your thirst, realize that your supplement might be to blame.  Some may perceive increased thirst as a favorable side effect in that it encourages you to stay hydrated and/or consume water to “flush out” any bacteria that end up dying after probiotic administration.

Since you may be drinking more as a result of the increased thirst, you might also end up experiencing frequent urination.  If the increased thirst fails to subside after several weeks of supplementing with your probiotic, it is recommended to discontinue your probiotic and have a doctor rule out other potential medical causes of your thirst increase (e.g. diabetes).  Switching to a different probiotic and/or decreasing your probiotic supplementation could also attenuate the excessive thirst (assuming it was caused by the probiotic).

Gastrointestinal infections: Although many researchers are investigating the effectiveness of probiotic supplements for the treatment of intestinal infections, it seems as though some individuals end up with an intestinal infection as a result of their probiotic supplement.  Most persons experiencing an intestinal infection as a result of probiotic supplementation have an underlying medical condition that made them susceptible to the specific infection.  For example, someone who’s immunocompromised as a result of HIV is expected to exhibit greater susceptibility to infectious disease as a result of probiotic supplementation.

In the event that an infection occurs after probiotic supplementation, a myriad of disconcerting symptoms may emerge including: abdominal pain, bloody stools, diarrhea, fever, skin rash, and vomiting.  These symptoms are caused in part by proliferation of the infectious agent, as well as inflammation of the gastrointestinal tract (throughout the stomach and small intestine).  If you suddenly became extremely sick after probiotic administration, seek emergency medical attention to rule out an underlying infection that may have flared up and/or been induced by the probiotic you’re using.

Insomnia: A relatively uncommon reaction to probiotic supplementation that some users report is insomnia.  If the insomnia only occurs for the first few weeks of your probiotic administration, it might be related to the death of older bacteria in which endotoxins are released, your autonomic nervous system (ANS) becomes imbalanced, and biogenic amines alter activity in your nervous system.  The insomnia may be accompanied by racing thoughts, restlessness, and brain fog or cognitive dysfunction.

For some individuals, the insomnia will subside after a couple weeks of taking probiotics and their sleep quality will significantly improve.  In the event that you experience insomnia for months after taking your probiotic supplement, it may be caused by the release of biogenic amines throughout your enteric nervous system.  Those that are sensitive to certain biogenic amines, especially histamine, are likely to have trouble falling asleep and/or staying asleep.

It is also possible that the probiotics you’re taking are causing stomach issues such as diarrhea or constipation that interfere with your ability to wind down and transition from a state of wakefulness to a slumber.  If your insomnia is worsened by probiotics, you might want to try altering the time of day you take your probiotic (e.g. morning vs. night), lowering your dose, or switching up the species.  You may also want to discontinue probiotic usage for awhile in hopes that your sleep normalizes.

Itchiness: An odd reaction that’s more common than expected among probiotic users is itchiness.  Some individuals end up trying a new probiotic supplement for the first time and notice that their skin becomes itchier than usual.  The itchiness may be of mild or moderately bothersome for certain people, however, others have described it as severe, incessant, and debilitating.

The most logical reason that you might become itchy from a probiotic supplement is that it’s triggering an allergy.  You might be allergic to one of the added ingredients within your probiotic formulation, or possibly allergic to the biogenic amines (such as histamine) being generated by the new bacterial species introduced to your gastrointestinal tract.  Individuals with histamine intolerance or sensitivity tend to be the ones who report severe itchiness, possibly accompanied by a rash and/or breakouts of acne.

Another reason for itchiness as a side effect of probiotics might be related to a Herxheimer reaction in which immune system activity increases to facilitate elimination of dead bacteria.  If you are experiencing a transient reaction to bacterial “die off” that’s causing the itchiness, it should decrease within several weeks.  If the itchiness fails to subside, you may want to reconsider probiotic supplementation or resort to using a different strain (less likely to modulate histaminergic activity).

Lightheadedness: It is fairly uncommon, but possible for some to experience lightheaded as a side effect of their probiotic supplementation.  The lightheadedness may be related to modulation of activity within the ENS (possibly through the release of biogenic amines) which exerts downstream effects upon CNS activity or alters vasodilation/vasoconstriction.  Lightheadedness might also be caused by probiotic-induced side effects such as diarrhea which leave a person depleted of electrolytes and dehydrated.

That said, in most cases, lightheadedness is of mild intensity, is easily managed by the probiotic user, and subsides over time.  If your lightheadedness is severe and you suspect that it’s caused by your probiotic supplement, it should be advised to discontinue probiotic usage and consult a medical doctor to evaluate your health.  Modifying your probiotic dosage, staying hydrated, and getting some extra rest when needed might also reduce lightheaded feelings.

Mood changes: There’s emerging evidence suggesting that altering bacterial composition of the gut might affect a person’s mood.  Modulating activity in the gut is thought to influence production of biogenic amines in the gut, some of which might cross the blood brain barrier to influence brain function and mood.  Other biogenic amines stimulate receptor sites in the enteric nervous system to support balance within the autonomic nervous system (between the SNS and PNS).

The predominant means by which gut bacteria influence brain function to modify our mood is through the vagal nerve.  Studies of dysbiosis (bacterial abnormalities in the gut) show that pathogenic bacteria affect vagal tone.  When healthy bacteria are introduced to the gut and dysbiosis is reversed, a person’s mood may change (perhaps to a substantial extent) as a result of enhanced vagal tone.

For this reason, researchers are investigating the effects of probiotics for depression, gut bacteria modulation for autism, and fermented foods for anxiety.  The effect of probiotics on your mood will likely be contingent upon the strain (species and subspecies) that you take.  In some cases, you might notice mood swings in the early days of supplementation as a result of bad bacteria dying off.  If probiotics are negatively affecting your mood over a long-term, a different strain and/or dosing modification should be considered.

Nausea: If you feel nauseated after taking probiotics, you are certainly not alone.  Many users report experiencing the side effect of nausea for 1-3 weeks after they begin supplementing for the first time.  The nausea could be a sign that your body is having a tough time adapting to the specific species of bacteria that you’re administering, or possibly resulting from administration of an unnecessarily high dose.

Another possibility is that the nausea is a byproduct of a Herxheimer-like reaction, especially if accompanied by other symptoms.  If you think that the probiotics have triggered some sort of “healing crisis” in your gut to cause nausea, you’ll want to stay hydrated, get plenty of rest, and with enough time the nausea should subside.  That said, ongoing nausea may signify contraindications, interactions, and/or an undiagnosed medical condition (e.g. infection).

