Why, How, and When to Take Probiotics? [Quick Guide]

Make sure to find a probiotic that contains bacterial species proven to help the symptoms you want to treat, that has an effective dosage and that comes from a reputable company.

Why, How, and When to Take Probiotics?

Smack dab in the middle of the supermarket aisle, probiotic carton in hand, you suddenly realize with the force of a Wile-E.-Coyote-anvil-to-the-face that you know absolutely nothing about actually taking probiotics — you don’t know anything about how or when to take probiotics at all.

You don’t know if you can take them with your medications.  

You don’t know if you need to take them with a snack.  Or with a meal.  Or on an empty stomach.

You don’t know if you need to take them in the morning or at night.

You don’t even know if you need to take them every day, or if it’s better to spread out your doses.  

So much for all your awesome plans to jump-start your health with a probiotic!  

You lower the bottle back onto the shelf and zip out of the store Road Runner style, hoping no one noticed you.   

This may sound like a silly story (and it kinda is) but, all Looney Tunes antics aside, feeling overwhelmed and helpless in making an informed decision about something that could have profound effects on your health is not funny at all.

All of us should have the information we need to empower ourselves to make our own choices about how to take care of our health.

And that’s why I put together this article.  I want to give you the research and information you need to choose how, why and when to take probiotics for yourself.

How Do You Know if You Need a Probiotic Supplement?

Alright, first thing is first.  You’re clearly interested in taking a probiotic!  But how do you know, for sure, that a probiotic supplement is actually a good choice for you?

Definitely Take a Probiotic If…

There are a few situations where the answer to the question of whether or not you should take a probiotic is straightforward.  If you have:

then go ahead and reach confidently for that supplement.  Probiotics have been well-studied for controlling the symptoms each of these conditions and have shown consistent positive results.  

Maybe Take a Probiotic If…

If you aren’t experiencing the symptoms of any of the above conditions, the story is a bit more complicated.  It doesn’t mean that a probiotic is necessarily a bad fit for you.  It simply means that it is not 100% clear that you should absolutely take one.

Studies suggest that probiotics may be helpful for all kinds of other conditions, ranging from acne and metabolic disorders to depression and cancer.  (Check out this article about the suspected benefits of probiotics to learn more about how and why probiotics can protect the health of organs outside your digestive tract.)  

Unfortunately, the data supporting probiotic use for other conditions is just not as strong as it is for digestive issues.  Don’t get me wrong — there is evidence.  It’s just not so overwhelming (yet?) that the whole medical community is on board with recommending probiotics as part of their treatment.

Less Evidence, But Still Take a Probiotic?

Now, typically, if you don’t have super strong data for taking a supplement, I’d say your best bet is to wait it out.  It’s usually a better idea keep an eye on the scientific data and only start taking a supplement after the studies really show it’s effective.

But I am very much willing to make an exception for probiotics.  Why?  Because they are just so safe and have very, very few side effects.

Study after study after study shows that taking probiotics comes with essentially no risk of serious side effects.  

The only two significant exceptions here are for those with extremely weak immune systems or those with an active Inflammatory Bowel Disease flare-up.  In these cases, probiotics may put you at a slightly higher risk of a serious infection.  If either of these applies to you, you should definitely talk to your doctor before taking a probiotic.


For everyone else, though, probiotics are thought to be so safe that I think there is no reason not to give them a try and see if they help you feel better.  

This is especially true if you are experiencing:
  • autoimmune conditions (non-digestive or in remission)
  • allergies
  • persistent acne
  • difficulty losing weight
  • diabetes
  • high cholesterol
  • heart disease
  • gingivitis or regular cavities
  • low bone density
  • poor muscle health/athletic performance
  • depression
  • migraines
  • anxiety
  • infertility

Quite frankly, probiotics pose so little risk that, even if you don’t feel particularly bad, I would say you could give them a shot just to see if they make you feel even better.  

Just know that you may not see particularly dramatic results in that case.

Up Next: What are Probiotics?  Benefits, Dangers and Best Sources

What are the Side Effects of Probiotics

You may have noticed I used the phrase “serious side effects”, not “side effects” above.  If that sent off your Spidey-sense, I totally understand!  Probiotics do, actually, have some mild side effects in some people.  But they are, typically, genuinely mild and short-lived.

What are the side effects of probiotics?

