The Ultimate Guide To Taking Probiotics

Probiotics have long been considered foundational to a healthy routine, but despite their lengthy history as a mainstream supplement, there’s still plenty of confusion about these itty-bitty gut bugs. Perpetual questions around which strains to choose, how many billions of bacteria to look for, and whether or not to refrigerate them can make taking probiotics feel as mind-boggling as trying to remember high school calculus.

If you could use some clarification on the puzzle of probiotics, read on. This expert-approved guide has the a’s to your microbiota q’s.

When to Take Your Probiotics 

There’s lots of chatter out there surrounding the best time of day to send probiotics down the hatch, and whether to do so with food. So are probiotics pals with breakfast, lunch, or dinner—or none of the above?

Turns out, time of day isn’t as important as whether you take them on an empty belly. “Probiotics have a better survival rate on an empty stomach or right before a meal, when stomach acid levels are lower,” says The Vitamin Shoppe dietitian Brittany Michels, M.S., R.D.N, L.D.N. “Avoid taking them after a meal.” The high amounts of stomach acid present then are bad news for probiotics’ survival.

The Science Behind Timing

Here’s what’s happening behind the scenes: When your stomach is empty or you’re about to eat, your stomach acid levels are at their lowest. That gives those beneficial bacteria a better chance of making it through to your intestines, where they can actually do their job.

Think of it like trying to get through a crowded room. When the room (your stomach) isn’t packed with digestive acids working overtime on a big meal, the probiotics have an easier time passing through to reach their destination—your gut.

Real-World Timing Tips

So when does this work best in your daily routine? Here are some simple ways to remember:

• First thing in the morning, about 30 minutes before breakfast, when your stomach is naturally less acidic
• Right before bed on an empty stomach (just make sure it’s been at least 2-3 hours since dinner)
• Shortly before any meal, giving the probiotics a head start before stomach acid ramps up

That said, the most important thing is consistency. If taking your probiotic with your morning coffee is the only way you’ll remember it, that’s better than skipping it altogether because you’re trying to find the “perfect” time.

How Many CFU to Choose

The epic numbers of microbes contained in probiotic supplements are enough to make your head spin. With such a wide range, you might be tempted to close your eyes and snag any old bottle, pin-the-tail-on-the-donkey-style. But according to the Cleveland Clinic, a general recommendation for adults is to choose a product with at least one billion colony-forming units (CFU).

Just how many billions, though, depends on your personal needs. “Probiotic depletion may be influenced by many factors, including but not limited to a lack of fermented foods in the diet, unmanaged stress, processed foods, alcohol, added sugar, inflammation, food intolerances, medication or antibiotic usage, and digestive disorders,” explains Michels. “The more depleting factors you have, the more support you need.”

Decoding the Billion-Count Mystery

Let’s break down what those numbers actually mean. When you see “10 billion CFU” on a label, you’re looking at 10 billion live bacteria that could potentially colonize your gut (at least temporarily). The “colony-forming units” part just means these are bacteria capable of reproducing and forming colonies.

Generally, daily supplements that contain between 15 and 50 billion CFU are common, according to Michels. Most people can start anywhere within this ballpark range. High billion counts (like up to 400 billion), meanwhile, are usually reserved for individuals needing serious gut rehab support (for example, post-antibiotic treatment). If you’re not sure exactly how many billions of bugs might benefit your gut, check with your doctor or a dietitian.

More Isn’t Always Better

Here’s something that might surprise you: grabbing the supplement with the highest CFU count on the shelf isn’t necessarily your best bet. What matters more is choosing the right strains for your specific health goals and making sure those bacteria are actually alive when you take them.

Think of it this way—would you rather have 100 billion bacteria of a strain that doesn’t address your needs, or 5 billion of exactly the right strain that’s been proven to help with what you’re dealing with? Quality and strain specificity trump sheer quantity every time.