For this reason, it is always advised to seek emergency medical care when experiencing nausea over an extended duration – especially if accompanied by other symptoms.  Trying a different probiotic strain (from the one they’re using) might be a good idea for certain individuals if the nausea is unmanageable.  Among individuals that want to continue using their probiotic despite feeling nauseous, an antiemetic adjunct could help.

Shakiness: A rare adverse reaction reported by a subset of probiotic users is intermittent bouts of shakiness.  It is unclear as to how a probiotic supplement might cause someone to experience the “shakes” or tremor, however, several theories have been proposed.  Some believe that shakiness could be a reaction to old bacteria within the gut “dying off” and getting replaced by new bacterial species (within the probiotic).

Prior to their death, the old gut bacteria might release toxic metabolites and/or manage to activate a person’s immune response.  Immune system activation could generate a host of reactions, including shakiness, flu-like symptoms, chills, sweating, etc.  Eventually the old, dead bacteria will get excreted, the body will adapt to the new bacteria colonizing within the gut, and the shakiness should subside.

That said, shakiness might not always be related to an immune reaction, it could be a sign of a contraindication, interaction, and/or toxicity (especially among high dose users).  Another possibility is that the probiotic supplement altered production of biogenic amines within the gut, ultimately causing anxiety and corresponding shakes.  If you’re feeling shaky and you know it’s a result of your probiotic, you may want to double check with a doctor that the probiotic is safe to use given your current medical status and/or medication regimen.

Skin rash: A side effect of probiotics that’s more common than many people suspect is skin rash.  Some individuals who report skin rashes after taking probiotics note that they are confined to a specific region of the body such as the neck, back, chest, or arms.  Other probiotic users have mentioned that the rash occurs throughout their entire body, including their face and is extremely itchy.

The rash you’re experiencing may appear as patches, splotches, or dots of redness and could be extremely itchy.  There are many possible reasons you might experience a rash after starting a probiotic supplement including: Herxheimer reactions (die off of old bacteria, triggering an immune response), modulation of biogenic amine levels by new bacterial strains (especially histamine), or even an interaction between probiotics and another substance you’re using.

You may also want to consider that a skin rash may occur from taking too high of a dose of your supplement, especially if you are simultaneously consuming fermented foods on a regular basis.  The smartest step to take if you experience a skin rash from your probiotic is to stop using it for awhile and consult a dermatologist for an evaluation.  If your rash goes away once you’ve stopped the probiotic, you may want to steer clear from supplementation for awhile and/or try an entirely different dose/strain combo.

Sleep problems: When first starting probiotics, you might notice changes in your sleep quality, sleep duration, and might experience weird dreams.  Some people mention that they’re not able to get as much quality sleep as they did before starting probiotics, whereas others report sleeping significantly better than they did prior to supplementation.  If you experience sleep problems from your probiotic supplement, one thing you might want to try is modifying the time of day at which you take it.

For example, if your probiotic makes you feel drowsy early in the day, but this early-day drowsiness interferes with your ability to fall asleep at night, you might want to try taking the probiotic at night.  Similarly, if the probiotic energizes you more than usual, try taking it in the early morning as opposed to late at night.  If modifying the time of administration isn’t helpful, another thing to try is reducing the dose of your supplement (e.g. take half rather than the full dose).

Sleep disturbances in the early phases of supplementation might also be a result of a Herxheimer reaction in which inflammation increases and an immune response is activated.  Consider that the production of biogenic amines within your gut from the specific strains of bacteria included in your probiotic might also be to blame for sleep abnormalities.  Tweaking the dose, time of administration, and/or bacterial constituents within your probiotic should help ameliorate some of the sleep deficits related to supplementation.

Stomach aches: Among the most popular probiotic side effects, especially those new to using probiotics, is stomach aches.  The stomach aches you experience could be caused by bacteria-induced changes in intestinal motility and/or gastric emptying.  Alterations in intestinal motility and/or gastric emptying could lead to abnormal intestinal contractions (e.g. spasms) or prevent stomach muscles from properly emptying the stomach of digested food.

Severe stomach aches are likely a byproduct of significant probiotic-induced bacterial changes throughout the gastrointestinal tract.  These changes in bacteria seem to affect the function of the entire GI tract, possibly more significantly in some users than others, and as a result, cause stomach aches.  In many cases, the stomach aches are accompanied by and/or influenced by other side effects such as: bloating, constipation, diarrhea, and/or gassiness.

In many cases, the stomach aches are transient and will eventually subside as the body adapts to the probiotic supplement (which could take weeks).  Avoiding foods that are likely to exacerbate your preexisting stomach ache should be helpful.  That said, if you’re continuing to experience unwanted, unremitting stomach aches, consider that you may be taking too high of a probiotic dose and/or bacterial species that aren’t an optimal fit for your particular biology.

Sweating: If you notice that you’re sweating more than usual and/or profusely (e.g. hyperhidrosis), realize that it could be an adverse reaction to your probiotic supplement.  For many who experience significant sweating after starting probiotics, it is possible that the new bacteria are overtaking old and/or pathogenic bacteria in your gut, ultimately causing bacterial “die off” which triggers an immune response that upregulates sweat production.  The immune-related increase in sweat production may persist until your body has fully detoxified from the dead bacteria and adapted to the new strains introduced from the probiotic.

It is also possible that the bacteria you’ve ingested had an indirect influence on systems implicated in production of sweat, whereby you’ve suddenly began sweating more frequently after supplementation.  Additionally, keep in mind that while sweating might be a temporary “detox,” it could also signify that you’re experiencing an interaction (between probiotics and another agent) and/or that your immune function is compromised.  Sweating as a long-term side effect of your probiotic may be a sign of an allergy and/or that you’re ingesting more CFUs than your body needs.

Tiredness: Supplementing with probiotics might cause some individuals to feel drowsy, tired, and/or more fatigued than usual.  This tiredness may be a temporary side effect resulting from bacterial “die off” and replacement, and if this is the case, it may persist for several weeks of supplementation until the body has fully adapted.  Feeling increasingly tired after taking a probiotic might also be related to modulation of biogenic amines within the enteric nervous system (ENS), ultimately affecting autonomic balance.

If your body is sensitive to the levels of certain biogenic amines being generated within your ENS, it is possible that this may alter activation of the CNS leading you to feel more tired than usual.  As was already mentioned, some individuals may experience changes in their sleep cycle from probiotics, and these sleep changes might lead to tiredness and/or grogginess throughout the day.  Altering the time of day at which you take your probiotic, modifying the dose (e.g. scaling back), or testing a different bacterial strain may help restore your energy levels.

