The Best Time To Take Probiotics

Some simple advice for scheduling your probiotic supplements.

Research shows that certain probiotic strains may not survive the harsh acidic environment of your stomach. If that’s true, how do you ensure the viability of the probiotic supplements you take? Should you take them with meals? Without meals? At bedtime? 

It turns out that concerns about probiotic viability are a bit of a red herring.

If you look to the internet for medical advice on these questions, you will get a lot of conflicting information.

The Best Time To Take Probiotics - AdobeStock 154987566 WEB gut probiotics supplements

Here’s a sampling of advice about probiotics from different sources:

  • Take probiotics just before a meal or as you begin your meal.
  • Take probiotics 20 minutes after you eat.
  • Take probiotics at bedtime.
  • Don’t take probiotics with a heavy meal.
  • Take probiotics with fats.
  • Don’t take probiotics with garlic, herbs or prescription medicine.

Crazy-making, right? Well, I have some good news for you that’s both uncomplicated and flexible…

Just find an approach that’s convenient for you. That makes it much more likely you will remember to take your probiotic supplements, which is what matters most if you want to get all the health benefits of probiotics.

Don’t Let Probiotic Myths Complicate Your Life

Misinformation about how to take probiotics are rampant on the internet. That’s because a lot of the information you read is based on conjecture, not on what the majority of research shows. And so much conflicting information can leave you feeling stressed and confused about your supplement routines.

Check this list of common advice about probiotics:

7 Probiotic Myths
Probiotic foods are better than probiotic supplements. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Stomach acid kills probiotics and makes them ineffective. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Take probiotics at a specific time of day. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Take probiotics with specific foods. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Never take probiotics and antibiotics together. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Certain kinds of probiotics work best for specific health issues. The Best Time To Take Probiotics - AdobeStock 255394930 Myth
Try different probiotics to find the one that works for you. The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Today I want to give you up-to-date, science-based information about how to best take probiotics. And I promise to keep it simple. I know from my own clinical practice that when medical advice gets too complicated, people have a much harder time sticking with it.

But first, let’s take a quick look at why probiotics are the number one supplement that I recommend to patients.

Why Take Probiotics?

The health benefits of probiotic supplements have been well-established in a very large body of clinical research. We know from the research that probiotics are helpful for a surprisingly wide range of health issues.  These include:

  • Digestive issues like IBS, IBD (Crohn’s and colitis), SIBO, leaky gut and more.
  • Non-digestive issues like mood, cognition, sleep, hormonal balance, autoimmune conditions and more.

How is it possible for one type of supplement to have so many health benefits?  This is because….

Probiotics Break This Destructive Cycle

An unhealthy balance of gut flora can lead to a poorly trained immune system and result in excessive inflammation.  This inflammation can further damage the good bacteria in your intestinal tract and damage your gut lining.  More inflammation and damage futhers the dysfunction, and so starts a self-feeding cycle. 

Probiotics help to break this destructive cycle and can lead to a self-perpetuating cycle of healing and improvement.

The Best Time To Take Probiotics - Poor Bacterial Loop

Probiotics Improve Gut Health

Probiotics have been shown to positively affect digestive health in several ways:

  • Increase the diversity, or health, of the living organisms in your digestive system.[1]
  • Fight pathogens (harmful bacteria and other bad bugs) and their toxins.[2, 3, Trusted SourcePubMedGo to source 4]
  • Promote a more rapid recovery from imbalances in your gut microbiota.[5]
  • Promote a healthy immune system response in your gut.[6, Trusted SourcePubMedGo to source 7]
  • Reduce gut inflammation (excessive inflammation is part of an overzealous immune response).[8]
  • Encourage the growth of healthy bacteria in your gut.[9]
  • Reduce leaky gut aka damage to your gut lining.[10, 11, Trusted SourcePubMedGo to source 12]

Probiotics Improve Many Other Health Issues

A healthy gut leads to better overall health (I wrote an entire book about this concept called Healthy Gut, Health You). Research also shows that probiotics can benefit a wide variety of health conditions.