For the first couple of weeks after starting a probiotic, you may experience:

  • bloating/gas
  • constipation
  • diarrhea
  • stomach ache
  • fatigue

Many people, however, experience no side effects whatsoever.  They only feel better!

Disclosure – This post contains affiliate links.  Click here for details.

What is the Best Probiotic to Use?

woman in front of two doors

Once you’ve got the enormous hurdle of “why” to take a probiotic supplement out of the way, you also have to decide on which supplement to take before you can move on to all the practical hows and whens of taking probiotics.

Unfortunately, I can’t just hook you up with a single ultimate one-size-fits-all whole-body-healing probiotic here.  As cool as that would be, the research shows that things are a bit (or, you know, way) more complicated than that.

Finding the Right Strain

Each probiotic supplement contains a unique combination of probiotic strains (species of bacteria) that have very different jobs and effects in your body.  Depending on your health and the symptoms you’re trying to address, sometimes these effects are lifesavers, and sometimes they do nothing at all.

For example, if you’re trying to improve your bone health, a probiotic bacterium that helps free up calcium from your food could do awesome things for you!  Your bones, after all, need plenty of calcium to grow dense and strong!

If, on the other hand, you are looking to prevent yeast infections, that same calcium-freeing bacteria would likely be of little or no help.

You really have to tailor the probiotic bacteria to your health needs.

In the table below, I’ve summarized the probiotic bacterial strains that research shows are actually helpful for individual conditions/symptoms.  I’ve also tracked down a great probiotic supplement that contains one or more of those strains for each condition that you can check out if you’d like!

Proven Beneficial Probiotic Strain(s)
Probiotic Brand with Beneficial Strain(s)

Gut Disorders and IBS

L. casei, L. plantarum, L. acidophilus, L. delbrueckii bulgaricus, B. longum, B. breve, B. infantis, S. salivarius

TrueNature Digestive Probiotic

TrueNature Digestive Probiotic

Infections and Antibiotic-Induced Diarrhea

L. acidophilus, L. plantarum, L. reuteri, L. rhamnosus, L. salivarius, E. faecium S. boulardii, L. casei rhamnosus

TrueNature Digestive Probiotic


TrueNature Digestive Probiotic

Immune Disorders

L. acidophilus, L. casei, L. fermentum, L. rhamnosus, L. reuteri, B. bifidum, L. paracasei, B. longum, B. animalis

Renew Life Ultimate Extra Care Probiotic

Renew Life Ultimate Flora Probiotic


E. faecium, S. termophilus, L. JBD301, L. planetarium, L. gasseri, L. reuteri, L. acidophilus, L. casei, P. pentosaceu, B. lactis

Bio Sense Probiotic

Bio Sense Probiotic

Metabolic Disorders

L. acidophilus, L. rhamnosus, L. plantarum WCFS1, L. bulgaricus, B. lactis Bb12, B. longum, E. faecium

Vitamin Bounty Pro 50 Probiotic

Vitamin Bounty Pro-50 Probiotic

Dental Cavities

L. rhamnosus, L. acidophilus, L. casei, L. paracasei, L. reuteri, L. johnsonii, W. cibaria, S. salivarius  

Hyperbiotics Pro-15 Probiotic Supplement

Hyperbiotics Pro-15


L. helveticus

Adult Grape Probonix

Probonix Liquid Probiotic Drops

Colon Cancer

L. casei

Garden of Life Dr Formulated Adult Probiotics Once Daily Ultra

Garden of Life Once Daily Ultra Probiotic

Neural and Mood Disorders

L. helveticus R0052, L. casei, B. longum R0175

DrFormula's NexabioticDrFormulas Nexabiotic

Poor Muscle Health

L. acidophilus, L. rhamnosus, L. casei, L. plantarum, L. fermentum, B. lactis, B. bifidum, S. thermophilus

NewRhythm Probiotic Supplement

New Rhythm Probiotic

Male Reproductive Disorders

L. paracasei

NatureMyst Controlled Release Probiotic

NatureMyst Controlled Release Probiotic

Female Reproductive Disorders

L. delbruekii, L. fermentum, L. rhamnosus GR-1, L. fermentum RC-14, L. acidophilus, B. lactis Bb12

Hyperbiotics Pro-15 Probiotic Supplement


Hyperbiotics Pro-15

Other Important Probiotic Factors

While the biggest player in determining if your probiotic is going to help your symptoms improve or not is the bacterial strain, there are two other factors that can make a big difference, as well.  These are:


An effective probiotic should guarantee a dose between 1 billion and 100 billion colony forming units (CFUs) (i.e. the number of bacteria that will actually be able to take hold and start growing in your gut) at the expiration date.