Vomiting: A rare adverse reaction that occurs in a very small percentage of probiotic users is vomiting.  The vomiting is typically preceded by nausea, and tends to occur among first-time probiotic users who initiate supplementation with high doses.  It is thought that by starting treatment with an extreme and/or abnormally high dose of probiotics, the body becomes overwhelmed, and vomits to purge itself of the supplement.

Another reason some users may end up vomiting is related to probiotic-induced generation of biogenic amines such as histamine.  Many bacterial strains increase concentrations of histamine in the gut, and among persons with low DAO (diamine oxidase) enzyme activity and/or HNMT (Histamine N-Methyl-Transferase) function, this may lead to a toxic effect and vomiting for detoxification.  Vomiting might also be caused by a Herxheimer-like reaction in which the probiotics are killing older bacteria in the gut, and in the process of doing so, the immune system is activated – causing the user to vomit.

If you’re vomiting after taking a probiotic, do not automatically assume that you’re experiencing a Herxheimer reaction.  Confirm that your batch of probiotics wasn’t somehow contaminated or expired, and verify that you aren’t allergic to any ingredients within your supplement.  Vomiting should be interpreted as a serious sign that your body is responding unfavorably to the probiotic – either as a result of the dose and/or bacterial species.

Have your doctor assess whether you could have a medical condition (e.g. viral or bacterial infection) in which probiotic usage is contraindicated.  Also review your supplement and/or medication regimen to rule out the possibility of an interaction effect.  In the meantime, since you won’t want to keep vomiting, discontinuing your probiotic for awhile is smart; reinstatement with an entirely different probiotic (strain/dose/manufacturer) in the future may be helpful.

Weight changes: A subset of individuals will report changes in body weight as a side effect of probiotic supplementation.  Some will report gaining more weight than expected, whereas others may report losing weight.  Studies in animal models show that bacterial constituents within the gut are correlated with body weight, and that modification of such bacteria can determine whether the animal gains or loses weight.

It is unknown as to whether probiotic administration has a significant effect upon the body weight of humans, however, it is reasonable to suspect that it could.  Slight weight gain from probiotic supplementation may be related to something as simple as increased appetite, bloating, or constipation.  Modest weight loss may stem from diarrhea, vomiting, or appetite reduction after ongoing supplementation.

Probiotics may also influence body weight through modulation of glucose levels, insulin secretion, and other hormones (e.g. ghrelin, leptin, etc.).  Though correcting dysbiosis is likely to facilitate therapeutic weight change and an overall health improvement, certain strains of healthy bacteria could lead to unexpected weight fluctuations.  A meta-analysis by Million, Angelakis, Armougom, et al. (2012) confirms that Lactobacillus species have host-specific effects associated with body weight change.

Research by Million and Raoult (2013) indicates that Lactobacillus species and strains induce weight gain in lean humans and weight loss in overweight/obese individuals.  The degree of weight change that you experience is likely contingent upon the species, subspecies and quantity of the probiotic you administer, as well as whether you are lean vs. obese prior to supplementation.  If you dislike the weight change you’re experiencing from your current supplement, you may wish to use a different species/strain.

  • Source: https://www.ncbi.nlm.nih.gov/pubmed/22634320
  • Source: https://www.ncbi.nlm.nih.gov/pubmed/23332210

Note: If you have a question regarding any particular side effect or adverse reaction on the above list, be sure to consult a medical professional for proper guidance.  Should you have an additional side effect and/or adverse reaction to report that wasn’t included in the aforestated list, share it in the comments section below.

Variables that influence Probiotic side effects

There are many variables that might influence the specific probiotic side effects that you experience, as well as their respective severities.  Examples of variables that could have a significant impact upon the side effects you experience from probiotic supplementation include: the specific probiotic, its dosage, administration details (e.g. time of day, empty vs. full stomach, etc.), as well as individual attributes (e.g. body size, genetics, medical status, etc.).  It is these variables that help explain why multiple probiotic users may report noticeably different reactions.

  1. Probiotic specifics

The specific probiotic that you’re using is likely to have a substantial impact on the side effects that you experience during supplementation.  Each probiotic supplement is unique in terms of: added ingredients, bacterial constituents, brand (manufacturer), number of CFUs per dose, formatting, and purity.  Always review these specifics when attempting to determine why you’re experiencing side effects from supplementation.

  • Added ingredients: While probiotic supplements are comprised of millions or billions of colony forming units (CFUs) to populate the gut with healthy bacteria, they may also contain additives. The additives are typically benign and aren’t likely to trigger a reaction, but certain individuals have sensitivities.  You may want to review the added ingredients in your probiotic supplement to ensure that you aren’t sensitive to any ingredient used in the engineering of the capsules or tablets harboring your bacteria. The label of your product should list all the ingredients, but if it doesn’t, you may need to contact the manufacturer or search online.
  • Bacterial species: Among the most significant influencers of probiotic side effects is the species and subspecies included within the probiotic supplement. Some probiotics are engineered to contain a single bacterial species such as Lactobacillus acidophilus, whereas others include a combination of several bacterial species (e.g. L. acidophilus, L. casei, L. reuteri, etc.).  Certain probiotics may even include multiple bacterial genus in a single concoction (e.g. Bifidobacterium plus Lactobacillus).  Consider that the quantities of each bacterial genus and/or species may influence how you respond to a product.  For example, you may experience fewer side effects from a product containing 75% B. longum and 25% L. reuteri (or vice-versa) than a 50/50 split.  Then again, you may also find that you experience fewer side effects from using a single species probiotic as opposed to one with multiple species.
  • Brand: The brand name and manufacturer of your probiotics should be taken into consideration if you experience side effects. You may try a probiotic supplement from one manufacturer and experience no side effects, yet purchase the same probiotic species from another supplier and experience a myriad of side effects.  Most brands differ in quality control, formatting of products, as well as added ingredients.  If you respond better to one brand of probiotic in terms of side effects, even though the bacterial constituents are the same, trust your experience.
  • CFUs: The number of colony forming units (CFUs) per dose of your probiotic might also influence whether you experience side effects and/or side effect severity. Probiotics engineered for children tend to incorporate between 5 and 10 billion CFUs per dose, whereas probiotics for adults tend to incorporate between 10 and 20 billion CFUs per dose.  The greater the number of CFUs ingested with your probiotic, the more significant its effect within your body is likely to be, thereby increasing odds of side effects.  The lower the CFUs per dose, the fewer total side effects you should experience.
  • Format: The formatting of your probiotic supplement might affect things like the speed at which bacteria are released from the supplement within your gut, as well as the survival rate of bacteria in the supplement. Most quality probiotics are encapsulated in a specialized “matrix” and/or enteric coating to minimize likelihood that the bacteria will be killed by stomach acid prior to entering the gastrointestinal tract.  If you’re taking a probiotic supplement with an encapsulation that isn’t protecting the bacteria on their way to your gut, none may survive and you might notice zero effect.  On the other hand, if your product is packed with 20 billion CFU per dose and engineered to maximize survival of the bacteria, you may notice more significant side effects (as a result of the higher dose).  Some supplements are designed to slowly degrade and release bacteria once reaching the gut, whereas others quickly release bacteria as a result of expedited degradation.  It is thought that the slower, steady-release formats are associated with fewer side effects.
  • Purity: You may want to check your product to ensure that it’s been verified by a third-party independent laboratory for quality. Third-party labs are able to confirm whether the probiotic supplement actually contains the ingredients and bacterial species (plus respective amounts) that are listed on the product label.  If your probiotic hasn’t been tested or evaluated by a laboratory, it could be laden with contaminants and/or might not contain what is claimed on the label.  Moreover, you’ll want to examine the expiration date of your probiotic and ensure that it hasn’t expired – as this could lead to reduced effect and/or side effects from expired constituents.
  1. Administration details