We currently have high level scientific support to show that probiotics can benefit:

  • IBS: Gas, bloating, diarrhea, constipation, abdominal pain
  • IBD: Crohn’s and ulcerative colitis
  • Mood: Depression and anxiety
  • Gut microbiota imbalance: SIBO, H. pylori, candida/fungus, pathogens
  • Leaky gut aka gut damage and permeability 

Limited, but encouraging, scientific support for:

  • Cognition
  • Sleep
  • Thyroid health
  • Female hormones
  • Autoimmune conditions
  • Metabolism
  • Blood pressure and cholesterol
  • Brain fog
  • Sleep

Ok, we’ve established that probiotics are good for your digestive health and your overall health. Let’s take a closer look at some myths and facts about taking probiotics.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Probiotic Foods are Better than Probiotic Supplements

Probiotic foods like kimchi, tempeh, kefir and lacto-fermented sauerkraut are great and I encourage you to include them in your diet. If you already have a healthy gut or if you eat A LOT of probiotic foods, these foods might give you enough healthy bacteria to meet your needs. However if you’re not eating a lot of probiotic foods or if you have specific health issues, probiotic supplements will provide you with more CFUs (colony forming units).

This chart shows the probiotic content of common probiotic foods.

Food Species Amount Equivalent Dose
Sauerkraut Leuconostoc mesenteroides Lactobacillus brevis Pediococcus pentosaceus Lactobacillus plantarum 3 billion CFU per cup ⅛ capsule Lacto-Bifido Blend Probiotic
Yogurt[13, 14] Lactobacillus acidophilus Streptococcus thermophilus Lactobacillus delbrueckii subsp. bulgaricus 2.5 billion CFU per  cup 1/10 capsule Lacto-Bifido Blend Probiotic
Lacto-fermented Pickles[15, 16] Lactobacillus casei Lactobacillus rhamnosus Lactobacillus plantarum Lactobacillus brevis 1.3 billion CFU per pickle .05 capsule Lacto-Bifido Blend Probiotic
Kefir[17] Lactobacillus brevis Lactobacillus acidophilus Lactobacillus casei Lactococcus lactis Saccharomyces cerevisiae 2.5 billion CFU per cup 1/10 capsule Lacto-Bifido Blend Probiotic
Kimchi[18, 19] Weissella koreensis Lactobacillus sakei Lactobacillus graminis Weissella cibaria Leuconostoc mesenteroides 11.5 billion CFU per ½ cup ½ capsule Lacto-Bifido Blend Probiotic

Bottom line: For the best therapeutic effect, take probiotic supplements.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Stomach Acid Kills Probiotics and Makes Them Ineffective

Actually, this one is partly true.

Research shows that stomach acid can kill some strains of probiotics. Up to 60% is often quoted.[20]

But here’s what you need to know before you start worrying about whether you are delivering living organisms to your digestive tract.

First, there’s actually a lot of variability in die off across probiotic strains. Some probiotic strains, like Saccharomyces boulardii,[21] Bifidobacterium animalis and Lactobacillus johnsonii[22 Trusted SourcePubMedGo to source] aren’t affected by stomach acid at all.

Also, a lot of this research takes place in test tubes, which can’t reproduce the dynamic complexity of your gastrointestinal tract. Some studies have attempted to correct this by using simulated models of the upper digestive tract. Research with these models show better survival rates of probiotic bacteria than in test tubes,[23] Trusted SourcePubMedGo to source however even a dynamic model can’t fully replicate what happens in our digestive system.[24]

Mechanistic studies like this often miss the big picture. In this case we have over 500 studies to show that when humans take probiotic supplements, there are a multitude of health benefits and few side effects. This is the science that we need to be paying attention to. Don’t get sidetracked by mechanistic studies done in test tubes and model digestive systems.

Finally, it may not actually matter much if some of the probiotic bacteria you take are killed  by stomach acid. That’s because there are a few fascinating studies to show that non-viable probiotics (probiotics that have been killed) also have health benefits.[25, 26] Trusted SourcePubMedGo to source Which just goes to show that we don’t yet fully understand the mechanisms behind how probiotics work inside the human digestive tract.

Bottom line: While stomach acid may have some impact on the viability of certain probiotic strains, probiotic supplements work well anyway.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Take Probiotics at a Specific Time of Day

A lot of advice about when to take probiotics is simply conjecture. Basically, if you are worried about the potential effects of stomach acid on probiotic supplements, then of course you start thinking up ways to save probiotic lives.

One study, which is often quoted, finds better survival rates for some probiotic strains if they are taken just before a meal.[27]. This study uses a model digestive tract and simply measures bacteria survival rates. This study doesn’t actually tell us anything about whether the probiotic supplements (living or dead) provided health benefits in humans.

With so many human clinical trials showing that probiotics work, no matter what time of day they are taken, it doesn’t make sense to focus on one mechanistic study.