Starting Your Probiotic Journey

If you’re brand new to probiotics, here’s a friendly approach:

• Week 1-2: Start with a lower dose (around 10-15 billion CFU) to let your gut adjust
• Week 3-4: If you’re feeling good, you can stick with that dose or gradually increase if needed
• Ongoing: Pay attention to how you feel and adjust accordingly

Your body will usually let you know if you need to dial things back—temporary gas or bloating in the first few days is normal, but it should ease up within a week or two.

Read More: Which Type of Probiotic Supplement Is Right for You?

Consider Your Specific Health Concerns

Not all probiotics are ideal for every health goal. “Probiotics are best taken when specific strains are used for specific concerns,” says Dr. Chris Damman, M.D., Clinical Associate Professor of Gastroenterology & Medicine at the University of Washington.

For example, if you’re looking to support immunity, you might try Lactobacillus paracasei, Lactobacillus casei, and Lactobacillus fermentium. One study found that people who took these strains for 12 weeks saw significant respiratory health and immunity benefits. Other research, meanwhile, has identified Saccharomyces boulardii as a potentially helpful strain for those experiencing chronic gut health symptoms, so look for that if it’s regularity you’re after.

Matching Strains to Your Goals

Let’s get practical about strain selection. Here’s what the research suggests for common concerns:

For digestive comfort:

• Bifidobacterium longum might help with bloating and occasional discomfort
• Lactobacillus acidophilus may support overall digestive balance
• Multi-strain formulas with both Lactobacillus and Bifidobacterium species often work well for general gut health

For immune support:

• Lactobacillus rhamnosus GG is one of the most researched strains for immune function
• Bifidobacterium animalis may help support your body’s natural defenses
• Look for products that combine multiple immune-supportive strains

After antibiotic use:

• Saccharomyces boulardii is a beneficial yeast (not bacteria) that can help during and after antibiotic courses
• Lactobacillus rhamnosus GG may help restore balance
• Starting these within a few days of beginning antibiotics might offer the most support

Reading Labels Like a Pro

Before hitting “add to cart,” you want to make sure you’re clear on your motives for taking a probiotic in the first place—and that the product you’re eyeing is specifically formulated to support those goals. Most supplement labels and e-commerce platforms offer basic information on a product’s health benefits.

Here’s what to look for on the label:

• Genus and species names (like Lactobacillus acidophilus)—the more specific, the better
• Strain designation (sometimes a number/letter combo after the species name)
• CFU count at expiration, not at manufacture
• Intended benefits based on research for those specific strains

The tricky part? Probiotic names can look like alphabet soup. Just remember: the first word (genus) and second word (species) together tell you what kind of bacteria you’re getting. Any numbers or letters after that identify the specific strain, which is where the research-backed benefits come in.

Where to Store Them

Probiotics have a reputation for being rather temperamental when it comes to temperature. So is it best to stash them in the fridge, or can they hang out with the beans and pasta in your pantry?

Read More: What’s the Deal With Refrigerated Probiotics?

In general, you can keep probiotics under whatever temperature conditions you purchased them (i.e. refrigerate them if you bought them refrigerated). That said, it’s always a good idea to check a product’s packaging for storage instructions.

Shelf-Stable vs. Refrigerated: What’s the Difference?

And if you’re wondering whether you should pick a shelf-stable or refrigerated supplement, know this: Neither one is superior. While it might seem that refrigerated products are more likely to retain their potency than shelf-stable options, there’s plenty of technology nowadays that protects the bacteria in shelf-stable products from heat, light, and oxygen, says dietitian Wendy Lord, R.D., a contributor to the health professional network Health Reporter.

Which you choose really comes down to personal preference (are you likely to forget your probiotic if it’s tucked away in the fridge?) and whether your healthcare provider has recommended you take certain strains in order to support your unique health needs and goals, Lord says.