The details associated with probiotic administration might also influence whether you experience side effects.  Some administration details to consider as influencing side effects include: the probiotic dosage, the cumulative duration over which you’ve been supplementing with your probiotic, whether you take it with food (or on an empty stomach), as well as the time of probiotic administration.  In most cases, individuals that have been taking probiotics at an appropriate dose for a long-term are less likely to experience side effects than new users taking mega-doses.

Dosage: What is the dose of probiotics that you take each day?  Most probiotics contain between 5 billion and 20 billion CFUs per dose and are intended to be taken once per day, but some individuals might administer them multiple times throughout the day.  In general, anyone taking higher doses of probiotics (e.g. 20 billion CFUs, multiple times per day) should expect to experience a greater number of side effects than persons using lower doses of probiotics (e.g. 5 billion CFUs, once per day).

When an extremely high dose of probiotics is taken, a greater number of preexisting gut bacteria are displaced by the CFUs within the probiotic, increasing odds of a Herxheimer reaction (which is associated with severe side effects).  Additionally, high doses will exert a more substantial effect on your biology through the GI tract by modulating biogenic amine production, vagal nerve activity, and/or hormone levels.  It is also thought that high doses may increase risk of interactions (with another supplement or medication) compared to lower doses.

Many individuals taking extremely low doses of probiotics will notice zero side effects.  Those taking moderate doses may notice some side effects, but they are typically modestly intense.  On the other hand, anyone using multiple doses or mega-doses of probiotics (e.g. above 20 billion CFUs per day) will probably encounter some side effects.

Duration of administration: How many days have you been supplementing with your probiotics?  The duration over which you’ve regularly taken a probiotic supplement may dictate whether you’re likely to experience side effects or adverse reactions.  If you’ve been using a probiotic over a short-term (e.g. a few days), your body probably hasn’t fully adjusted itself to accommodate the new influx of bacteria delivered to the GI tract from the supplement.

Initially, your body may be overwhelmed with the billions of new bacteria colonizing in your gut, possibly a reason as to why you may experience side effects.  In addition, old bacteria might die upon competing with the new bacteria for resources, thereby triggering Herxheimer-related reactions.  It is also likely that a short-term user won’t know the optimal tolerable dose of probiotics for his/her body, possibly leading to side effects from administering too high of a dose.

By comparison, long-term users will have already worked their way through any possible transient Herxheimer reactions and/or adaptation-related effects, each of which typically occur in the first few weeks of supplementation.  What’s more, long-term users will likely have a good idea as to what their body can tolerate in terms of probiotic dosing, strains, etc. – and probably would’ve stopped using probiotics if they experienced debilitating, unremitting side effects.

Food and/or drinks vs. empty stomach: It is possible that taking your probiotics on an empty stomach may yield slightly different side effects compared to taking them with food (or after a meal).  If you take probiotics on an empty stomach, your gastric acid production will be lower and as a result, more CFUs from your probiotic supplement (especially if non-enterically coated) are likely to survive and colonize within your gut.  The increased survival rate of CFUs should yield a more substantial effect within the GI tract, ultimately increasing likelihood and/or severity of side effects.

On the other hand, individuals taking probiotics after a large meal will have higher levels of gastric acid.  The elevated levels of gastric acid are likely to degrade more CFUs (or perhaps all of them in a non-enterically coated capsule) before they’re able to populate the gut.  In accordance with the lower survival rate of CFUs after a large meal (mediated by gastric acid), fewer bacteria colonize within the gut and for this reason, fewer side effects occur.

Though there will be less differences in side effects associated with empty stomach vs. food – among those using enterically formatted supplements (designed to resist stomach acid), it is still hypothesized that empty stomach users would exhibit increases in survival rates of CFUs, and predictably, more side effects.  It should also be noted that consumption of beverages could influence side effects of probiotics similar to food regarding stomach acid-induced degradation of the bacteria (prior to reaching your GI tract).  For example, someone drinking their probiotic with juices, sodas, or sugary drinks may experience fewer (or no) side effects as a result of their drink’s acidity, which in turn may degrade the supplement before CFUs are able to colonize within the gut.

If few or no CFUs survive because of what you drank along with your probiotic, you shouldn’t expect any favorable effect nor side effects.  You may also want to consider that food/beverage characteristics such as: acidity, quantity consumed, and recency of consumption (in respect to supplementation) – might increase or decrease the severity of your side effects.  Moreover, if any of the foods/drinks you consumed were fermented, there could be some sort of interaction or synergistic effect with your probiotic supplement to provoke side effects.

Regularity of administration:  How regularly do you supplement with probiotics?  The frequency at which you supplement with probiotics could influence whether you’re likely to experience unwanted side effects and/or adverse reactions.  Dosing schedules may vary depending on the person, but could include:  once-per-day dosing, twice-per-day dosing, every-other-day dosing, once-per-week dosing, and once-per month dosing.