There’s no harm in taking your probiotic supplement right before a meal and it’s even possible that this may provide some benefit. But don’t stress about it.

Also, I’ve seen a few silly suggestions like: “Take probiotics at bedtime if you suffer from insomnia.” Preliminary evidence suggests that probiotics can help with sleep quality,[28, 29, 30, Trusted SourcePubMedGo to source 31] however they don’t work in the same way as a sleeping pill. Take probiotics for a couple of weeks (at any time of the day) and you may start to experience sleep improvements.

Bottom line: Take probiotics when it’s convenient for you.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Take Probiotics with Specific Foods

Again, we have one study in a model digestive tract that shows that more probiotic bacteria survive when “consumed” with fats.[32]

And once again, we need to consider this study in light of all of the research that confirms the health benefits of probiotics. Nearly all of these studies prescribed a specific dose of probiotics without any requirements for how patients should consume them.

Bottom line: Take your probiotic supplement with or without food.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Never Take Probiotics and Antibiotics Together

This is common advice that’s also based on conjecture.

We know that antibiotics kill good bacteria, so it follows that taking probiotics and antibiotics together is pointless, right? Actually, no. Our biology is wonderfully complex and we shouldn’t think about it in terms of simple mechanics.

Rather than cancelling each other out, research shows that taking probiotics and antibiotics together is a more effective treatment than taking antibiotics alone.

The most relevant study to show this effect is a systematic review of 20,215 patients with H. pylori infections.[33] Patients who took probiotics and antibiotics together were able to clear their infections better than patients who only took antibiotics.

This sort of finding has been found in SIBO and other gut infections too.[34, 35, Trusted SourcePubMedGo to source 36] Probiotic co-administration with antibiotics tends to enhance treatment results.

Bottom line: It’s beneficial to take probiotics and antibiotics together.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Certain Kinds of Probiotics Work Best for Specific Health Issues

Years ago, I was planning to use a special probiotic for my constipated patients. This was after the first, and only study of its kind, was published showing probiotics could improve constipation. Then, something interesting happened. Six months later, a different probiotic formula was shown to improve constipation. Then, soon after, another study showing another different probiotic also improved constipation. 

I watched this same thing happen with probiotics and mood, probiotics and SIBO, etc…. Eventually I came to understand probiotics aren’t that specific, nor that complicated. 

It’s simply not necessary to match specific probiotic strains to specific health issues. Just imagine how complicated that would be for anyone with multiple symptoms!

As I explained earlier in this article,  probiotics work synergistically to restore gut health, reduce inflammation and modulate the immune system. And while there are differences between probiotic strains, all probiotics confer similar health benefits by treating the underlying reason for your symptoms.

Bottom line: Choose any high quality probiotic supplement.

The Best Time To Take Probiotics - AdobeStock 255394930 Myth

Try Different Probiotics to Find the One That Works for You

Here is something I’d like to share, that most supplement companies don’t want you to know.  While there are many probiotic strains, all of these strains can be organized into 3 categories.  Meaning nearly every probiotic product can be classified into one of three categories:[37]

  1. Lactobacillus & Bifidobacterium predominated blends
  2. Saccharomyces Boulardii
  3. Soil-based probiotics (Bacillus species)

It’s not necessary to try lots of different probiotic formulations. However, if you want to achieve maximum probiotic diversity, I do recommend that you take one product from all three probiotic categories. In my experience this approach to probiotic therapy has made the difference between patients experiencing minimal results and impressive results. 

Bottom line: Get off the probiotic merry-go round! For a powerful, therapeutic approach to probiotics, try my Probiotic Protocol.

In Conclusion

For all these reasons, take your probiotic supplements in whatever way is easiest for you. The benefits of taking probiotics at a specific time of day is likely minimal at best.  You can take probiotics once or twice daily.  Many patients find it convenient to take probiotics with water in the morning and at bedtime. Others prefer to take probiotic supplements with meals.