Storage Mistakes That Sabotage Your Probiotics

Even with the best supplement, poor storage can turn those billions of bacteria into, well… not much. Here’s how to keep your probiotics happy:

For refrigerated probiotics:

• Keep them in the main part of your fridge, not the door (temperature fluctuates too much there)
• Don’t leave them on the counter for extended periods
• If traveling, use a small cooler pack for short trips

For shelf-stable probiotics:

• Store in a cool, dry place away from direct sunlight
• Keep the cap tightly sealed between uses
• Avoid humid environments like bathrooms (that steam from your shower isn’t doing your probiotics any favors)
• Don’t leave them in a hot car

Travel Tips for Probiotic Users

Planning a trip? Your probiotics can come along. For shelf-stable options, just toss them in your carry-on or suitcase as usual. For refrigerated varieties, consider these workarounds:

• Switch to a shelf-stable formula for the duration of your trip
• Use insulated travel bags with ice packs for short trips (a day or two)
• Ask your hotel to store them in their mini-fridge upon arrival
• Take a break during travel and restart when you’re home (not ideal, but better than letting them spoil)

The Importance of Quality

As with every supplement, don’t forget to look for indicators of third-party testing. Approval labels from companies like NSF, Consumer Labs, and USP are a sign of quality and purity of ingredients.

Another sign of quality: diversity. “The gut flora is diverse, so supplements should have a variety of bacterial strains as well.”

Why Third-Party Testing Matters

Here’s the thing about probiotics: unlike medications, the FDA doesn’t strictly regulate them for safety and effectiveness before they hit store shelves. That makes third-party testing your best friend when shopping for quality.

When you see certifications from organizations like NSF International, U.S. Pharmacopeia (USP), or ConsumerLab.com, it means an independent lab has verified that what’s on the label actually matches what’s in the bottle. They’re checking that the bacteria are alive, that the CFU count is accurate, and that there aren’t any sneaky contaminants hiding in there.

At The Vitamin Shoppe, our proprietary brands undergo 320 quality assurance steps with ingredient purity and potency verified by independent third-party laboratories—giving you confidence that you’re getting exactly what you pay for.

Multi-Strain vs. Single-Strain Formulas

Research from the NIH suggests that products containing both Lactobacillus and Bifidobacterium species often show better results for certain conditions compared to single-strain supplements. Your gut naturally houses hundreds of different bacterial species, so it makes sense that giving it a variety of beneficial strains might offer more comprehensive support.

That said, for very specific health goals—like taking Lactobacillus rhamnosus GG during antibiotic treatment—a targeted single-strain product might be your best bet. It really depends on what you’re trying to achieve.

Clean Label Considerations

Lastly, make sure you don’t get more than you bargained for if you’re allergic to certain foods or dyes. “Check the ingredient list to confirm absence of allergens, fillers, artificial colors, or preservatives,” Michels recommends.

Pay special attention to:

• Dairy ingredients (many probiotics are cultured in dairy, though dairy-free options exist)
• Soy, gluten, or corn if you have sensitivities
• Artificial colors or flavors in gummy or chewable formulas
• Added sugars (some probiotic products contain unnecessary sweeteners)

Expiration Dates Actually Matter

Unlike some supplements where the expiration date is more of a suggestion, with probiotics it’s crucial. Bacteria are living organisms, and they gradually die off over time—even in the best storage conditions.

When you buy probiotics, check two things:

1. How long until expiration? The closer to the expiration date, the fewer live bacteria you’re actually getting
2. Does the label show CFU at expiration or at manufacture? Reputable brands list the CFU count you can expect at the end of the shelf life, not just when they bottled it

For the best results, buy probiotics with at least several months before expiration and use them consistently rather than letting the bottle sit around for ages.

Convenience Matters Too

Let’s be real: the best probiotic is the one you’ll actually take consistently. That’s why The Vitamin Shoppe offers multiple ways to make probiotics part of your routine:

• Auto Delivery saves you 10% on every subscription order with flexible delivery every 30-180 days
• 2-hour in-store or curbside pickup when you need them fast
• Same-day delivery via Instacart in participating areas
• Free shipping on orders $35+ (or $25+ for subscriptions)

Find a formula that fits your health goals and a delivery method that fits your lifestyle, and you’re much more likely to stick with it long enough to see benefits. Schedule a free virtual nutrition consultation with our Health Enthusiasts if you need help choosing the right probiotic for your specific needs.