High-frequency administration of probiotics may trigger a greater number of side effects in some users, especially if excessive quantities of bacterial species populate the gut over a short timespan.  There may be a biological threshold for each individual regarding the number of CFUs that can be introduced in a short-term without side effects.  For example, most people may be able to tolerate 10 billion CFUs per day, but if 100 billion CFUs are ingested within a 48-hour period – side effects should be expected not only from initial elevations in bacterial count, but from death of older bacteria that was necessary to accommodate the new bacteria.

Others might report that daily administration of probiotics (even at standard doses) is too much for their body to handle, especially at high doses, ultimately causing severe side effects and/or adverse reactions.  Certain users report tolerating probiotics better when administering them on an every-other-day, once-every-few-days, or even once per week.  That said, many will report short-term side effects from daily administration, followed by zero side effects as the body eventually acclimates itself to the bacterial species and CFU load.

In some cases, regular dosing may yield fewer unwanted side effects than erratic or infrequent dosing.  Those who never commit to regular dosing may not give their bodies a chance to fully adjust to the bacterial species and/or CFU load.  For example, if you were to supplement with a low-dose probiotic once per week, your gut may revert back to a state of dysbiosis in the 6 days between doses, ultimately never fully acclimating to the new bacteria – possibly causing side effects with each administration.

Time of administration: The time of day at which you administer a probiotic supplement could influence how you react to it and/or perceive side effects.  As a hypothetical example, let’s assume that the probiotic you’re using makes you feel slightly tired after administration.  If you were to take this probiotic in the morning before work or school, the fatigue may be bothersome in that it impairs your ability to maintain energy and focus to complete cognitively-demanding work.

Oppositely, if you administered the arousal-reducing probiotic in the evening, you might’ve never had a problem with the fatigue because you weren’t expected to perform cognitively-demanding tasks nor maintain peak energy.  Additionally, had you administered the same probiotic in the afternoon, you may have noted a slight reduction in energy, but not as significant as in the morning.  In other words, the biological effect of probiotics may be synergistic or antagonistic to your circadian rhythm, ultimately influencing your perception of its side effects.

  1. Individual factors

Hypothetically, let’s assume that two individuals were assigned to initiate probiotic supplementation on the same day and continue supplementing for a 3-month duration.  Let’s also assume that both of the individuals are using probiotics from the same supplier/brand at equal strength doses, and that each administers his/her probiotic supplements every day at 7:00 AM on an empty stomach.  Based on the fact that probiotic specifics (composition, format, ingredients, etc.) and administration details are identical, most would expect side effects to be relatively similar among the two.

Despite our suspicion that side effects would be similar among these two individuals, we may learn that one experiences a severe skin rash with itchiness, while the other endures bloating, diarrhea, fatigue, and nausea.  In this hypothetical example, differences in specific side effects can be explained by individual factors such as: age, antibiotic usage, body size, co-administered substances, genetics, medical conditions, pH level, and preexisting bacteria.  Individual factors can have a profound impact upon whether someone is able to tolerate probiotics supplementation.

Age: Probiotic dosing recommendations typically differ based on the age of the recipient.  Children and/or adolescents are recommended to take lower doses (e.g. 5 billion CFUs) than healthy adults, whereas recommended doses for healthy adults (e.g. 20 billion CFUs) might be too large for elderly individuals to tolerate.  Younger individuals are recommended to use lower doses of probiotics because their bodies aren’t fully developed and are smaller in size.  Administering adult doses of probiotics to a child may overwhelm his/her GI tract, spike levels of biogenic amines in the peripheral, and/or induce a noticeable “die off” reaction whereby side effects become noticeable.  Elderly individuals might also have adverse reactions to high doses of probiotics as a result of age-related: health conditions (and medications to treat them) and compromised immune function.  In summary, healthy adults should have an easier time tolerating probiotics compared to children and elderly.

Antibiotic history: The history of a person’s antibiotic usage might influence how they respond to probiotic supplementation.  Someone that’s been treated heavily with antibiotics over an extended duration may exhibit chronic dysbiosis from depletion of healthy flora.  Administration of probiotics following chronic or long-term antibiotic administration may induce severe side effects or adverse reactions as a result of pathogenic bacteria fighting the new bacteria in attempt to remain colonized within the gut.  In the process, endotoxins may be released and/or bacteria may “die off” to provoke disconcerting side effects.  You may want to critically review your antibiotic history and consider that the total duration and recency of your usage might influence how you respond to probiotic supplementation.

Body size: When supplementing with a probiotic, it is possible that your body size (height/weight) and composition (muscle/fat) could have an influence on side effect occurrence.  For example, some studies discovered that lean individuals (with low body fat and more muscle) experience weight gain from administration of certain lactobacillus subspecies whereas those same species cause weight loss in overweight persons.  Based on this finding, it’s reasonable to suspect that there’s some interplay between body composition, the gut, and probiotic effects.  In addition to side effect variation in respect to body composition, it is theorized that larger sized individuals (e.g. tall and/or heavy) might be capable of tolerating higher doses of probiotics than smaller sized people (e.g. short and/or skinny).

Co-administered substances: If you’re using other substances (drugs and/or supplements) along with probiotics, there’s a chance that these co-administered agents may influence the number and/or severity of side effects that you experience.  Co-administered substances have the potential to alter a person’s pH (acidity vs. alkalinity), as well as interact with the pharmacokinetics and pharmacodynamics of medications and supplements.  It is also possible that co-administered substances are reducing the severity of probiotic-related side effects and/or that a person may wrongfully attribute his/her side effects to a probiotic when in actuality, they were caused by the other substance.

  • pH alteration: Many co-administered agents can modify the acidity and/or alkalinity of your pH, possibly expediting or prolonging degradation of the probiotic within your gut. Any agents that increase acidity could kill bacteria within your probiotic prior to their colonization within your GI tract, thereby negating both the therapeutic “flora restoring” effects and side effects.  Understand that enterically-coated probiotics may be less susceptible to rapid degradation from a co-administered substance-induced increase in gastric acid.
  • Pharmacokinetics: It is also necessary to consider that probiotics might affect the pharmacokinetics (absorption, metabolism, distribution, and elimination) of another co-administered agent, ultimately provoking more or fewer side effects than expected. In other words, probiotics might slightly modify the rate at which a drug is metabolized or distributed as a result of probiotic-related altered bacterial composition within the gut.  This slight change in metabolism and distribution could significantly alter side effects experienced by the user – either amplifying them or reducing them.
  • Pharmacodynamics: The effects exerted by probiotics within the enteric nervous system (ENS) are thought to affect processes throughout the body, including functions within the brain. Any co-administered substances you’re using along with a probiotic may be amplifying or attenuating the effects or probiotics within the body.  For example, if probiotics are increasing production of histamine within your gut, you might experience an itchy skin rash, however, if you’re co-administering an antihistamine, it may offset some of the side effects of the probiotic – making them unnoticeable to the user.  On the other hand, if you were taking a medication that spiked histamine with a histamine-upregulating probiotic, you may experience an itchier and more extreme skin rash than you otherwise would’ve.  Also realize that not all drugs will directly offset the mechanisms of probiotic-related side effects.  For example, if your probiotic gives you insomnia, a hypnotic medication may override the insomnia despite acting upon different biological targets.  The effects elicited by probiotics within the body might also be amplified with co-administration of fermented products, yet offset completely by co-administration of antibiotics.