References (click to expand)

[1] Nutrients Trusted SourcePubMedGo to source 2020 Apr 16;12(4):1107. doi: 10.3390/nu12041107.
[2] Eur J Pediatr. Trusted SourcePubMedGo to source 2013 Oct;172(10):1321-6. doi: 10.1007/s00431-013-2041-4. Epub 2013 May 24.
[3] Scand J Infect Dis. Trusted SourcePubMedGo to source 2006;38(6-7):479-81.
[4] Parasitol Res. Trusted SourcePubMedGo to source 2011 Mar;108(3):541-5. doi: 10.1007/s00436-010-2095-4. Epub 2010 Oct 5.
[5] BMJ Open. Trusted SourcePubMedGo to source 2014 Aug 25;4(8):e005047. doi: 10.1136/bmjopen-2014-005047.
[6] Microorganisms. Trusted SourcePubMedGo to source 2018 Apr 25;6(2). pii: E35. doi: 10.3390/microorganisms6020035.
[7] Iran J Pharm Res. Trusted SourcePubMedGo to source Fall 2019;18(Suppl1):31-50. doi: 10.22037/ijpr.2020.112232.13620.
[8] Pharmacol Res Trusted SourcePubMedGo to source. 2019 Apr;142:303-313. doi: 10.1016/j.phrs.2019.02.016. Epub 2019 Feb 19.
[9] Front Immunol. Trusted SourcePubMedGo to source 2019 Oct 1;10:2348. doi: 10.3389/fimmu.2019.02348. eCollection 2019.
[10] Sci Rep. Trusted SourcePubMedGo to source 2017 Jan 3;7:40128. doi: 10.1038/srep40128.
[11] Clin Infect Dis. Trusted SourcePubMedGo to source 2014 Apr;58(8):1107-15. doi: 10.1093/cid/ciu065. Epub 2014 Feb 5.
[12] J Int Soc Sports Nutr. Trusted SourcePubMedGo to source 2012 Sep 20;9(1):45. doi: 10.1186/1550-2783-9-45.
[13] Front Microbiol. Trusted SourcePubMedGo to source 2018 Aug 24;9:1785. doi: 10.3389/fmicb.2018.01785. eCollection 2018.
[14] LAYE, I., KARLESKIND, D. and MORR, C. (1993), Chemical, Microbiological and Sensory Properties of Plain Nonfat Yogurt. Journal of Food Science, 58: 991-995. doi:10.1111/j.1365-2621.1993.tb06096.x
[20] Int J Food Microbiol. Trusted SourcePubMedGo to source 2005 Apr 1;99(3):287-96.
[21] Benef Microbes. Trusted SourcePubMedGo to source 2011 Dec 1;2(4):295-303. doi: 10.3920/BM2011.0022.
[22] Int J Food Microbiol. Trusted SourcePubMedGo to source 2005 Apr 1;99(3):287-96.
[23] Microorganisms. Trusted SourcePubMedGo to source 2018 Apr 25;6(2):35. doi: 10.3390/microorganisms6020035.
[24] Food Res Int. Trusted SourcePubMedGo to source 2018 May;107:423-436. doi: 10.1016/j.foodres.2018.02.055. Epub 2018 Feb 27.
[25] Microb Ecol Health Dis. Trusted SourcePubMedGo to source 2012 Jun 18;23. doi: 10.3402/mehd.v23i0.18567. eCollection 2012.
[26] Int J Mol Sci. Trusted SourcePubMedGo to source 2019 May 23;20(10). pii: E2534. doi: 10.3390/ijms20102534.
[27] Benef Microbes. Trusted SourcePubMedGo to source 2011 Dec 1;2(4):295-303. doi: 10.3920/BM2011.0022.
[28] Benef Microbes. Trusted SourcePubMedGo to source 2017 Apr 26;8(2):153-162. doi: 10.3920/BM2016.0150.
[29] Front Psychiatry. Trusted SourcePubMedGo to source 2019 Mar 27;10:164. doi: 10.3389/fpsyt.2019.00164. eCollection 2019.
[30] Acta Med Indones. Trusted SourcePubMedGo to source 2015 Jul;47(3):201-8.
[31] Aust N Z J Psychiatry. Trusted SourcePubMedGo to source 2017 Aug;51(8):810-821. doi: 10.1177/0004867416686694. Epub 2017 Jan 10.
[32] Benef Microbes. Trusted SourcePubMedGo to source 2011 Dec 1;2(4):295-303. doi: 10.3920/BM2011.0022.
[33] Clin Res Hepatol Gastroenterol. Trusted SourcePubMedGo to source 2017 Sep;41(4):466-475. doi: 10.1016/j.clinre.2017.04.004. Epub 2017 May 25.
[34] Dig Dis Sci. Trusted SourcePubMedGo to source 2019 Sep 23. doi: 10.1007/s10620-019-05830-0. [Epub ahead of print]
[35] Scand J Gastroenterol. Trusted SourcePubMedGo to source 2015;50(11):1376-81. doi: 10.3109/00365521.2015.1050691. Epub 2015 May 19.
[36] Infect Control Hosp Epidemiol. Trusted SourcePubMedGo to source 2018 Jul;39(7):771-781. doi: 10.1017/ice.2018.84. Epub 2018 Apr 26.
[37] IPA guidelines to qualify a microorganism as probiotic

What do you think? I would like to hear your thoughts or experience with this.