If the label only lists the CFUs at packaging, you have no real idea how many bacteria are still alive by the time you take your last capsule!

Supplement Reliability

Your supplement should come from a reputable brand.  The label should be clear and understandable.  You want to know exactly what bacterial strains, and how many of them, are in each and every dose.  

Ideally, your supplement should also be independently tested to make sure the detailed label on the outside of the package matches the supplement inside.  

Once you’ve found the right strain(s) at the right dose in a reputable package, you’re ready to move on to how and when to take your new probiotic!

To learn more about why specific doses and independent supplement testing are important for choosing a probiotic, check out our guide to the best probiotic supplements for a leaky gut.

How Often Should You Take a Probiotic?

Calendar Close Up

Okay, this might feel like a cop-out to you, but the honest answer to how often you should take your probiotic supplement is: as often as it says to on the package, or as often as your doctor tells you to.

If you chose a supplement with an effective dose per serving (1 billion to 100 billion CFUs) this will likely be one supplement/one dose per day.  After all, that is how the supplements were designed — get an effective number of probiotic bacteria in one go!

Of course, you do have some wiggle room.

Taking Multiple Doses to Get More Probiotic Bacteria

If a single dose of your probiotic is at the lower end of the effective range (1-55 billion CFUs, say), you may, eventually, be able to increase your intake to two doses per day safely.  You should only do this, though, if:

If you decide to do double your daily dosage, make sure you spread the doses out.  Researchers aren’t sure, yet, if doses above 100 billion CFUs in one go might have more serious side effects.  So, you should make sure not to take two or more servings at once if that will bump your intake up over the 100 billion mark.

Taking Multiple Doses to Get Less Probiotic Bacteria

If you are having side effects from a full dose, you can split a single dose up into several smaller doses.  Don’t do this long-term, though.

If you take a smaller dose than recommended, too few bacteria may make it to your intestines to have the effect they are supposed to.  This means that if you consistently take less than the recommended amount, you may end up just wasting your probiotic altogether. 

If you start with smaller doses, try to slowly work your way up to the recommended dose as your digestive tract gets used to the extra probiotic bacteria.

You can, of course, stop at any point before the full recommended dose if you start seeing real improvements in your symptoms.

Should You Take a Probiotic Supplement with Food?

Breakfast spread on marble counter-top

Supplement packages and probiotic articles regularly recommend taking your probiotic on an empty stomach, shortly before a meal.  This recommendation seems to be entirely based on a single study that used a model of a human digestive tract to see how many bacteria survived.  

In this study, the researchers found that hardly any probiotic bacteria survived when the supplement was sent through the model when the “stomach” was completely full of food.  Some survived if the stomach was empty.  Most survived, though, when small amounts of food were added to the stomach at the same time as the probiotic.

Clearly, this isn’t airtight proof that a probiotic right before a meal on an empty stomach is ideal.  After all, it was only a model of a human digestive tract.  Plus, they could only test a couple of foods — milk and oatmeal.  

What happens if the meal is salad?  Pasta?  We don’t know.  Not to mention they only tested supplements not housed in special capsules made to survive your stomach acid.  So, we also don’t know how those specially coated capsules react to food in your belly.

That being said, it is the best evidence we have right now.  So, as far as we know now, your best bet is to take your probiotic supplement on an empty stomach and then eat a meal that contains healthy fats.

When to Take Probiotics: Should You Take Probiotics in the Morning or at Night?

Man's hand holding a mini alarm clock

If there is little research into whether you should take your probiotic supplement with food or not, there seems to be even less research on what time of the day is best.  (Impressive, huh!)

From a practical standpoint, though, taking your probiotic in the morning may be a good way to go.  It should be pretty easy to meet the “empty stomach directly before a meal” recommendation at breakfast.  

Since you’ve fasted overnight, you know your stomach is empty at breakfast.  And many typical breakfast foods include some fat (cow’s milk or plant-based milk in your cereal, eggs, butter on your toast, etc.)  