When attempting to determine how a co-administered substance could influence probiotic side effects, you may also want to consider whether the co-administered agent is administered simultaneously (with the probiotic) OR if there is a time gap between respective administration of each, and if so, the specific time gap.  Additionally, the frequency of usage associated with the co-administered substance, as well as its dosing may influence whether it is likely to modify the side effects of a probiotic.  Moreover, all individuals should evaluate whether they may be wrongfully attributing the side effects they’re experiencing to a probiotic, when in fact, those side effects resulted from co-administered agents.

Genetics: A person’s genetic and epigenetic expression may affect how they react to probiotic supplementation.  Genes implicated in degradation of biogenic amines may have a significant impact on how a person reacts to his/her probiotic.  For example, some probiotics may contain bacterial species that upregulate the production of histamine in the gut.

If a person using a histamine-modulating probiotic exhibits genetic polymorphisms associated with DAO (diamine oxidase) or HNMT (histamine N-methyltransferase), each of which are involved in histamine metabolism, he/she might have trouble handling the extra histamine, resulting in allergy-like side effects such as itchiness, skin rashes, nausea, etc. – all from the high histamine.  To get more complex, if a person is using other substances with probiotics that undergo hepatic metabolism, and certain genetic polymorphisms are present of hepatic enzymes (e.g. CYP2D6), the probiotic and co-administered substance may have a stronger interaction.

Other genes and/or gene complexes besides those involved in degradation of amines and/or hepatic metabolism could influence how someone might respond to certain species of probiotics.  Research may discover that individuals with a particular set of genes respond better when supplementing with one particular species of probiotics, compared to individuals with a different gene complex.  Genes likely contribute more to sensitivities and/or ability to tolerate various probiotics than many suspect.

Medical conditions:  While probiotics are regarded as safe for many individuals, and are sometimes used as an adjunct intervention for the treatment of some medical conditions, the usage of probiotics is contraindicated among those with certain diagnoses.  Anyone using a probiotic with a medical condition that is contraindicated with probiotics may be at risk for more serious side effects and/or adverse reactions compared to those in good health.  What’s more, the medications used to treat various medical conditions could interact with the probiotics (and vice-versa) to amplify the intensity of side effects.  Listed below are some medical conditions that may be contraindicated with probiotic supplements.

  • Allergies: Despite the claim that probiotics may reduce symptoms of allergies, some individuals might notice an increase in allergic responses after regular probiotic usage. A clinical trial investigating the efficacy of probiotics for the treatment of childhood allergies discovered that probiotic recipients exhibited sensitivities to allergies that were not seen in placebo users.  For this reason, you may want to realize that if you have severe allergies, probiotics might amplify their severity.
  • Food allergies: If you have a food sensitivity or allergy, you may be more at risk for experiencing an adverse reaction or side effects from probiotics. Medical documentation notes that Lactobacillus-containing probiotic supplements are contraindicated among those with a lactose intolerance or sensitivity.  Additionally, since some probiotic supplements may contain the yeast S. boulardii, adverse reactions can occur among persons with an underlying yeast allergy.
  • Gastrointestinal disorders: Many individuals with GI and digestive disorders claim to derive some benefit from supplementation with probiotics. That said, there’s no evidence to suggest that probiotics provide clinically relevant symptomatic reduction for any GI condition.  In addition, it appears as though a subset of persons with GI-related conditions may be at greater risk for probiotic-induced side effects and/or adverse reactions than the general population.  Examples of several conditions that may worsen from probiotic usage include: constipation, inflammatory bowel disease, irritable bowel syndrome, and ulcerative colitis.
  • Hepatic dysfunction: Research suggests that probiotics interact with liver function via the gut-liver axis. The gut-liver axis allows for an interaction between metabolites generated by gut bacteria and Toll-like receptors in the liver.  Dysbiosis within the gut is thought to generate endotoxins (e.g. lipopolysaccharides), whereby liver function becomes worse.  While administration of probiotics may prove useful for managing hepatic impairment, it is possible that the wrong strain and/or too high of a starting dose may temporarily induce endotoxemia as a result of a bacterial “die off” (in the process of replacing pathogenic microbes with healthier ones).
  • Immune dysfunction: Anyone with a compromised immune system is generally advised to avoid probiotic supplementation altogether or use them with extreme caution. Conditions that may lower the immune system such as: AIDS/HIV, autoimmunity, cancer, diabetes, hepatic insufficiency, hepatitis, renal insufficiency, and various immune-related syndromes are at greater risk for side effects and adverse reactions.  Although rare, case reports suggest that probiotic administration to persons with immune dysfunction may cause bacteremia (bacteria within the blood) or fungemia (fungi within the blood).  Both bacteremia and fungemia are problematic in that they can lead to sepsis, a life-threatening condition in which the body’s response to an infection injures its own organs.  Medical professionals note that probiotics may cause pathological or difficult-to-treat infection among those with immune abnormalities.
  • Neuropsychiatric disorders: Individuals that have been diagnosed with neuropsychiatric disorders such as: autism spectrum disorder, anxiety, bipolar disorder, depression, and schizophrenia – may be at greater risk of experiencing side effects than others. Persons with neuropsychiatric conditions are often extremely sensitive to modulation of activity in the autonomic nervous system, peripheral nervous system, and central nervous system – all of which probiotics could affect.  Something as simple as increasing concentrations of particular amines in the gut may exacerbate the severity of neuropsychiatric symptoms.  The medications used to treat neuropsychiatric disorders may also interact with probiotics to provoke interaction-related effects.
  • Short-bowel syndrome: The medical condition known as short bowel syndrome (SBS) results (in most cases) from removal of a large portion (at least two-thirds) of the small intestine. It is known that probiotics (especially lactobacillus strains) are contraindicated among individuals with SBS.  Researchers suspect that altered gut integrity and composition among persons with SBS may induce bacteremia following probiotic administration.

pH level: The pH of your body could also influence the side effects (as well as effectiveness) of your probiotic supplement.  Most research suggests that probiotics are likely to degrade fast in a highly acidic environment and survive longer with less acidity (greater alkalinity).  If you’re using a probiotic that isn’t engineered to protect the bacterial constituents from stomach acid, your pH may play a big role in determining whether those bacteria actually survive and colonize within your gut.  If they don’t colonize due to high acidity, you probably won’t experience any side effects because the degradation of your supplement will have occurred too quickly.  That said, if your body is more alkaline than acidic, non-enterically-coated probiotics may exhibit better survival rates, ultimately increasing odds of side effects.