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!

11 thoughts on “The Best Time To Take Probiotics

  1. “a lot of the information you read is based on conjecture, not on what the majority of research shows”
    I’m curious as to what actual research is out there regarding the benefits of meal spacing. I have been a “grazer” most of my life. I started keto and was pretty much eating just 2 meals per day. Somewhen in the last few years, I developed methane sibo. It seems to me that I feel better when I’m grazing (and including carbs).
    As one of the recommended maintenance protocols recommends meal spacing, I was wondering if there are any studies supporting this or if it’s just recommended based on what the logic SHOULD be.

    1. I think you’ve hit on it. Listen to your body. Fasting can be helpful, and there is some research to support that, but no for everyone.

  2. I am going to start a course of your three suggested probiotic strains to address my leaky gut. I was going to also take 1.5g of L-glutamine each day as well to help with gut repair. Is this a good idea and should I do it at the same time as I take all three probiotics or should I take the probiotics first to see how I respond? Many thanks for all your great work and advice!

      1. Hi Dr Ruscio: Thanks for the advice. I have just started and will give it a couple of weeks to see how I feel on the probiotics and add in the L-glutamine. I’ve also heard that powdered colostrum is very healing but I suppose one thing at a time! Many thanks 🙂

  3. I’ve become a firm believer in “listen to your body.” I don’t take probiotic supplements for the simple reason that I have a limited budget, so instead I make a lot of much cheaper home-fermented veggies and eat a substantial serving of them every day, really more like a side-dish than just a condiment. But I’m pretty much a one-meal-a-day eater, a rather large plateful. I seldom have room to eat absolutely everything I put on my plate, and when I stop because I just can’t eat every last bite, most of the time my leftovers consist primarily of the fermented food(s). That’s not a deliberate, conscious choice, just a consistent spontaneous pattern that I’ve noticed. Then several hours later I’m in the mood for a snack and my left-over delicious fermenties are exactly what I have a taste for, typically along with a cup of homemade bone broth. I just figure that my body is telling me something about what works best for me personally, and I’m happy to cooperate with that.

  4. In June I was prescribed metronidazole and Fluconazole which tore up my stomach. I did not know to take probiotics. I had diarrhea for 3 weeks and when I was told to get on probiotics it seemed to detox my system even more. I would be going 3-4 times a day. Finally, Culturelle stopped my diarrhea but now I’m 19 pounds lighter. I was 119. I’ve had a colonoscopy and endoscopy and stool sample which all came back fine. GI Doctor told me to get on refrigerated probiotic. I’m currently taking Solutions RX Superior Probiotics. But now I am constipated. They seem to make me want to go 2-3 times a day but they are hard and I can’t pass them. So now Doctor told me miralax. Which I used to be chronic constipation person. I’m very depressed now and anemic. Iron pills gave me diarrhea now I have to take liquid iron. I can’t sleep, etc. Any advice you could give me about which probiotic to use for constipation and how to get my gut flora back. Taking these probiotics makes my stomach rumble a lot. My stomach never tumbled before all this. I used to go once a day and now it’s like the probiotic wants me to go 2-3 times a day but it’s hard and can’t pass. I used to be a happy, healthy person and now I am not. But confused now because my probiotic has 20 billion CFU with 3% prebiotic. But it only has 6 strains which looks like from Lactobacillus and bifidobacterium strains.

    1. Hi Annie,

      I’m so sorry to hear you’ve been dealing with all of this – it sounds frustrating. Dr R typically recommends a lacto-bifido blend, s. boulardii, and a soil-based probiotic all used together. You can see the ones he recommends here: In terms of regaining your gut health, I would definitely recommend giving Dr R’s book, Healthy Gut Healthy You, a read as it tackles that exact question and lays out a DIY protocol. You can find it here:
      Hope this helps!

  5. I know from personal experience and that of some family and friends some people do much better with probiotics that are histamine free to start off. Once the gut has healed up some can tolerate others. Until then the ones that have histamine or cause histamine to be released just make them sicker.

Leave a Reply

Your email address will not be published. Required fields are marked *