Of course, if you tend not to snack in the afternoon and have several hours (3-4) between lunch and dinner, or if you regularly have a late night snack 3-4 hours after dinner, there seems to be no reason to think taking your probiotic with one of these evening meals shouldn’t be effective.

Read: Best Prebiotic Supplements for Leaky Gut Healing

Should You Take a Probiotic with a Prebiotic?

Finally, a practical question I can give you a single, definitive answer for!  Yes, you should take your probiotic with a prebiotic.

Prebiotics, or dietary fibers, are long chains of sugar molecules that probiotic bacteria use for food, fuel and building blocks.  Having plenty of fiber (either from a healthy diet full of lots of plant foods, or a prebiotic supplement) can definitely help make your probiotic supplement more effective by helping the bacteria that make it to your intestines grow and thrive.

Check out our article on choosing the best prebiotic supplements to learn more about the interactions between prebiotics, probiotics and your health!

Should You Take a Probiotic Supplement with other Medications?

Close Up of Pink Tablets in Blister Wraper

And… now I’m back to a complicated question.  Well, that was short-lived!

The best, if somewhat unsatisfying, answer I can give you to whether or not you should take a probiotic with other medications is: it depends on the medication.  Probiotics can influence how well some medications work.

There are two main reasons for this:

  • probiotic bacteria may change the structure of your medications before you absorb them
  • probiotics can change how your liver functions

Probiotics Can Chemically Change Medications

Probiotic bacteria may be able to break down or chemically change the structure of some medicines before they leave your digestive tract.  

Bacteria are, after all, living organisms with all kinds of active metabolic pathways and, living in your gut, they come into contact with anything you swallow before it gets into your body.  

If your probiotics happen to have enzymes that can change the structure of a medicine you take, it may change how that medication works in your body.  It may make the drug not work at all.  It may make it work too well.  That’s difficult to say ahead of time.

Probiotics Can Change Your Liver Function

The second way probiotics can interact with medications is by changing how your liver works.  Your liver is responsible for breaking down and chemically changing your medications in your body.  

Some medications only work in your body if your liver changes them.  Others are made so that your liver can break them down and keep you from overdosing.

This means that changes in how your liver works could potentially have huge effects on how well your medications work.  It is, again, difficult to predict the effects ahead of time.

A few drugs have been tested and researchers know they can interact with probiotic bacteria, though.  These include:

  • CPT11  
  • Nitrazepam  
  • Clonazepam  
  • Misonidazole  
  • Chloramphenicol  
  • Zonisamide  
  • Digoxin  
  • Sulindac  
  • Sulfnpyrazone

Keep in mind that this list is by no means complete!  Theoretically, the function of basically any drug could be influenced by adding extra probiotic bacteria to your digestive tract.

If you take any prescription medications or any over-the-counter medications, regularly, make sure to talk to your doctor or pharmacist about any potential risks before starting a probiotic supplement!

Should You Take a Probiotic if You are Pregnant or Breastfeeding?

Based on the current evidence, there is no reason you can’t take a probiotic supplement if you are pregnant or breastfeeding.  Studies show no negative side effects of probiotics during pregnancy or nursing, on either mother or baby.

In fact, both mom and baby may enjoy benefits.  Probiotics during pregnancy may:

Sounds like a win-win-win!

So, there you have it!  All the current research about how, why and when to take probiotics in simple, practical terms!  

I hope this helps you feel empowered to walk back into that supermarket with your head held high to pick up that probiotic supplement. 

Take Home Message

If you are experiencing digestive symptoms, such as IBS or antibiotic-induced diarrhea, you should almost certainly take a probiotic.  For other conditions, you should weigh the small risk of mild side effects against the potential improvements in your symptoms. 

Make sure to find a probiotic that contains bacterial species proven to help the symptoms you want to treat, that has an effective dosage and that comes from a reputable company. 

Take the dosage(s) recommended on the packaging of your probiotic.  

Adding your probiotic to your breakfast is likely a good strategy for making sure it is effective.  You may also take your probiotic in the evening, though.

Probiotics are safe to take with prebiotics and while you are pregnant and breastfeeding.  Be sure to ask your doctor if taking a probiotic is safe for you if you take other medications.

If you are interested in giving some kids’ probiotics a go, then I strongly recommend the options listed in this article: The Best Probiotics for Kids: An Expert’s Guide for Moms

Read Next: Best Leaky Gut Supplements for Leaky Gut Treatment


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