Pre-existing bacteria: The bacterial composition of your gut prior to using probiotics might make a difference in terms of how you respond to probiotic supplementation.  It is thought that a person’s diet (macros/micros, caloric intake, etc.), environment, genes, and lifestyle (stress, exercise, etc.) influence the microbial composition of his/her gut.  Since one person may exhibit an entirely different composition of gut bacteria prior to probiotic supplementation compared to another individual, it is necessary to consider that these differences may influence side effects (or lack thereof) to the probiotic.

For example, if someone already has a high level of Lactobacillus species in their gut (as a result of regular yogurt consumption), he/she may not notice any side effects from supplementing with a Lactobacillus-based probiotic because the body will have already adjusted to this bacterial species.  Oppositely, someone exhibiting low levels of Lactobacillus species in the gut prior to supplementation with a Lactobacillus-based probiotic may experience noticeable side effects due to the drastic changes in gut bacteria composition from supplementation.  Overall, the composition of your gut bacteria prior to probiotic usage might dictate compatibility and/or adjustment-related effects associated with introduction of new strains, whereby you may be more or less prone to side effects.

Probiotics: Do the benefits outweigh the side effects?

If you’re taking probiotics, it’s always smart to evaluate whether the benefits of supplementation outweigh side effects and/or unwanted reactions.  Unless you have a medical condition or are using a substance that could interact with your probiotic (or vice-versa), you’re unlikely to experience side effects or adverse reactions.  A majority of probiotic users will experience some benefit without any side effects – especially if they’ve been using for a sufficient duration for their body to adapt to the supplement (e.g. 2 to 4 weeks).

Obviously, those who are deriving significant or even slight benefit from probiotic administration will want to continue supplementing.  On the other hand, a subset of probiotic users might experience zero side effects, but also no significant benefit from supplementation.  They may continue taking their probiotic assuming that it’s healthy, but in their subjective experience, nothing has changed to improve GI function or health.

If you happen to be an individual who takes a probiotic without noticing any benefit, you may want to test a different bacterial species and/or manufacturer.  No beneficial effects nor side effects may indicate that the probiotic you’re using is being degraded by stomach acid before the CFUs have a chance to populate your GI tract.  Then again, if you’ve tested a bunch of probiotics without noticing any significant benefit, it doesn’t make much sense to continue spending money on supplements for regular usage – you may want to discontinue.

Another percentage of users will attain some perceived benefit from probiotic usage, but simultaneously experience side effects.  Since most individuals report mild, manageable side effects, it may be worth continuing your supplement for the more prominent health benefit.  That said, if the probiotic side effects you are experiencing are more severe than any benefit, it’s probably smart to cease probiotic supplementation.

Lastly, in rare cases, individuals supplementing with probiotics may experience all side effects without any discernable benefit.  If you’re experiencing things like brain fog, constipation, diarrhea, nausea, stomach aches, etc. on a regular basis, and feel way worse after taking probiotics, your best bet is to stop using them.  One valuable way to track your experience with probiotics is to maintain a journal.

Journaling is a great way to record things like: your probiotic dosage, bacterial composition of your probiotic, interactions with other medications, and how you are functioning on a day-to-day basis.  Furthermore, if you ever need to report any side effects or experiences to a medical professional, you’ll have kept track of all the details within a journal.  With a journal, you’ll have an easy time reviewing the side effects and/or therapeutic efficacy of probiotics over an extended duration.

Possible ways to reduce Probiotics side effects

In the event that you’re experiencing side effects from probiotic supplementation, there may be some effective ways in which you can mitigate them.  Examples of strategies to mitigate side effects of probiotics include: dosage modification, altering administration details, and switching the bacterial species and/or brand.  Prior to implementing any of the side effect mitigation strategies below, discuss the safety and theorized efficacy of each with a medical professional.  Also realize that usefulness of side effect mitigation strategies may be subject to significant individual variation.

  1. Rule out contraindications: If you’re experiencing side effects or unexpected reactions to probiotics, the first thing you should do is consult a medical professional to rule out medical conditions for which probiotic administration is contraindicated. You should also have a doctor confirm that your medication and/or supplement regimen is safe to be administered simultaneously with probiotics. A contraindication or interaction that you weren’t aware of might explain why you are having a difficult time tolerating probiotics.  Realize that if you have a food allergy such as to lactose or yeast, certain probiotics are contraindicated such as those containing lactobacillus and S. boulardii, respectively.
  2. Dosage modification: Generally, the greater the dose of probiotics administered, the more potent its effect on biological processes, thereby amplifying side effects. If you started taking a probiotic with 20 billion CFUs per dose, you may want to scale back to just 5 or 10 billion CFUs per dose and reassess severity of your side effects. Most individuals will tolerate a smaller dose easier than a larger one.  Similarly, if you’re administering a probiotic several times per day, cut back to just once per day.  The goal should be to take the minimal effective dose or lowest possible amount that promotes gut health without causing side effects.
  3. Gradual titration of dosing: Another strategy to minimize likelihood of side effects and/or adverse reactions from probiotics is to initiate supplementation at an extremely low dose (e.g. 5 billion CFUs per day) and gradually titrate the dose upwards over a duration of several weeks (possibly longer) until the recommended daily dose is reached (e.g. 20 billion CFUs per day). By starting supplementation at a low dose, you give your body time to adjust itself to the influx of new bacteria within its GI tract, plus the biological effects induced by those bacteria. You also reduce the likelihood of a severe Herxheimer-like reaction because the lower dose won’t likely provoke excessive “die off” all at once.  In addition, gradually titrating the dose of your probiotics in small increments (e.g. 5 to 10 to 15 to 20 billion CFUs) should give you insight regarding the dosage you can tolerate best without side effects.
  4. Frequency of supplementation: Some individuals administer probiotics on a frequent basis such as multiple times per day or once per day, however, it is possible that this frequent administration might be overkill and trigger side effects. If you use probiotics once or multiple times per day and are experiencing side effects, you may want to try scaling back your frequency of administration. You might find that an every-other-day, every-third-day, weekly, or even once every other week administration schedule works best for your biology.  Your body may not need billions of CFUs every single day to maintain gut health and your high-frequency supplementation may explain your side effects.
  5. Administration tweaks: Modifying the details associated with administration of your probiotic may make you less prone to experiencing side effects and/or could make the side effects easier to manage. Although it was already mentioned to reduce and titrate the dosing, plus reduce the frequency of your administration, you can also alter the: time of administration (morning, afternoon, dinner), whether you take your probiotic with or without food (or certain drinks), and/or the time gap between supplementing with a probiotic and administering another substance. For example, if you find that taking your probiotic in the morning causes drowsiness, you may want to try taking it in the evening and determine whether the side effect becomes easier to manage.  Additionally, if you’re taking a probiotic with food and find that it makes you nauseous, try taking it on an empty stomach.
  6. Eliminate unnecessary substances: Side effects of probiotics can often be reduced by eliminating regular concurrent administration of substances (drugs and/or supplements) that aren’t medically necessary. By eliminating unnecessary co-administered substances from your regimen, you’re less likely to experience: interaction-related effects (between the substance and a probiotic) and/or amplification of probiotic side effects through synergistic biological mechanisms (shared with the other agent). It is also possible that other substances you’re using are causing side effects that you’ve misattributed to probiotics, and once they’re eliminated, you find that probiotics are easier to tolerate.  If there are any substances that you cannot eliminate due to having a medical condition, it is recommended to administer them at least 2 hours apart from probiotics to avoid pharmacokinetic (and possibly pharmacodynamic) interactions.
  7. Add-on substances: In the event that you’re getting extreme benefit from a specific probiotic supplement and/or species, but also experiencing side effects, you may want to consider adjunctive agents to specifically negate the unwanted effects. For example, if you’re taking B. longum at 40 billion CFU per day and it’s significantly enhancing your cognitive function, but simultaneously giving you insomnia (no matter when you take it), you might want to consider strategic “as-needed” supplementation with a circadian modulator like melatonin, or a safe sedative hypnotic (in accordance with professional medical instruction). Another example might be administering activated charcoal (several hours after your probiotic – assuming it’s not an extended release) to help mop up (via “adsorption”) endotoxins resulting from probiotic-related “die off.”
  8. Test a different manufacturer: Some individuals find that they’re able to tolerate the same species and dose of a particular probiotic much better from one brand over another. It is known that certain manufacturers engineer their probiotics with distinctive encapsulations, ingredients, and other constituents that differ from those associated with another manufacturer. For this reason, you might take a probiotic containing Bifidobacterium animalis at a dose of 20 billion CFU from one supplement company, and experience a mix of benefit with disconcerting side effects.  However, you might try the same probiotic species and dose from another company, and experience all benefit without side effects.  Assuming you want to give a particular species and/or subspecies of gut bacteria a try, you may want to test it from multiple manufacturers (especially if you’re experiencing side effects).
  9. Switch the species: If you’ve experienced side effects from one particular probiotic, there’s reason to believe that these side effects might be contingent upon its composition in terms of species and/or subspecies. For example, it is known that many probiotics contain lactobacillus bacteria and sometimes include the yeast S. Boulardii, each of which can induce allergic reactions in persons with lactose and yeast sensitivities, respectively. You may find that switching from a species like Lactobacillus acidophilus to Bifidobacterium longum significantly enhances your GI function without any side effects.  There are many different species to test, some of which you may respond better to than others.  Another thing you can do is switch from a single-strain probiotic to a multi-strain, or from a multi-strain probiotic to a specific single strain – to determine whether one works better than the other.
  10. Continue using: Anyone that’s new to using probiotics (e.g. first-time users) may experience side effects when they first initiate supplementation. Assuming you’ve ruled out interactions and contraindications with your doctor and probiotics are considered safe to use, you may want to continue using them if you’re experiencing side effects.  In some cases, side effects occur during the first 1 to 4 weeks of treatment due to significant changes in the composition of your gut microbiota, and from the body detoxifying itself from pathogenic bacteria.  With continued usage, you may notice that side effects experienced in the first few days or weeks of treatment diminish and/or cease altogether over a longer-term.
  11. Discontinue: If you’ve tried many different types of probiotics, altered the doses, and modified your administration regimen, but are still experiencing side effects – you may want to discontinue probiotics altogether. It’s possible that for one reason or another, you just don’t react well to probiotic supplementation of any kind. In this case, you could always consider alternative interventions for modifying your gut including: fermented foods (e.g. kimchi), beverages (e.g. kombucha), or prebiotics.  There are many ways to influence the composition of your gut microbiome that don’t involve administration of any bacteria, including: dietary modification, increases in exercise, reducing stress, et al.

Have you experienced side effects of probiotics?

If you’ve experienced side effects from taking probiotics, mention the specific side effects you endured and their respective severities within the comments section below.  To help others get a better understanding of your situation, provide some personal details such as: the bacterial composition of your probiotic, the manufacturer of your supplement, and the dose you were taking each day (e.g. 20 billion CFUs).  Also report the duration over which you administered your probiotic, whether you were using any other substances (drugs and/or supplements) along with it, and/or if you have any medical conditions that might’ve made you more susceptible to side effects.

For those that have used a probiotic supplement over an extended duration, have side effects: diminished, remained the same, or worsened over time?  It may also be helpful to document whether you have a history of regular antibiotic usage and/or if you exhibit any genetic abnormalities that could explain adverse reactions to probiotics (e.g. HNMT polymorphisms that inhibit your ability to cope with increased histamine).  Is there any particular probiotic brand (manufacturer) and/or species that you consistently tolerate better than others?

What was your reason for supplementing with probiotics in the first place?  Do you get the sense that your probiotic supplement is actually working and/or delivering some sort of therapeutic effect?  If you experience probiotic side effects and have any strategies for coping with them (other than the ones discussed within this article), make note of them in your comment – it may help someone else.  Moreover, when it comes to supplementing with anything, including probiotics (which are well-tolerated by most), always listen to your body and trust that if you’re experiencing severe side effects, it’s probably smart to discontinue.

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